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Hattori N, Takamatsu H, Iida N, Asano N, Yamashita S, Oba GM, Kimura K, Yoshida A, Kobayashi E, Nakayama R, Matsumoto M, Nakamura M, Kawai A, Ushijima T. Epigenetic disruption of adipogenic gene enhancers in dedifferentiated liposarcomas and its therapeutic value. Front Oncol 2025; 15:1419877. [PMID: 40371227 PMCID: PMC12074953 DOI: 10.3389/fonc.2025.1419877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 04/09/2025] [Indexed: 05/16/2025] Open
Abstract
Liposarcoma (LPS) is the most common soft-tissue sarcoma in adults, and well-differentiated liposarcoma (WDLPS) and dedifferentiated liposarcoma (DDLPS) are the most frequent subtypes. These LPSs are considered to develop due to disturbances in the adipogenic differentiation of mesenchymal stem cells. However, the molecular mechanisms underlying the disturbances remain unclear. Here, we aimed to identify the mechanism and explore its therapeutic advantages focusing upon their epigenetic alterations, known to be important in differentiation. First, we conducted a genome-wide DNA methylation analysis using 15 LPSs (6 WDLPSs and 9 DDLPSs) and 6 normal adipose tissues. Unsupervised hierarchical cluster analysis using DNA methylation profiles at enhancers classified the samples into the three histological types, whereas analysis using promoters did not. Principal component analysis revealed that normal adipose tissues and WDLPSs were grouped closely, whereas DDLPSs were scattered. Genomic regions hypermethylated in DDLPSs were enriched for enhancers, especially super-enhancers (13.5% of hypermethylated regions and 7.0% of the whole genome), which were located in the genes involved in adipogenesis, such as PPARG2 and its target genes (FABP4 and PLIN1). In addition, marked decreases in PPARG2 and FABP4 expression were confirmed in DDLPSs. Then, treatment of PPARG2-expressing DDLPS cell lines with 5-aza-2'-deoxycytidine, a DNA demethylating agent, and rosiglitazone, a PPARγ agonist, was shown to induce differentiation with enhanced expression of FABP4. These findings indicate that aberrant DNA methylation of adipogenic gene enhancers plays a crucial role in the development of DDLPS and can be a therapeutic target.
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Affiliation(s)
- Naoko Hattori
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Laboratory of Integrative Metabolic Regulation, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Hironori Takamatsu
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Naoko Iida
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Naofumi Asano
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Satoshi Yamashita
- Department of Life Engineering, Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Japan
| | - Gina Miku Oba
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Kozue Kimura
- Laboratory of Integrative Metabolic Regulation, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Eisuke Kobayashi
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Robert Nakayama
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Morio Matsumoto
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Masaya Nakamura
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Akira Kawai
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Toshikazu Ushijima
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
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Chen M, Zhou Y, Fu Z, Wu C. Transcription factor occupancy limits DNA methylation and determines ICAM1 expression in breast cancer. Acta Biochim Biophys Sin (Shanghai) 2025. [PMID: 40230289 DOI: 10.3724/abbs.2024237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2025] Open
Abstract
The interaction between TF binding and DNA methylation is increasingly recognized as a key player in the regulation of gene expression. However, the role of this interaction in regulating ICAM1 expression in breast cancer has not been elucidated. CpG methylation in the ICAM1 promoter is negatively correlated with ICAM1 expression, and ICAM1 expression is significantly positively correlated with DNMT and TET3 expression in breast cancer. TF binding attenuates ICAM1 promoter CpG methylation and promotes ICAM1 transcription. DNA methylation regulation enhances ICAM1 expression in breast cancer by promoting the transcription of transcription factors. In terms of mechanisms, RELA and STATs recruit TET3 to prevent DNMT-mediated DNA methylation, thereby maintaining CpG island hypomethylation in the ICAM1 promoter. Therefore, TF occupancy limits DNA methylation and affects ICAM1 expression in breast cancer.
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Affiliation(s)
- Mingcang Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
- Metabolic Disease Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ying Zhou
- Department of Peripheral Vascular, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chunyu Wu
- Department of Breast Surgery (Integrated Traditional and Western Medicine), Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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3
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Monteagudo-Sánchez A, Richard Albert J, Scarpa M, Noordermeer D, Greenberg MC. The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation. Nucleic Acids Res 2024; 52:10934-10950. [PMID: 39180406 PMCID: PMC11472158 DOI: 10.1093/nar/gkae724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/23/2024] [Accepted: 08/21/2024] [Indexed: 08/26/2024] Open
Abstract
During mammalian embryogenesis, both the 5-cytosine DNA methylation (5meC) landscape and three dimensional (3D) chromatin architecture are profoundly remodeled during a process known as 'epigenetic reprogramming.' An understudied aspect of epigenetic reprogramming is how the 5meC flux, per se, affects the 3D genome. This is pertinent given the 5meC-sensitivity of DNA binding for a key regulator of chromosome folding: CTCF. We profiled the CTCF binding landscape using a mouse embryonic stem cell (ESC) differentiation protocol that models embryonic 5meC dynamics. Mouse ESCs lacking DNA methylation machinery are able to exit naive pluripotency, thus allowing for dissection of subtle effects of CTCF on gene expression. We performed CTCF HiChIP in both wild-type and mutant conditions to assess gained CTCF-CTCF contacts in the absence of 5meC. We performed H3K27ac HiChIP to determine the impact that ectopic CTCF binding has on cis-regulatory contacts. Using 5meC epigenome editing, we demonstrated that the methyl-mark is able to impair CTCF binding at select loci. Finally, a detailed dissection of the imprinted Zdbf2 locus showed how 5meC-antagonism of CTCF allows for proper gene regulation during differentiation. This work provides a comprehensive overview of how 5meC impacts the 3D genome in a relevant model for early embryonic events.
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Affiliation(s)
| | | | - Margherita Scarpa
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91998 Gif-sur-Yvette, France
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4
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Monteagudo-Sánchez A, Noordermeer D, Greenberg MVC. The impact of DNA methylation on CTCF-mediated 3D genome organization. Nat Struct Mol Biol 2024; 31:404-412. [PMID: 38499830 DOI: 10.1038/s41594-024-01241-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/05/2024] [Indexed: 03/20/2024]
Abstract
Cytosine DNA methylation is a highly conserved epigenetic mark in eukaryotes. Although the role of DNA methylation at gene promoters and repetitive elements has been extensively studied, the function of DNA methylation in other genomic contexts remains less clear. In the nucleus of mammalian cells, the genome is spatially organized at different levels, and strongly influences myriad genomic processes. There are a number of factors that regulate the three-dimensional (3D) organization of the genome, with the CTCF insulator protein being among the most well-characterized. Pertinently, CTCF binding has been reported as being DNA methylation-sensitive in certain contexts, perhaps most notably in the process of genomic imprinting. Therefore, it stands to reason that DNA methylation may play a broader role in the regulation of chromatin architecture. Here we summarize the current understanding that is relevant to both the mammalian DNA methylation and chromatin architecture fields and attempt to assess the extent to which DNA methylation impacts the folding of the genome. The focus is in early embryonic development and cellular transitions when the epigenome is in flux, but we also describe insights from pathological contexts, such as cancer, in which the epigenome and 3D genome organization are misregulated.
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Affiliation(s)
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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6
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Grau J, Schmidt F, Schulz MH. Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models. Nucleic Acids Res 2023; 51:e95. [PMID: 37650641 PMCID: PMC10570048 DOI: 10.1093/nar/gkad693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/20/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
Several studies suggested that transcription factor (TF) binding to DNA may be impaired or enhanced by DNA methylation. We present MeDeMo, a toolbox for TF motif analysis that combines information about DNA methylation with models capturing intra-motif dependencies. In a large-scale study using ChIP-seq data for 335 TFs, we identify novel TFs that show a binding behaviour associated with DNA methylation. Overall, we find that the presence of CpG methylation decreases the likelihood of binding for the majority of methylation-associated TFs. For a considerable subset of TFs, we show that intra-motif dependencies are pivotal for accurately modelling the impact of DNA methylation on TF binding. We illustrate that the novel methylation-aware TF binding models allow to predict differential ChIP-seq peaks and improve the genome-wide analysis of TF binding. Our work indicates that simplistic models that neglect the effect of DNA methylation on DNA binding may lead to systematic underperformance for methylation-associated TFs.
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Affiliation(s)
- Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Florian Schmidt
- Goethe-University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
- Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken 66123, Germany
- Systems Biology and Data Analytics, Genome Institute of Singapore, Singapore 13862, Singapore
- ImmunoScape Pte Ltd, Singapore 228208, Singapore
| | - Marcel H Schulz
- Goethe-University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
- Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken 66123, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University, Frankfurt am Main, Germany
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7
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Vega-Benedetti AF, Loi E, Moi L, Zavattari P. DNA methylation alterations at RE1-silencing transcription factor binding sites and their flanking regions in cancer. Clin Epigenetics 2023; 15:98. [PMID: 37301955 PMCID: PMC10257853 DOI: 10.1186/s13148-023-01514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND DNA methylation changes, frequent early events in cancer, can modulate the binding of transcription factors. RE1-silencing transcription factor (REST) plays a fundamental role in regulating the expression of neuronal genes, and in particular their silencing in non-neuronal tissues, by inducing chromatin modifications, including DNA methylation changes, not only in the proximity of its binding sites but also in the flanking regions. REST has been found aberrantly expressed in brain cancer and other cancer types. In this work, we investigated DNA methylation alterations at REST binding sites and their flanking regions in a brain cancer (pilocytic astrocytoma), two gastrointestinal tumours (colorectal cancer and biliary tract cancer) and a blood cancer (chronic lymphocytic leukemia). RESULTS Differential methylation analyses focused on REST binding sites and their flanking regions were conducted between tumour and normal samples from our experimental datasets analysed by Illumina microarrays and the identified alterations were validated using publicly available datasets. We discovered distinct DNA methylation patterns between pilocytic astrocytoma and the other cancer types in agreement with the opposite oncogenic and tumour suppressive role of REST in glioma and non-brain tumours. CONCLUSIONS Our results suggest that these DNA methylation alterations in cancer may be associated with REST dysfunction opening the enthusiastic possibility to develop novel therapeutic interventions based on the modulation of this master regulator in order to restore the aberrant methylation of its target regions into a normal status.
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Affiliation(s)
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Loredana Moi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy.
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8
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Del Moral-Morales A, Salgado-Albarrán M, Sánchez-Pérez Y, Wenke NK, Baumbach J, Soto-Reyes E. CTCF and Its Multi-Partner Network for Chromatin Regulation. Cells 2023; 12:1357. [PMID: 37408191 DOI: 10.3390/cells12101357] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
Architectural proteins are essential epigenetic regulators that play a critical role in organizing chromatin and controlling gene expression. CTCF (CCCTC-binding factor) is a key architectural protein responsible for maintaining the intricate 3D structure of chromatin. Because of its multivalent properties and plasticity to bind various sequences, CTCF is similar to a Swiss knife for genome organization. Despite the importance of this protein, its mechanisms of action are not fully elucidated. It has been hypothesized that its versatility is achieved through interaction with multiple partners, forming a complex network that regulates chromatin folding within the nucleus. In this review, we delve into CTCF's interactions with other molecules involved in epigenetic processes, particularly histone and DNA demethylases, as well as several long non-coding RNAs (lncRNAs) that are able to recruit CTCF. Our review highlights the importance of CTCF partners to shed light on chromatin regulation and pave the way for future exploration of the mechanisms that enable the finely-tuned role of CTCF as a master regulator of chromatin.
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Affiliation(s)
- Aylin Del Moral-Morales
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Marisol Salgado-Albarrán
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Yesennia Sánchez-Pérez
- Subdirección de Investigación, Instituto Nacional de Cancerología, Mexico City 14080, Mexico
| | - Nina Kerstin Wenke
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
- Computational BioMedicine Lab., University of Southern Denmark, DK-5230 Odense, Denmark
| | - Ernesto Soto-Reyes
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
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9
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Kreibich E, Kleinendorst R, Barzaghi G, Kaspar S, Krebs AR. Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation. Mol Cell 2023; 83:787-802.e9. [PMID: 36758546 DOI: 10.1016/j.molcel.2023.01.017] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/21/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023]
Abstract
Enhancers are cis-regulatory elements that control the establishment of cell identities during development. In mammals, enhancer activation is tightly coupled with DNA demethylation. However, whether this epigenetic remodeling is necessary for enhancer activation is unknown. Here, we adapted single-molecule footprinting to measure chromatin accessibility and transcription factor binding as a function of the presence of methylation on the same DNA molecules. We leveraged natural epigenetic heterogeneity at active enhancers to test the impact of DNA methylation on their chromatin accessibility in multiple cell lineages. Although reduction of DNA methylation appears dispensable for the activity of most enhancers, we identify a class of cell-type-specific enhancers where DNA methylation antagonizes the binding of transcription factors. Genetic perturbations reveal that chromatin accessibility and transcription factor binding require active demethylation at these loci. Thus, in addition to safeguarding the genome from spurious activation, DNA methylation directly controls transcription factor occupancy at active enhancers.
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Affiliation(s)
- Elisa Kreibich
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Rozemarijn Kleinendorst
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Guido Barzaghi
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Sarah Kaspar
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Arnaud R Krebs
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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10
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Loyfer N, Magenheim J, Peretz A, Cann G, Bredno J, Klochendler A, Fox-Fisher I, Shabi-Porat S, Hecht M, Pelet T, Moss J, Drawshy Z, Amini H, Moradi P, Nagaraju S, Bauman D, Shveiky D, Porat S, Dior U, Rivkin G, Or O, Hirshoren N, Carmon E, Pikarsky A, Khalaileh A, Zamir G, Grinbaum R, Abu Gazala M, Mizrahi I, Shussman N, Korach A, Wald O, Izhar U, Erez E, Yutkin V, Samet Y, Rotnemer Golinkin D, Spalding KL, Druid H, Arner P, Shapiro AMJ, Grompe M, Aravanis A, Venn O, Jamshidi A, Shemer R, Dor Y, Glaser B, Kaplan T. A DNA methylation atlas of normal human cell types. Nature 2023; 613:355-364. [PMID: 36599988 PMCID: PMC9811898 DOI: 10.1038/s41586-022-05580-6] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 11/18/2022] [Indexed: 01/05/2023]
Abstract
DNA methylation is a fundamental epigenetic mark that governs gene expression and chromatin organization, thus providing a window into cellular identity and developmental processes1. Current datasets typically include only a fraction of methylation sites and are often based either on cell lines that underwent massive changes in culture or on tissues containing unspecified mixtures of cells2-5. Here we describe a human methylome atlas, based on deep whole-genome bisulfite sequencing, allowing fragment-level analysis across thousands of unique markers for 39 cell types sorted from 205 healthy tissue samples. Replicates of the same cell type are more than 99.5% identical, demonstrating the robustness of cell identity programmes to environmental perturbation. Unsupervised clustering of the atlas recapitulates key elements of tissue ontogeny and identifies methylation patterns retained since embryonic development. Loci uniquely unmethylated in an individual cell type often reside in transcriptional enhancers and contain DNA binding sites for tissue-specific transcriptional regulators. Uniquely hypermethylated loci are rare and are enriched for CpG islands, Polycomb targets and CTCF binding sites, suggesting a new role in shaping cell-type-specific chromatin looping. The atlas provides an essential resource for study of gene regulation and disease-associated genetic variants, and a wealth of potential tissue-specific biomarkers for use in liquid biopsies.
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Affiliation(s)
- Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ayelet Peretz
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilana Fox-Fisher
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sapir Shabi-Porat
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Merav Hecht
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tsuria Pelet
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joshua Moss
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Zeina Drawshy
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | | | - Dvora Bauman
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Shveiky
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shay Porat
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uri Dior
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gurion Rivkin
- Department of Orthopedics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Omer Or
- Department of Orthopedics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nir Hirshoren
- Department of Otolaryngology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Einat Carmon
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Surgery, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Alon Pikarsky
- Surgery Division, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Abed Khalaileh
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gideon Zamir
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ronit Grinbaum
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Machmud Abu Gazala
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ido Mizrahi
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Noam Shussman
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Korach
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ori Wald
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uzi Izhar
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eldad Erez
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vladimir Yutkin
- Department of Urology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yaacov Samet
- Department of Vascular Surgery, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Devorah Rotnemer Golinkin
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kirsty L Spalding
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Druid
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Forensic Medicine, The National Board of Forensic Medicine, Stockholm, Sweden
| | - Peter Arner
- Department of Medicine (H7) and Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - A M James Shapiro
- Department of Surgery and the Clinical Islet Transplant Program, University of Alberta, Edmonton, Alberta, Canada
| | - Markus Grompe
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alex Aravanis
- GRAIL, Inc., Menlo Park, CA, USA
- Illumina, Inc., San Diego, CA, USA
| | | | | | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
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11
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Dehingia B, Milewska M, Janowski M, Pękowska A. CTCF shapes chromatin structure and gene expression in health and disease. EMBO Rep 2022; 23:e55146. [PMID: 35993175 PMCID: PMC9442299 DOI: 10.15252/embr.202255146] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/31/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Abstract
CCCTC-binding factor (CTCF) is an eleven zinc finger (ZF), multivalent transcriptional regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations of its ZFs. The great majority of the ~50,000 genomic locations bound by the CTCF protein in a given cell type is intergenic, and a fraction of these sites overlaps with transcriptional enhancers. Furthermore, a proportion of the regions bound by CTCF intersect genes and promoters. This suggests multiple ways in which CTCF may impact gene expression. At promoters, CTCF can directly affect transcription. At more distal sites, CTCF may orchestrate interactions between regulatory elements and help separate eu- and heterochromatic areas in the genome, exerting a chromatin barrier function. In this review, we outline how CTCF contributes to the regulation of the three-dimensional structure of chromatin and the formation of chromatin domains. We discuss how CTCF binding and architectural functions are regulated. We examine the literature implicating CTCF in controlling gene expression in development and disease both by acting as an insulator and a factor facilitating regulatory elements to efficiently interact with each other in the nuclear space.
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Affiliation(s)
- Bondita Dehingia
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental BiologyPolish Academy of SciencesWarsawPoland
| | - Małgorzata Milewska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental BiologyPolish Academy of SciencesWarsawPoland
| | - Marcin Janowski
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental BiologyPolish Academy of SciencesWarsawPoland
| | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental BiologyPolish Academy of SciencesWarsawPoland
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12
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Enhancer methylation dynamics drive core transcriptional regulatory circuitry in pan-cancer. Oncogene 2022; 41:3474-3484. [PMID: 35655092 DOI: 10.1038/s41388-022-02359-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/11/2022] [Accepted: 05/19/2022] [Indexed: 12/16/2022]
Abstract
Accumulating evidence has demonstrated that enhancer methylation has strong and dynamic regulatory effects on gene expression. Some transcription factors (TFs) can auto- and cross-regulate in a feed-forward manner, and cooperate with their enhancers to form core transcriptional regulatory circuitries (CRCs). However, the elaborated regulatory mechanism between enhancer methylation and CRC remains the tip of the iceberg. Here, we revealed that DNA methylation could drive the tissue-specific enhancer basal transcription and target gene expression in human cancers. By integrating methylome, transcriptome, and 3D genomic data, we identified enhancer methylation triplets (enhancer methylation-enhancer transcription-target gene expression) and dissected potential regulatory patterns within them. Moreover, we observed that cancer-specific core TFs regulated by enhancers were able to shape their enhancer methylation forming the enhancer methylation-driven CRCs (emCRCs). Further parsing of clinical implications showed rewired emCRCs could serve as druggable targets and prognostic risk markers. In summary, the integrative analysis of enhancer methylation regulome would facilitate portraying the cancer epigenomics landscape and developing the epigenetic anti-cancer approaches.
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13
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Lancaster EE, Vladimirov VI, Riley BP, Landry JW, Roberson-Nay R, York TP. LARGE-SCALE INTEGRATION OF DNA METHYLATION AND GENE EXPRESSION ARRAY PLATFORMS IDENTIFIES BOTH cis AND trans RELATIONSHIPS. Epigenetics 2022; 17:1753-1773. [PMID: 35608069 PMCID: PMC9621057 DOI: 10.1080/15592294.2022.2079293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Although epigenome-wide association studies (EWAS) have been successful in identifying DNA methylation (DNAm) patterns associated with disease states, any further characterization of etiologic mechanisms underlying disease remains elusive. This knowledge gap does not originate from a lack of DNAm–trait associations, but rather stems from study design issues that affect the interpretability of EWAS results. Despite known limitations in predicting the function of a particular CpG site, most EWAS maintain the broad assumption that altered DNAm results in a concomitant change of transcription at the most proximal gene. This study integrated DNAm and gene expression (GE) measurements in two cohorts, the Adolescent and Young Adult Twin Study (AYATS) and the Pregnancy, Race, Environment, Genes (PREG) study, to improve the understanding of epigenomic regulatory mechanisms. CpG sites associated with GE in cis were enriched in areas of transcription factor binding and areas of intermediate-to-low CpG density. CpG sites associated with trans GE were also enriched in areas of known regulatory significance, including enhancer regions. These results highlight issues with restricting DNAm-transcript annotations to small genomic intervals and question the validity of assuming a cis DNAm–GE pathway. Based on these findings, the interpretation of EWAS results is limited in studies without multi-omic support and further research should identify genomic regions in which GE-associated DNAm is overrepresented. An in-depth characterization of GE-associated CpG sites could improve predictions of the downstream functional impact of altered DNAm and inform best practices for interpreting DNAm–trait associations generated by EWAS.
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Affiliation(s)
- Eva E Lancaster
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23220
| | | | - Brien P Riley
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23220.,Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23220
| | - Joseph W Landry
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23220
| | - Roxann Roberson-Nay
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23220.,Department of Psychology, Virginia Commonwealth University, Richmond, VA 23220
| | - Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23220.,Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA 23220
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14
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Silver MJ, Saffari A, Kessler NJ, Chandak GR, Fall CHD, Issarapu P, Dedaniya A, Betts M, Moore SE, Routledge MN, Herceg Z, Cuenin C, Derakhshan M, James PT, Monk D, Prentice AM. Environmentally sensitive hotspots in the methylome of the early human embryo. eLife 2022; 11:e72031. [PMID: 35188105 PMCID: PMC8912923 DOI: 10.7554/elife.72031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/18/2022] [Indexed: 11/26/2022] Open
Abstract
In humans, DNA methylation marks inherited from gametes are largely erased following fertilisation, prior to construction of the embryonic methylome. Exploiting a natural experiment of seasonal variation including changes in diet and nutritional status in rural Gambia, we analysed three datasets covering two independent child cohorts and identified 259 CpGs showing consistent associations between season of conception (SoC) and DNA methylation. SoC effects were most apparent in early infancy, with evidence of attenuation by mid-childhood. SoC-associated CpGs were enriched for metastable epialleles, parent-of-origin-specific methylation and germline differentially methylated regions, supporting a periconceptional environmental influence. Many SoC-associated CpGs overlapped enhancers or sites of active transcription in H1 embryonic stem cells and fetal tissues. Half were influenced but not determined by measured genetic variants that were independent of SoC. Environmental 'hotspots' providing a record of environmental influence at periconception constitute a valuable resource for investigating epigenetic mechanisms linking early exposures to lifelong health and disease.
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Affiliation(s)
- Matt J Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Ayden Saffari
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Noah J Kessler
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Gririraj R Chandak
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Caroline HD Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General HospitalSouthamptonUnited Kingdom
| | - Prachand Issarapu
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Akshay Dedaniya
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Modupeh Betts
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Sophie E Moore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
- Department of Women and Children's Health, King's College LondonLondonUnited Kingdom
| | - Michael N Routledge
- School of Medicine, University of LeedsLeedsUnited Kingdom
- School of Food and Biological Engineering, Jiangsu UniversityZhenjiangChina
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Maria Derakhshan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Philip T James
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - David Monk
- Biomedical Research Centre, University of East AngliaNorwichUnited Kingdom
- Bellvitge Institute for Biomedical ResearchBarcelonaSpain
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
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15
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Yeh CY, Huang WH, Chen HC, Meir YJJ. Capturing Pluripotency and Beyond. Cells 2021; 10:cells10123558. [PMID: 34944066 PMCID: PMC8700150 DOI: 10.3390/cells10123558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
During the development of a multicellular organism, the specification of different cell lineages originates in a small group of pluripotent cells, the epiblasts, formed in the preimplantation embryo. The pluripotent epiblast is protected from premature differentiation until exposure to inductive cues in strictly controlled spatially and temporally organized patterns guiding fetus formation. Epiblasts cultured in vitro are embryonic stem cells (ESCs), which recapitulate the self-renewal and lineage specification properties of their endogenous counterparts. The characteristics of totipotency, although less understood than pluripotency, are becoming clearer. Recent studies have shown that a minor ESC subpopulation exhibits expanded developmental potential beyond pluripotency, displaying a characteristic reminiscent of two-cell embryo blastomeres (2CLCs). In addition, reprogramming both mouse and human ESCs in defined media can produce expanded/extended pluripotent stem cells (EPSCs) similar to but different from 2CLCs. Further, the molecular roadmaps driving the transition of various potency states have been clarified. These recent key findings will allow us to understand eutherian mammalian development by comparing the underlying differences between potency network components during development. Using the mouse as a paradigm and recent progress in human PSCs, we review the epiblast's identity acquisition during embryogenesis and their ESC counterparts regarding their pluripotent fates and beyond.
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Affiliation(s)
- Chih-Yu Yeh
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
| | - Wei-Han Huang
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
| | - Hung-Chi Chen
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Correspondence: (H.-C.C.); (Y.-J.J.M.)
| | - Yaa-Jyuhn James Meir
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: (H.-C.C.); (Y.-J.J.M.)
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16
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Somatic Reprogramming-Above and Beyond Pluripotency. Cells 2021; 10:cells10112888. [PMID: 34831113 PMCID: PMC8616127 DOI: 10.3390/cells10112888] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/11/2022] Open
Abstract
Pluripotent stem cells, having long been considered the fountain of youth, have caught the attention of many researchers from diverse backgrounds due to their capacity for unlimited self-renewal and potential to differentiate into all cell types. Over the past 15 years, the advanced development of induced pluripotent stem cells (iPSCs) has displayed an unparalleled potential for regenerative medicine, cell-based therapies, modeling human diseases in culture, and drug discovery. The transcription factor quartet (Oct4, Sox2, Klf4, and c-Myc) reprograms highly differentiated somatic cells back to a pluripotent state recapitulated embryonic stem cells (ESCs) in different aspects, including gene expression profile, epigenetic signature, and functional pluripotency. With the prior fruitful studies in SCNT and cell fusion experiments, iPSC finds its place and implicates that the differentiated somatic epigenome retains plasticity for re-gaining the pluripotency and further stretchability to reach a totipotency-like state. These achievements have revolutionized the concept and created a new avenue in biomedical sciences for clinical applications. With the advent of 15 years’ progress-making after iPSC discovery, this review is focused on how the current concept is established by revisiting those essential landmark studies and summarizing its current biomedical applications status to facilitate the new era entry of regenerative therapy.
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17
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Fu Q, North PE, Ke X, Huang YW, Fritz KA, Majnik AV, Lane RH. Adverse Maternal Environment and Postweaning Western Diet Alter Hepatic CD36 Expression and Methylation Concurrently with Nonalcoholic Fatty Liver Disease in Mouse Offspring. J Nutr 2021; 151:3102-3112. [PMID: 34486661 PMCID: PMC8485909 DOI: 10.1093/jn/nxab249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 07/01/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The role of an adverse maternal environment (AME) in conjunction with a postweaning Western diet (WD) in the development of nonalcoholic fatty liver disease (NAFLD) in adult offspring has not been explored. Likewise, the molecular mechanisms associated with AME-induced NAFLD have not been studied. The fatty acid translocase or cluster of differentiation 36 (CD36) has been implicated to play a causal role in the pathogenesis of WD-induced steatosis. However, it is unknown if CD36 plays a role in AME-induced NAFLD. OBJECTIVE This study was designed to evaluate the isolated and additive impact of AME and postweaning WD on the expression and DNA methylation of hepatic Cd36 in association with the development of NAFLD in a novel mouse model. METHODS AME constituted maternal WD and maternal stress, whereas the control (Con) group had neither. Female C57BL/6J mice were fed a WD [40% fat energy, 29.1% sucrose energy, and 0.15% cholesterol (wt/wt)] 5 wk prior to pregnancy and throughout lactation. Non invasive variable stressors (random frequent cage changing, limited bedding, novel object, etc.) were applied to WD dams during the last third of pregnancy to produce an AME. Con dams consumed the control diet (CD) (10% fat energy, no sucrose or cholesterol) and were not exposed to stress. Male offspring were weaned onto either CD or WD, creating 4 experimental groups: Con-CD, Con-WD, AME-CD, and AME-WD, and evaluated for metabolic and molecular parameters at 120 d of age. RESULTS AME and postweaning WD independently and additively increased the development of hepatic steatosis in adult male offspring. AME and WD independently and additively upregulated hepatic CD36 protein and mRNA expression and hypomethylated promoters 2 and 3 of the Cd36 gene. CONCLUSIONS Using a mouse AME model together with postweaning WD, this study demonstrates a role for CD36 in AME-induced NAFLD in offspring and reveals 2 regions of environmentally induced epigenetic heterogeneity within Cd36.
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Affiliation(s)
- Qi Fu
- Department of Research Administration, Children's Mercy Hospital, Kansas City, MO, USA
| | - Paula E North
- Department of Pediatric Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Xingrao Ke
- Department of Research Administration, Children's Mercy Hospital, Kansas City, MO, USA
| | - Yi-Wen Huang
- Department of Obstetrics & Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Katie A Fritz
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
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18
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Krebs AR. Studying transcription factor function in the genome at molecular resolution. Trends Genet 2021; 37:798-806. [DOI: 10.1016/j.tig.2021.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022]
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19
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A Comprehensive Toolbox to Analyze Enhancer-Promoter Functions. Methods Mol Biol 2021. [PMID: 34382181 DOI: 10.1007/978-1-0716-1597-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Knowledge in gene transcription and chromatin regulation has been intensely studied for decades, but thanks to next-generation sequencing (NGS) techniques there has been a major leap forward in the last few years. Historically, identification of specific enhancer elements has led to the identification of master transcription factors (TFs) in the 1990s. Genetic and biochemical experiments have identified the key regulators controlling RNA polymerase II (RNAPII) transcription and structurally analyses have elucidated detailed mechanisms. NGS and the development of chromatin immunoprecipitation (ChIP) have accelerated the gain of knowledge in the recent years. By now, we have a dazzling wealth of techniques that are currently used to put gene expression into a genome-wide context. This book is an attempt to assemble useful protocols for many researchers within and nearby research areas. In general, these innovative techniques focus on enhancer and promoter studies. The techniques should also be of interest for related fields such as DNA repair and replication.
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20
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Min JL, Hemani G, Hannon E, Dekkers KF, Castillo-Fernandez J, Luijk R, Carnero-Montoro E, Lawson DJ, Burrows K, Suderman M, Bretherick AD, Richardson TG, Klughammer J, Iotchkova V, Sharp G, Al Khleifat A, Shatunov A, Iacoangeli A, McArdle WL, Ho KM, Kumar A, Söderhäll C, Soriano-Tárraga C, Giralt-Steinhauer E, Kazmi N, Mason D, McRae AF, Corcoran DL, Sugden K, Kasela S, Cardona A, Day FR, Cugliari G, Viberti C, Guarrera S, Lerro M, Gupta R, Bollepalli S, Mandaviya P, Zeng Y, Clarke TK, Walker RM, Schmoll V, Czamara D, Ruiz-Arenas C, Rezwan FI, Marioni RE, Lin T, Awaloff Y, Germain M, Aïssi D, Zwamborn R, van Eijk K, Dekker A, van Dongen J, Hottenga JJ, Willemsen G, Xu CJ, Barturen G, Català-Moll F, Kerick M, Wang C, Melton P, Elliott HR, Shin J, Bernard M, Yet I, Smart M, Gorrie-Stone T, Shaw C, Al Chalabi A, Ring SM, Pershagen G, Melén E, Jiménez-Conde J, Roquer J, Lawlor DA, Wright J, Martin NG, Montgomery GW, Moffitt TE, Poulton R, Esko T, Milani L, Metspalu A, Perry JRB, Ong KK, Wareham NJ, Matullo G, Sacerdote C, Panico S, Caspi A, Arseneault L, Gagnon F, Ollikainen M, Kaprio J, Felix JF, Rivadeneira F, Tiemeier H, et alMin JL, Hemani G, Hannon E, Dekkers KF, Castillo-Fernandez J, Luijk R, Carnero-Montoro E, Lawson DJ, Burrows K, Suderman M, Bretherick AD, Richardson TG, Klughammer J, Iotchkova V, Sharp G, Al Khleifat A, Shatunov A, Iacoangeli A, McArdle WL, Ho KM, Kumar A, Söderhäll C, Soriano-Tárraga C, Giralt-Steinhauer E, Kazmi N, Mason D, McRae AF, Corcoran DL, Sugden K, Kasela S, Cardona A, Day FR, Cugliari G, Viberti C, Guarrera S, Lerro M, Gupta R, Bollepalli S, Mandaviya P, Zeng Y, Clarke TK, Walker RM, Schmoll V, Czamara D, Ruiz-Arenas C, Rezwan FI, Marioni RE, Lin T, Awaloff Y, Germain M, Aïssi D, Zwamborn R, van Eijk K, Dekker A, van Dongen J, Hottenga JJ, Willemsen G, Xu CJ, Barturen G, Català-Moll F, Kerick M, Wang C, Melton P, Elliott HR, Shin J, Bernard M, Yet I, Smart M, Gorrie-Stone T, Shaw C, Al Chalabi A, Ring SM, Pershagen G, Melén E, Jiménez-Conde J, Roquer J, Lawlor DA, Wright J, Martin NG, Montgomery GW, Moffitt TE, Poulton R, Esko T, Milani L, Metspalu A, Perry JRB, Ong KK, Wareham NJ, Matullo G, Sacerdote C, Panico S, Caspi A, Arseneault L, Gagnon F, Ollikainen M, Kaprio J, Felix JF, Rivadeneira F, Tiemeier H, van IJzendoorn MH, Uitterlinden AG, Jaddoe VWV, Haley C, McIntosh AM, Evans KL, Murray A, Räikkönen K, Lahti J, Nohr EA, Sørensen TIA, Hansen T, Morgen CS, Binder EB, Lucae S, Gonzalez JR, Bustamante M, Sunyer J, Holloway JW, Karmaus W, Zhang H, Deary IJ, Wray NR, Starr JM, Beekman M, van Heemst D, Slagboom PE, Morange PE, Trégouët DA, Veldink JH, Davies GE, de Geus EJC, Boomsma DI, Vonk JM, Brunekreef B, Koppelman GH, Alarcón-Riquelme ME, Huang RC, Pennell CE, van Meurs J, Ikram MA, Hughes AD, Tillin T, Chaturvedi N, Pausova Z, Paus T, Spector TD, Kumari M, Schalkwyk LC, Visscher PM, Davey Smith G, Bock C, Gaunt TR, Bell JT, Heijmans BT, Mill J, Relton CL. Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation. Nat Genet 2021; 53:1311-1321. [PMID: 34493871 PMCID: PMC7612069 DOI: 10.1038/s41588-021-00923-x] [Show More Authors] [Citation(s) in RCA: 267] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/12/2021] [Indexed: 12/25/2022]
Abstract
Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype-phenotype map than previously anticipated.
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Affiliation(s)
- Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Koen F Dekkers
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | | | - René Luijk
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Elena Carnero-Montoro
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
| | - Daniel J Lawson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Gemma Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Biostatistics and Health Informatics, King's College London, London, UK
| | - Wendy L McArdle
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Karen M Ho
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Chronic Disease Epidemiology unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Carolina Soriano-Tárraga
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Eva Giralt-Steinhauer
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Dan Mason
- Bradford Institute for Health Research, Bradford, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Karen Sugden
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Silva Kasela
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alexia Cardona
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Felix R Day
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Giovanni Cugliari
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Clara Viberti
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Simonetta Guarrera
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Michael Lerro
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Richa Gupta
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pooja Mandaviya
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Yanni Zeng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Toni-Kim Clarke
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Vanessa Schmoll
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Carlos Ruiz-Arenas
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Faisal I Rezwan
- Department of Computer Science, Aberystwyth University, Aberystwyth, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Tian Lin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Yvonne Awaloff
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Marine Germain
- INSERM UMR_S 1219, Bordeaux Population Health Center, University of Bordeaux, Bordeaux, France
| | - Dylan Aïssi
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Ramona Zwamborn
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kristel van Eijk
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Annelot Dekker
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, the Netherlands
- CiiM and TWINCORE, Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany
| | - Guillermo Barturen
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
| | - Francesc Català-Moll
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | - Martin Kerick
- Instituto de Parasitología y Biomedicina López Neyra, CSIC, Granada, Spain
| | - Carol Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, Australia
| | - Phillip Melton
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Australia
- School of Global Population Health, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jean Shin
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Manon Bernard
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Idil Yet
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Melissa Smart
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | | | - Chris Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Neurology, King's College Hospital, London, UK
| | - Ammar Al Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Neurology, King's College Hospital, London, UK
- United Kingdom Dementia Research Institute, King's College London, London, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Jordi Jiménez-Conde
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Jaume Roquer
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - John Wright
- Bradford Institute for Health Research, Bradford, UK
| | | | - Grant W Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Terrie E Moffitt
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical School, Durham, NC, USA
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Richie Poulton
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - John R B Perry
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Ken K Ong
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Carlotta Sacerdote
- Italian Institute for Genomic Medicine, Turin, Italy
- Piemonte Centre for Cancer Prevention, Turin, Italy
| | - Salvatore Panico
- Dipartimento Di Medicina Clinica E Chirurgia, Federico II University, Naples, Italy
| | - Avshalom Caspi
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical School, Durham, NC, USA
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Louise Arseneault
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - France Gagnon
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Miina Ollikainen
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Social and Behavioral Science, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Marinus H van IJzendoorn
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Department of Clinical, Educational and Health Psychology, Division on Psychology and Language Sciences, Faculty of Brain Sciences, University College London, London, UK
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Chris Haley
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Alison Murray
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Institute of Clinical research, University of Southern Denmark, Odense, Denmark
- Centre of Women's, Family and Child Health, University of South-Eastern Norway, Kongsberg, Norway
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health (Section of Epidemiology), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Camilla S Morgen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Susanne Lucae
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Juan Ramon Gonzalez
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Sunyer
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Diana van Heemst
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Eco J C de Geus
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, GRIAC Research Institute Groningen, Groningen, the Netherlands
| | - Bert Brunekreef
- Institute for Risk Assessment Sciences, Universiteit Utrecht, Utrecht, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, the Netherlands
| | - Marta E Alarcón-Riquelme
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Craig E Pennell
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, Australia
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | | | | | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Tomas Paus
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, Canada
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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21
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Lu J, Cannizzaro E, Meier-Abt F, Scheinost S, Bruch PM, Giles HAR, Lütge A, Hüllein J, Wagner L, Giacopelli B, Nadeu F, Delgado J, Campo E, Mangolini M, Ringshausen I, Böttcher M, Mougiakakos D, Jacobs A, Bodenmiller B, Dietrich S, Oakes CC, Zenz T, Huber W. Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia. NATURE CANCER 2021; 2:853-864. [PMID: 34423310 PMCID: PMC7611543 DOI: 10.1038/s43018-021-00216-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/10/2021] [Indexed: 11/10/2022]
Abstract
Chronic Lymphocytic Leukemia (CLL) has a complex pattern of driver mutations and much of its clinical diversity remains unexplained. We devised a method for simultaneous subgroup discovery across multiple data types and applied it to genomic, transcriptomic, DNA methylation and ex-vivo drug response data from 217 Chronic Lymphocytic Leukemia (CLL) cases. We uncovered a biological axis of heterogeneity strongly associated with clinical behavior and orthogonal to the known biomarkers. We validated its presence and clinical relevance in four independent cohorts (n=547 patients). We find that this axis captures the proliferative drive (PD) of CLL cells, as it associates with lymphocyte doubling rate, global hypomethylation, accumulation of driver aberrations and response to pro-proliferative stimuli. CLL-PD was linked to the activation of mTOR-MYC-oxidative phosphorylation (OXPHOS) through transcriptomic, proteomic and single cell resolution analysis. CLL-PD is a key determinant of disease outcome in CLL. Our multi-table integration approach may be applicable to other tumors whose inter-individual differences are currently unexplained.
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Affiliation(s)
- Junyan Lu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Ester Cannizzaro
- Department of Medical Oncology and Hematology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Fabienne Meier-Abt
- Department of Medical Oncology and Hematology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Sebastian Scheinost
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Peter-Martin Bruch
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- University of Heidelberg, Heidelberg, Germany
| | - Holly AR Giles
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Almut Lütge
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Jennifer Hüllein
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Lena Wagner
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Brian Giacopelli
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH
| | - Ferran Nadeu
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Julio Delgado
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematopathology Unit, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Elías Campo
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematopathology Unit, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Maurizio Mangolini
- Wellcome Trust/MRC Cambridge Stem Cell Institute & Department of Haematology, University of Cambridge, Cambridge CB2 0AH, UK
| | - Ingo Ringshausen
- Wellcome Trust/MRC Cambridge Stem Cell Institute & Department of Haematology, University of Cambridge, Cambridge CB2 0AH, UK
| | - Martin Böttcher
- Department of Internal Medicine 5, Hematology and Oncology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Dimitrios Mougiakakos
- Department of Internal Medicine 5, Hematology and Oncology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Andrea Jacobs
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Bernd Bodenmiller
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Sascha Dietrich
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- University of Heidelberg, Heidelberg, Germany
- Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christopher C. Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
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22
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Mounger J, Ainouche ML, Bossdorf O, Cavé-Radet A, Li B, Parepa M, Salmon A, Yang J, Richards CL. Epigenetics and the success of invasive plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200117. [PMID: 33866809 PMCID: PMC8059582 DOI: 10.1098/rstb.2020.0117] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Biological invasions impose ecological and economic problems on a global scale, but also provide extraordinary opportunities for studying contemporary evolution. It is critical to understand the evolutionary processes that underly invasion success in order to successfully manage existing invaders, and to prevent future invasions. As successful invasive species sometimes are suspected to rapidly adjust to their new environments in spite of very low genetic diversity, we are obliged to re-evaluate genomic-level processes that translate into phenotypic diversity. In this paper, we review work that supports the idea that trait variation, within and among invasive populations, can be created through epigenetic or other non-genetic processes, particularly in clonal invaders where somatic changes can persist indefinitely. We consider several processes that have been implicated as adaptive in invasion success, focusing on various forms of 'genomic shock' resulting from exposure to environmental stress, hybridization and whole-genome duplication (polyploidy), and leading to various patterns of gene expression re-programming and epigenetic changes that contribute to phenotypic variation or even novelty. These mechanisms can contribute to transgressive phenotypes, including hybrid vigour and novel traits, and may thus help to understand the huge successes of some plant invaders, especially those that are genetically impoverished. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Jeannie Mounger
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33617, USA
| | - Malika L. Ainouche
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Armand Cavé-Radet
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Bo Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Madalin Parepa
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Armel Salmon
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Ji Yang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Christina L. Richards
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33617, USA
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
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23
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Vanzan L, Soldati H, Ythier V, Anand S, Braun SMG, Francis N, Murr R. High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites. Nat Commun 2021; 12:3337. [PMID: 34099689 PMCID: PMC8184831 DOI: 10.1038/s41467-021-23630-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
Binding of mammalian transcription factors (TFs) to regulatory regions is hindered by chromatin compaction and DNA methylation of their binding sites. Nevertheless, pioneer transcription factors (PFs), a distinct class of TFs, have the ability to access nucleosomal DNA, leading to nucleosome remodelling and enhanced chromatin accessibility. Whether PFs can bind to methylated sites and induce DNA demethylation is largely unknown. Using a highly parallelized approach to investigate PF ability to bind methylated DNA and induce DNA demethylation, we show that the interdependence between DNA methylation and TF binding is more complex than previously thought, even within a select group of TFs displaying pioneering activity; while some PFs do not affect the methylation status of their binding sites, we identified PFs that can protect DNA from methylation and others that can induce DNA demethylation at methylated binding sites. We call the latter super pioneer transcription factors (SPFs), as they are seemingly able to overcome several types of repressive epigenetic marks. Finally, while most SPFs induce TET-dependent active DNA demethylation, SOX2 binding leads to passive demethylation, an activity enhanced by the co-binding of OCT4. This finding suggests that SPFs could interfere with epigenetic memory during DNA replication.
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Affiliation(s)
- Ludovica Vanzan
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Hadrien Soldati
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Victor Ythier
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Diagnostic Department, Clinical Pathology Division, University Hospital of Geneva, Geneva, Switzerland
| | - Santosh Anand
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Department of Informatics, Systems and Communications (DISCo), University of Milano-Bicocca, Milan, Italy
| | - Simon M G Braun
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Nicole Francis
- Institut de Recherches Cliniques de Montréal (IRCM) and Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
| | - Rabih Murr
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
- Institute for Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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24
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Huff TC, Sant DW, Camarena V, Van Booven D, Andrade NS, Mustafi S, Monje PV, Wang G. Vitamin C regulates Schwann cell myelination by promoting DNA demethylation of pro-myelinating genes. J Neurochem 2021; 157:1759-1773. [PMID: 32219848 PMCID: PMC7530063 DOI: 10.1111/jnc.15015] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/12/2022]
Abstract
Ascorbic acid (vitamin C) is critical for Schwann cells to myelinate peripheral nerve axons during development and remyelination after injury. However, its exact mechanism remains elusive. Vitamin C is a dietary nutrient that was recently discovered to promote active DNA demethylation. Schwann cell myelination is characterized by global DNA demethylation in vivo and may therefore be regulated by vitamin C. We found that vitamin C induces a massive transcriptomic shift (n = 3,848 genes) in primary cultured Schwann cells while simultaneously producing a global increase in genomic 5-hydroxymethylcytosine (5hmC), a DNA demethylation intermediate which regulates transcription. Vitamin C up-regulates 10 pro-myelinating genes which exhibit elevated 5hmC content in both the promoter and gene body regions of these loci following treatment. Using a mouse model of human vitamin C metabolism, we found that maternal dietary vitamin C deficiency causes peripheral nerve hypomyelination throughout early development in resulting offspring. Additionally, dietary vitamin C intake regulates the expression of myelin-related proteins such as periaxin (PRX) and myelin basic protein (MBP) during development and remyelination after injury in mice. Taken together, these results suggest that vitamin C cooperatively promotes myelination through 1) increased DNA demethylation and transcription of pro-myelinating genes, and 2) its known role in stabilizing collagen helices to form the basal lamina that is necessary for myelination.
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Affiliation(s)
- Tyler C. Huff
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - David W. Sant
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Vladimir Camarena
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nadja S. Andrade
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sushmita Mustafi
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Paula V. Monje
- Department of Neurological Surgery, Indiana University, Indianapolis, IN, USA
| | - Gaofeng Wang
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
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25
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Yu X, Kong DX. EnMCB: an R/bioconductor package for predicting disease progression based on methylation correlated blocks using ensemble models. Bioinformatics 2021; 37:4282-4284. [PMID: 34050729 DOI: 10.1093/bioinformatics/btab415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 04/27/2021] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Based on the concept that adjacent CpG sites in the same DNA strand may be modified by a methyltransferase or demethylase together, current study found that the combination of multiple CpGs into a single block may improve cancer diagnosis. However, there is no R package available for building models based on methylation correlated blocks. RESULTS Here, we present a package named stacked ensemble of machine learning models for methylation correlated blocks (EnMCB) to build signatures based on DNA methylation correlated blocks for survival prediction. The Cox regression, support vector regression, mboost and elastic-net model were combined in the ensemble model. Methylation profiles from Cancer Genome Atlas were used as real datasets. The package automatically partitions the genome into blocks of tightly co-methylated CpG sites, termed methylation correlated blocks. After partitioning and modeling, the diagnostic capacities for predicting patients' survival are given. AVAILABILITY EnMCB is freely available for download at GitHub (https://github.com/whirlsyu/EnMCB/) and Bioconductor (http://bioconductor.org/packages/release/bioc/html/EnMCB.html). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xin Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - De-Xin Kong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
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26
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Species-Specific Relationships between DNA and Chromatin Properties of CpG Islands in Embryonic Stem Cells and Differentiated Cells. Stem Cell Reports 2021; 16:899-912. [PMID: 33770494 PMCID: PMC8072027 DOI: 10.1016/j.stemcr.2021.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/22/2022] Open
Abstract
CpG islands often exhibit low DNA methylation, high histone H3 lysine 4 trimethylation, low nucleosome density, and high DNase I hypersensitivity, yet the rules by which CpG islands are sensed remain poorly understood. In this study, we first evaluated the relationships between the DNA and the chromatin properties of CpG islands in embryonic stem cells using modified bacterial artificial chromosomes. Then, using a bioinformatic approach, we identified strict CpG-island density and length thresholds in mouse embryonic stem and differentiated cells that consistently specify low DNA methylation levels. Surprisingly, the human genome exhibited a dramatically different relationship between DNA properties and DNA methylation levels of CpG islands. Further analysis allowed speculation that this difference is accommodated in part by evolutionary changes in the nucleotide composition of orthologous promoters. Thus, a change in the rules by which CpG-island properties are sensed may have co-evolved with compensatory genome adaptation events during mammalian evolution. Strict DNA property rules can predict low DNA methylation at murine CpG islands Mice and humans differ greatly in how DNA properties influence DNA methylation Evolutionary adaptation of CpG islands compensates for the species differences
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27
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Elmer JL, Hay AD, Kessler NJ, Bertozzi TM, Ainscough EAC, Ferguson-Smith AC. Genomic properties of variably methylated retrotransposons in mouse. Mob DNA 2021; 12:6. [PMID: 33612119 PMCID: PMC7898769 DOI: 10.1186/s13100-021-00235-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs in mice that exhibit inter-individual variability in this methylation (VM-IAPs) with implications for genome function. RESULTS Here we validate these metastable epialleles and discover a novel class that exhibit tissue specificity (tsVM-IAPs) in addition to those with uniform methylation in all tissues (constitutive- or cVM-IAPs); both types have the potential to regulate genes in cis. Screening for variable methylation at other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We identify sequences enriched within cVM-IAPs, but determine that these are not sufficient to confer epigenetic variability. CTCF is enriched at VM-IAPs with binding inversely correlated with DNA methylation. We uncover dynamic physical interactions between cVM-IAPs with low methylation ranges and other genomic loci, suggesting that VM-IAPs have the potential for long-range regulation. CONCLUSION Our findings indicate that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs can result in inter-individual variability in transcriptional outcomes with implications for phenotypic variation.
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Affiliation(s)
- Jessica L. Elmer
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Amir D. Hay
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Noah J. Kessler
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Tessa M. Bertozzi
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
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28
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Yu X, Yang Q, Wang D, Li Z, Chen N, Kong DX. Predicting lung adenocarcinoma disease progression using methylation-correlated blocks and ensemble machine learning classifiers. PeerJ 2021; 9:e10884. [PMID: 33628643 PMCID: PMC7894106 DOI: 10.7717/peerj.10884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/12/2021] [Indexed: 01/20/2023] Open
Abstract
Applying the knowledge that methyltransferases and demethylases can modify adjacent cytosine-phosphorothioate-guanine (CpG) sites in the same DNA strand, we found that combining multiple CpGs into a single block may improve cancer diagnosis. However, survival prediction remains a challenge. In this study, we developed a pipeline named "stacked ensemble of machine learning models for methylation-correlated blocks" (EnMCB) that combined Cox regression, support vector regression (SVR), and elastic-net models to construct signatures based on DNA methylation-correlated blocks for lung adenocarcinoma (LUAD) survival prediction. We used methylation profiles from the Cancer Genome Atlas (TCGA) as the training set, and profiles from the Gene Expression Omnibus (GEO) as validation and testing sets. First, we partitioned the genome into blocks of tightly co-methylated CpG sites, which we termed methylation-correlated blocks (MCBs). After partitioning and feature selection, we observed different diagnostic capacities for predicting patient survival across the models. We combined the multiple models into a single stacking ensemble model. The stacking ensemble model based on the top-ranked block had the area under the receiver operating characteristic curve of 0.622 in the TCGA training set, 0.773 in the validation set, and 0.698 in the testing set. When stratified by clinicopathological risk factors, the risk score predicted by the top-ranked MCB was an independent prognostic factor. Our results showed that our pipeline was a reliable tool that may facilitate MCB selection and survival prediction.
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Affiliation(s)
- Xin Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qian Yang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dong Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhaoyang Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Nianhang Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - De-Xin Kong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
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29
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Ming X, Zhu B, Li Y. Mitotic inheritance of DNA methylation: more than just copy and paste. J Genet Genomics 2021; 48:1-13. [PMID: 33771455 DOI: 10.1016/j.jgg.2021.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
Decades of investigation on DNA methylation have led to deeper insights into its metabolic mechanisms and biological functions. This understanding was fueled by the recent development of genome editing tools and our improved capacity for analyzing the global DNA methylome in mammalian cells. This review focuses on the maintenance of DNA methylation patterns during mitotic cell division. We discuss the latest discoveries of the mechanisms for the inheritance of DNA methylation as a stable epigenetic memory. We also highlight recent evidence showing the rapid turnover of DNA methylation as a dynamic gene regulatory mechanism. A body of work has shown that altered DNA methylomes are common features in aging and disease. We discuss the potential links between methylation maintenance mechanisms and disease-associated methylation changes.
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Affiliation(s)
- Xuan Ming
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yingfeng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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30
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Brulport A, Vaiman D, Bou-Maroun E, Chagnon MC, Corre LL. Hepatic transcriptome and DNA methylation patterns following perinatal and chronic BPS exposure in male mice. BMC Genomics 2020; 21:881. [PMID: 33297965 PMCID: PMC7727143 DOI: 10.1186/s12864-020-07294-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/28/2020] [Indexed: 11/21/2022] Open
Abstract
Background Bisphenol S (BPS) is a common bisphenol A (BPA) substitute, since BPA is virtually banned worldwide. However, BPS and BPA have both endocrine disrupting properties. Their effects appear mostly in adulthood following perinatal exposures. The objective of the present study was to investigate the impact of perinatal and chronic exposure to BPS at the low dose of 1.5 μg/kg body weight/day on the transcriptome and methylome of the liver in 23 weeks-old C57BL6/J male mice. Results This multi-omic study highlights a major impact of BPS on gene expression (374 significant deregulated genes) and Gene Set Enrichment Analysis show an enrichment focused on several biological pathways related to metabolic liver regulation. BPS exposure also induces a hypomethylation in 58.5% of the differentially methylated regions (DMR). Systematic connections were not found between gene expression and methylation profile excepted for 18 genes, including 4 genes involved in lipid metabolism pathways (Fasn, Hmgcr, Elovl6, Lpin1), which were downregulated and featured differentially methylated CpGs in their exons or introns. Conclusions This descriptive study shows an impact of BPS on biological pathways mainly related to an integrative disruption of metabolism (energy metabolism, detoxification, protein and steroid metabolism) and, like most high-throughput studies, contributes to the identification of potential exposure biomarkers. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07294-3.
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Affiliation(s)
- Axelle Brulport
- Université de Bourgogne Franche-Comté, LNC UMR1231, F-21000, Dijon, France.,AgroSup, LNC UMR1231, 1 Esplanade Erasme, 21000, Dijon, France.,Nutrition Physiology and Toxicology Team (NUTox), INSERM, LNC UMR1231, F-21000, Dijon, France
| | - Daniel Vaiman
- From Gametes to Birth Team (FGTB), INSERM, U1016, Institut Cochin, F-75014, Paris, France.,CNRS UMR8104, F-75014, Paris, France.,Université Sorbonne Paris Cité, F-75014, Paris, France
| | - Elias Bou-Maroun
- Université de Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Procédés Alimentaires et Microbiologiques, F-21000, Dijon, France
| | - Marie-Christine Chagnon
- Université de Bourgogne Franche-Comté, LNC UMR1231, F-21000, Dijon, France.,AgroSup, LNC UMR1231, 1 Esplanade Erasme, 21000, Dijon, France.,Nutrition Physiology and Toxicology Team (NUTox), INSERM, LNC UMR1231, F-21000, Dijon, France
| | - Ludovic Le Corre
- Université de Bourgogne Franche-Comté, LNC UMR1231, F-21000, Dijon, France. .,AgroSup, LNC UMR1231, 1 Esplanade Erasme, 21000, Dijon, France. .,Nutrition Physiology and Toxicology Team (NUTox), INSERM, LNC UMR1231, F-21000, Dijon, France.
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31
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de Gannes M, Ko CI, Zhang X, Biesiada J, Niu L, Koch SE, Medvedovic M, Rubinstein J, Puga A. Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes That Govern Cardiomyocyte Maturation. Toxicol Sci 2020; 178:325-337. [PMID: 33017471 DOI: 10.1093/toxsci/kfaa153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Congenital heart disease (CHD), the leading birth defect worldwide, has a largely unknown etiology, likely to result from complex interactions between genetic and environmental factors during heart development, at a time when the heart adapts to diverse physiological and pathophysiological conditions. Crucial among these is the regulation of cardiomyocyte development and postnatal maturation, governed by dynamic changes in DNA methylation. Previous work from our laboratory has shown that exposure to the environmental toxicant tetrachlorodibenzo-p-dioxin (TCDD) disrupts several molecular networks responsible for heart development and function. To test the hypothesis that the disruption caused by TCDD in the heart results from changes in DNA methylation and gene expression patterns of cardiomyocytes, we established a stable mouse embryonic stem cell line expressing a puromycin resistance selectable marker under control of the cardiomyocyte-specific Nkx2-5 promoter. Differentiation of these cells in the presence of puromycin induces the expression of a large suite of cardiomyocyte-specific markers. To assess the consequences of TCDD treatment on gene expression and DNA methylation in these cardiomyocytes, we subjected them to transcriptome and methylome analyses in the presence of TCDD. Unlike control cardiomyocytes maintained in vehicle, the TCDD-treated cardiomyocytes showed extensive gene expression changes, with a significant correlation between differential RNA expression and DNA methylation in 111 genes, many of which are key elements of pathways that regulate cardiovascular development and function. Our findings provide an important clue toward the elucidation of the complex interactions between genetic and epigenetic mechanisms after developmental TCDD exposure that may contribute to CHD.
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Affiliation(s)
- Matthew de Gannes
- Department of Environmental Health and Center for Environmental Genetics
| | - Chia-I Ko
- Department of Environmental Health and Center for Environmental Genetics
| | - Xiang Zhang
- Department of Environmental Health and Center for Environmental Genetics
| | - Jacek Biesiada
- Department of Environmental Health and Center for Environmental Genetics
| | - Liang Niu
- Department of Environmental Health and Center for Environmental Genetics
| | - Sheryl E Koch
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
| | - Mario Medvedovic
- Department of Environmental Health and Center for Environmental Genetics
| | - Jack Rubinstein
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
| | - Alvaro Puga
- Department of Environmental Health and Center for Environmental Genetics
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32
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Li S, Tollefsbol TO. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods 2020; 187:28-43. [PMID: 33039572 DOI: 10.1016/j.ymeth.2020.10.002] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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33
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Adrian-Kalchhauser I, Sultan SE, Shama LNS, Spence-Jones H, Tiso S, Keller Valsecchi CI, Weissing FJ. Understanding 'Non-genetic' Inheritance: Insights from Molecular-Evolutionary Crosstalk. Trends Ecol Evol 2020; 35:1078-1089. [PMID: 33036806 DOI: 10.1016/j.tree.2020.08.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 12/23/2022]
Abstract
Understanding the evolutionary and ecological roles of 'non-genetic' inheritance (NGI) is daunting due to the complexity and diversity of epigenetic mechanisms. We draw on insights from molecular and evolutionary biology perspectives to identify three general features of 'non-genetic' inheritance systems: (i) they are functionally interdependent with, rather than separate from, DNA sequence; (ii) precise mechanisms vary phylogenetically and operationally; and (iii) epigenetic elements are probabilistic, interactive regulatory factors and not deterministic 'epialleles' with defined genomic locations and effects. We discuss each of these features and offer recommendations for future empirical and theoretical research that implements a unifying inherited gene regulation (IGR) approach to studies of 'non-genetic' inheritance.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Centre for Fish and Wildlife Health, Department for Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland.
| | - Sonia E Sultan
- Biology Department, Wesleyan University, Middletown, CT 06459, USA
| | - Lisa N S Shama
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, Hafenstrasse 43, 25992 List, Germany
| | - Helen Spence-Jones
- Centre for Biological Diversity, School of Biology, University of St Andrews, St. Andrews, UK
| | - Stefano Tiso
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | | | - Franz J Weissing
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
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34
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Fang C, Rao S, Crispino JD, Ntziachristos P. Determinants and role of chromatin organization in acute leukemia. Leukemia 2020; 34:2561-2575. [PMID: 32690881 PMCID: PMC7999176 DOI: 10.1038/s41375-020-0981-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
DNA is compacted into higher order structures that have major implications in gene regulation. These structures allow for long-range interactions of DNA elements, such as the association of promoters with their cognate enhancers. In recent years, mutations in genes that control these structures, including the cohesin-complex and the insulator-binding protein CTCF, have been found in a spectrum of hematologic disorders, and especially in acute leukemias. Cohesin and CTCF are critical for mediating looping and establishing boundaries within chromatin. Cells that harbor mutations in these genes display aberrant chromatin architecture and resulting differences in gene expression that contribute to leukemia initiation and progression. Here, we provide detailed discussion of the nature of 3D interactions and the way that they are disrupted in acute leukemia. Continued research in this area will provide new insights into the mechanisms of leukemogenesis and may shed light on novel treatment strategies.
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Affiliation(s)
- Celestia Fang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sridhar Rao
- Versiti Blood Research Institute, Milwaukee, WI, 53226, USA
| | - John D Crispino
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Division of Hematology, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Division of Hematology, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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Aristizabal MJ, Anreiter I, Halldorsdottir T, Odgers CL, McDade TW, Goldenberg A, Mostafavi S, Kobor MS, Binder EB, Sokolowski MB, O'Donnell KJ. Biological embedding of experience: A primer on epigenetics. Proc Natl Acad Sci U S A 2020; 117:23261-23269. [PMID: 31624126 PMCID: PMC7519272 DOI: 10.1073/pnas.1820838116] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Biological embedding occurs when life experience alters biological processes to affect later life health and well-being. Although extensive correlative data exist supporting the notion that epigenetic mechanisms such as DNA methylation underlie biological embedding, causal data are lacking. We describe specific epigenetic mechanisms and their potential roles in the biological embedding of experience. We also consider the nuanced relationships between the genome, the epigenome, and gene expression. Our ability to connect biological embedding to the epigenetic landscape in its complexity is challenging and complicated by the influence of multiple factors. These include cell type, age, the timing of experience, sex, and DNA sequence. Recent advances in molecular profiling and epigenome editing, combined with the use of comparative animal and human longitudinal studies, should enable this field to transition from correlative to causal analyses.
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Affiliation(s)
- Maria J Aristizabal
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, and BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V52 4H4, Canada
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
| | - Ina Anreiter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
| | - Thorhildur Halldorsdottir
- Centre of Public Health Sciences, Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Candice L Odgers
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
- Department of Psychological Science, University of California, Irvine, CA 92697
- Sanford School of Public Policy, Duke University, Durham, NC 27708
| | - Thomas W McDade
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
- Department of Anthropology, Northwestern University, Evanston, IL 60208
- Institute for Policy Research, Northwestern University, Evanston, IL 60208
| | - Anna Goldenberg
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
- Department of Computer Science, Hospital for Sick Children, Vector Institute, University of Toronto, Toronto, ON, M5G OA4, Canada
| | - Sara Mostafavi
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
- Department of Statistics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, and BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V52 4H4, Canada
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
| | - Elisabeth B Binder
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329
| | - Marla B Sokolowski
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada;
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
| | - Kieran J O'Donnell
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada;
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Hospital Research Centre, Department of Psychiatry, McGill University, Montreal, QC, H4H 1R3, Canada
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36
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Patel M, Patel D, Datta S, Singh U. CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity. BMC Genet 2020; 21:84. [PMID: 32727353 PMCID: PMC7392725 DOI: 10.1186/s12863-020-00894-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/23/2020] [Indexed: 12/03/2022] Open
Abstract
Background The human CGGBP1 binds to GC-rich regions and interspersed repeats, maintains homeostasis of stochastic cytosine methylation and determines DNA-binding of CTCF. Interdependence between regulation of cytosine methylation and CTCF occupancy by CGGBP1 remains unknown. Results By analyzing methylated DNA-sequencing data obtained from CGGBP1-depleted cells, we report that some transcription factor-binding sites, including CTCF, resist stochastic changes in cytosine methylation. By analysing CTCF-binding sites we show that cytosine methylation changes at CTCF motifs caused by CGGBP1 depletion resist stochastic changes. These CTCF-binding sites are positioned at locations where the spread of cytosine methylation in cis depends on the levels of CGGBP1. Conclusion Our findings suggest that CTCF occupancy and functions are determined by CGGBP1-regulated cytosine methylation patterns.
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Affiliation(s)
- Manthan Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Divyesh Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Subhamoy Datta
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Umashankar Singh
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, 382355, Gujarat, India.
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37
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Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY. The DNA methylation landscape of advanced prostate cancer. Nat Genet 2020; 52:778-789. [PMID: 32661416 PMCID: PMC7454228 DOI: 10.1038/s41588-020-0648-8] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/20/2020] [Indexed: 02/08/2023]
Abstract
Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes only detectable with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hyper-methylation and somatic mutations in TET2, DNMT3B, IDH1, and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer and provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.
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Affiliation(s)
- Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - William S Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Yale School of Medicine, New Haven, CT, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Denise Playdle
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Rajdeep Das
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Chou
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Junjie T Hua
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Travis J Barnard
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adina M Bailey
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA
| | - Marc D Perry
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ha X Dang
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA
| | - Rendong Yang
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Ruhollah Moussavi-Baygi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - S Laura Chang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen E Houlahan
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Division of Hematology/Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Cancer Agency, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert E Reiter
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew B Rettig
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA.,Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Owen Witte
- Department of Microbiology, Immunology, and Molecular Genetics at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - M Yvonne Kim
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hui Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa Chesner
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Tanushree Shenoy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Irfan A Asangani
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Nupam P Mahajan
- Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Surgery, Washington University, St. Louis, MO, USA
| | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA.,Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA.,Department of Urologic Surgery, University of California Davis, Sacramento, CA, USA
| | | | | | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Housheng H He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC, USA
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Arul M Chinnaiyan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Biomedical Engineering, Washington University, St. Louis, MO, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. .,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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38
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Do C, Dumont ELP, Salas M, Castano A, Mujahed H, Maldonado L, Singh A, DaSilva-Arnold SC, Bhagat G, Lehman S, Christiano AM, Madhavan S, Nagy PL, Green PHR, Feinman R, Trimble C, Illsley NP, Marder K, Honig L, Monk C, Goy A, Chow K, Goldlust S, Kaptain G, Siegel D, Tycko B. Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs. Genome Biol 2020; 21:153. [PMID: 32594908 PMCID: PMC7322865 DOI: 10.1186/s13059-020-02059-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 05/27/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Mapping of allele-specific DNA methylation (ASM) can be a post-GWAS strategy for localizing regulatory sequence polymorphisms (rSNPs). The advantages of this approach, and the mechanisms underlying ASM in normal and neoplastic cells, remain to be clarified. RESULTS We perform whole genome methyl-seq on diverse normal cells and tissues and three cancer types. After excluding imprinting, the data pinpoint 15,112 high-confidence ASM differentially methylated regions, of which 1838 contain SNPs in strong linkage disequilibrium or coinciding with GWAS peaks. ASM frequencies are increased in cancers versus matched normal tissues, due to widespread allele-specific hypomethylation and focal allele-specific hypermethylation in poised chromatin. Cancer cells show increased allele switching at ASM loci, but disruptive SNPs in specific classes of CTCF and transcription factor binding motifs are similarly correlated with ASM in cancer and non-cancer. Rare somatic mutations affecting these same motif classes track with de novo ASM. Allele-specific transcription factor binding from ChIP-seq is enriched among ASM loci, but most ASM differentially methylated regions lack such annotations, and some are found in otherwise uninformative "chromatin deserts." CONCLUSIONS ASM is increased in cancers but occurs by a shared mechanism involving disruptive SNPs in CTCF and transcription factor binding sites in both normal and neoplastic cells. Dense ASM mapping in normal plus cancer samples reveals candidate rSNPs that are difficult to find by other approaches. Together with GWAS data, these rSNPs can nominate specific transcriptional pathways in susceptibility to autoimmune, cardiometabolic, neuropsychiatric, and neoplastic diseases.
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Affiliation(s)
- Catherine Do
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA.
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA.
| | - Emmanuel L P Dumont
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Martha Salas
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Angelica Castano
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Huthayfa Mujahed
- Department of Medicine, Huddinge, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Leonel Maldonado
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21287, USA
| | - Arunjot Singh
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sonia C DaSilva-Arnold
- Department of Obstetrics and Gynecology, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Govind Bhagat
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA
- Division of Gastroenterology and Celiac Center, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Soren Lehman
- Department of Medicine, Huddinge, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Angela M Christiano
- Departments of Dermatology and Genetics and Development, Columbia University Medical Center, New York, NY, 10032, USA
| | - Subha Madhavan
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | | | - Peter H R Green
- Division of Gastroenterology and Celiac Center, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Rena Feinman
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Cornelia Trimble
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21287, USA
| | - Nicholas P Illsley
- Department of Obstetrics and Gynecology, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - Karen Marder
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Lawrence Honig
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Catherine Monk
- Departments of Psychiatry and Behavioral Medicine and Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Andre Goy
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Kar Chow
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Samuel Goldlust
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - George Kaptain
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
| | - David Siegel
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA.
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, 07601, USA.
- Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC, 20057, USA.
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39
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Enhancer DNA methylation: implications for gene regulation. Essays Biochem 2020; 63:707-715. [PMID: 31551326 DOI: 10.1042/ebc20190030] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/13/2022]
Abstract
DNA methylation involves the addition of a methyl group to the fifth carbon of the pyrimidine cytosine ring (5-methylcytosine, 5mC). 5mC is widespread in vertebrate genomes where it is predominantly found within CpG dinucleotides. In mammals, 5mC participates in long-term silencing processes such as X-chromosome inactivation, genomic imprinting, somatic silencing of germline genes, and silencing of repetitive DNA elements. The evidence for 5mC as a dynamic gene-regulatory mechanism is mostly limited to specific examples, and is far from being completely understood. Recent work from diverse model systems suggests that 5mC might not always act as a dominant repressive mechanism and that hypermethylated promoters and enhancers can be permissive to transcription in vivo and in vitro. In this review, we discuss the links between 5mC and enhancer activity, and evaluate the role of this biochemical mechanism in various biological contexts.
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40
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Sensitivity of transcription factors to DNA methylation. Essays Biochem 2020; 63:727-741. [PMID: 31755929 PMCID: PMC6923324 DOI: 10.1042/ebc20190033] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022]
Abstract
Dynamic binding of transcription factors (TFs) to regulatory elements controls transcriptional states throughout organism development. Epigenetics modifications, such as DNA methylation mostly within cytosine-guanine dinucleotides (CpGs), have the potential to modulate TF binding to DNA. Although DNA methylation has long been thought to repress TF binding, a more recent model proposes that TF binding can also inhibit DNA methylation. Here, we review the possible scenarios by which DNA methylation and TF binding affect each other. Further in vivo experiments will be required to generalize these models.
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41
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Harnessing targeted DNA methylation and demethylation using dCas9. Essays Biochem 2020; 63:813-825. [PMID: 31724704 DOI: 10.1042/ebc20190029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022]
Abstract
DNA methylation is an essential DNA modification that plays a crucial role in genome regulation during differentiation and development, and is disrupted in a range of disease states. The recent development of CRISPR/catalytically dead CRISPR/Cas9 (dCas9)-based targeted DNA methylation editing tools has enabled new insights into the roles and functional relevance of this modification, including its importance at regulatory regions and the role of aberrant methylation in various diseases. However, while these tools are advancing our ability to understand and manipulate this regulatory layer of the genome, they still possess a variety of limitations in efficacy, implementation, and targeting specificity. Effective targeted DNA methylation editing will continue to advance our fundamental understanding of the role of this modification in different genomic and cellular contexts, and further improvements may enable more accurate disease modeling and possible future treatments. In this review, we discuss strategies, considerations, and future directions for targeted DNA methylation editing.
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42
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Li L, Maire CL, Bilenky M, Carles A, Heravi-Moussavi A, Hong C, Tam A, Kamoh B, Cho S, Cheung D, Li I, Wong T, Nagarajan RP, Mungall AJ, Moore R, Wang T, Kleinman CL, Jabado N, Jones SJM, Marra MA, Ligon KL, Costello JF, Hirst M. Epigenomic programming in early fetal brain development. Epigenomics 2020; 12:1053-1070. [PMID: 32677466 PMCID: PMC7857341 DOI: 10.2217/epi-2019-0319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/19/2020] [Indexed: 12/21/2022] Open
Abstract
Aim: To provide a comprehensive understanding of gene regulatory networks in the developing human brain and a foundation for interpreting pathogenic deregulation. Materials & methods: We generated reference epigenomes and transcriptomes of dissected brain regions and primary neural progenitor cells (NPCs) derived from cortical and ganglionic eminence tissues of four normal human fetuses. Results: Integration of these data across developmental stages revealed a directional increase in active regulatory states, transcription factor activities and gene transcription with developmental stage. Consistent with differences in their biology, NPCs derived from cortical and ganglionic eminence regions contained common, region specific, and gestational week specific regulatory states. Conclusion: We provide a high-resolution regulatory network for NPCs from different brain regions as a comprehensive reference for future studies.
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Affiliation(s)
- Luolan Li
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cecile L Maire
- Department of Medical Oncology, Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Misha Bilenky
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Annaïck Carles
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | | | - Chibo Hong
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Angela Tam
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Baljit Kamoh
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Stephanie Cho
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Dorothy Cheung
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Irene Li
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Tina Wong
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Raman P Nagarajan
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Andrew J Mungall
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Ting Wang
- Department of Genetics, Washington University, St Louis, MO 63108, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Steven JM Jones
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Keith L Ligon
- Department of Medical Oncology, Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Martin Hirst
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
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Ginno PA, Gaidatzis D, Feldmann A, Hoerner L, Imanci D, Burger L, Zilbermann F, Peters AHFM, Edenhofer F, Smallwood SA, Krebs AR, Schübeler D. A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity. Nat Commun 2020; 11:2680. [PMID: 32471981 PMCID: PMC7260214 DOI: 10.1038/s41467-020-16354-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/24/2020] [Indexed: 12/21/2022] Open
Abstract
DNA methylation is considered a stable epigenetic mark, yet methylation patterns can vary during differentiation and in diseases such as cancer. Local levels of DNA methylation result from opposing enzymatic activities, the rates of which remain largely unknown. Here we developed a theoretical and experimental framework enabling us to infer methylation and demethylation rates at 860,404 CpGs in mouse embryonic stem cells. We find that enzymatic rates can vary as much as two orders of magnitude between CpGs with identical steady-state DNA methylation. Unexpectedly, de novo and maintenance methylation activity is reduced at transcription factor binding sites, while methylation turnover is elevated in transcribed gene bodies. Furthermore, we show that TET activity contributes substantially more than passive demethylation to establishing low methylation levels at distal enhancers. Taken together, our work unveils a genome-scale map of methylation kinetics, revealing highly variable and context-specific activity for the DNA methylation machinery.
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Affiliation(s)
- Paul Adrian Ginno
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Angelika Feldmann
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Leslie Hoerner
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dilek Imanci
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Frank Edenhofer
- Leopold-Franzens-University Innsbruck & CMBI, Innsbruck, Austria
| | | | - Arnaud R Krebs
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- EMBL Heidelberg, Heidelberg, Germany
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- Faculty of Sciences, University of Basel, Basel, Switzerland.
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Dynamic CpG methylation delineates subregions within super-enhancers selectively decommissioned at the exit from naive pluripotency. Nat Commun 2020; 11:1112. [PMID: 32111830 PMCID: PMC7048827 DOI: 10.1038/s41467-020-14916-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 02/08/2020] [Indexed: 12/29/2022] Open
Abstract
Clusters of enhancers, referred as to super-enhancers (SEs), control the expression of cell identity genes. The organisation of these clusters, and how they are remodelled upon developmental transitions remain poorly understood. Here, we report the existence of two types of enhancer units within SEs typified by distinctive CpG methylation dynamics in embryonic stem cells (ESCs). We find that these units are either prone for decommissioning or remain constitutively active in epiblast stem cells (EpiSCs), as further established in the peri-implantation epiblast in vivo. Mechanistically, we show a pivotal role for ESRRB in regulating the activity of ESC-specific enhancer units and propose that the developmentally regulated silencing of ESRRB triggers the selective inactivation of these units within SEs. Our study provides insights into the molecular events that follow the loss of ESRRB binding, and offers a mechanism by which the naive pluripotency transcriptional programme can be partially reset upon embryo implantation.
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45
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Borkowska J, Domaszewska-Szostek A, Kołodziej P, Wicik Z, Połosak J, Buyanovskaya O, Charzewski L, Stańczyk M, Noszczyk B, Puzianowska-Kuznicka M. Alterations in 5hmC level and genomic distribution in aging-related epigenetic drift in human adipose stem cells. Epigenomics 2020; 12:423-437. [PMID: 32031421 DOI: 10.2217/epi-2019-0131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: To clarify mechanisms affecting the level and distribution of 5-hydroxymethylcytosine (5hmC) during aging. Materials & methods: We examined levels and genomic distribution of 5hmC along with the expression of ten-eleven translocation methylcytosine dioxygenases (TETs) in adipose stem cells in young and age-advanced individuals. Results: 5hmC levels were higher in adipose stem cells of age-advanced than young individuals (p = 0.0003), but were not associated with age-related changes in expression of TETs. 5hmC levels correlated with population doubling time (r = 0.62; p = 0.01). We identified 58 differentially hydroxymethylated regions. Hypo-hydroxymethylated differentially hydroxymethylated regions were approximately twofold enriched in CCCTC-binding factor binding sites. Conclusion: Accumulation of 5hmC in aged cells can result from inefficient active demethylation due to altered TETs activity and reduced passive demethylation due to slower proliferation.
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Affiliation(s)
- Joanna Borkowska
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Anna Domaszewska-Szostek
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Paulina Kołodziej
- Department of Geriatrics & Gerontology, Medical Centre of Postgraduate Education, 61/63 Kleczewska Street, 01-826 Warsaw, Poland
| | - Zofia Wicik
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Jacek Połosak
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Olga Buyanovskaya
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Lukasz Charzewski
- Faculty of Physics, University of Warsaw, 5 Pasteur Street, 02-093 Warsaw, Poland
| | - Marek Stańczyk
- Department of General Surgery, Wolski Hospital, 17 Kasprzaka Street, 01-211 Warsaw, Poland
| | - Bartłomiej Noszczyk
- Department of Plastic Surgery, Medical Centre of Postgraduate Education, 99/103 Marymoncka Street, 01-813 Warsaw, Poland
| | - Monika Puzianowska-Kuznicka
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland.,Department of Geriatrics & Gerontology, Medical Centre of Postgraduate Education, 61/63 Kleczewska Street, 01-826 Warsaw, Poland
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46
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Feng L, Zhou J, Xia B, Tian BF. The Positive Effect of TET2 on the Osteogenic Differentiation of Human Adipose-Derived Mesenchymal Stem Cells. Cell Reprogram 2020; 22:3-13. [PMID: 31829736 DOI: 10.1089/cell.2019.0045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Li Feng
- Department of Traumatic Orthopedics, Jining No. 1 People's Hospital, Jining, China
| | - Jing Zhou
- Department of Gynecology, Jining No. 1 People's Hospital, Jining, China
| | - Bo Xia
- Department of Traumatic Orthopedics, Jining No. 1 People's Hospital, Jining, China
| | - Bao-Fang Tian
- Department of Traumatic Orthopedics, Jining No. 1 People's Hospital, Jining, China
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47
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Wada T, Wallerich S, Becskei A. Stochastic Gene Choice during Cellular Differentiation. Cell Rep 2019; 24:3503-3512. [PMID: 30257211 DOI: 10.1016/j.celrep.2018.08.074] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 05/02/2018] [Accepted: 08/24/2018] [Indexed: 01/06/2023] Open
Abstract
Genes in higher eukaryotes are regulated by long-range interactions, which can determine what combination of genes is expressed in a chromosomal segment. The choice of the genes can display exclusivity, independence, or co-occurrence. We introduced a simple measure to quantify this interdependence in gene expression and differentiated mouse embryonic stem cells to neurons to measure the single-cell expression of the gene isoforms in the protocadherin (Pcdh) cluster, a key component of neuronal diversity. As the neuronal progenitors mature into neurons, expression of the gene isoforms in the Pcdh array is initially concurrent. Even though the number of the expressed genes is increasing during differentiation, the expression shifts toward exclusivity. The expression frequency correlates highly with CTCF binding to the promoters and follows dynamically the changes in the binding during the differentiation. These findings aid in understanding the interplay between cellular differentiation and stochastic gene choice.
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Affiliation(s)
- Takeo Wada
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel 4056, Switzerland
| | - Sandrine Wallerich
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel 4056, Switzerland
| | - Attila Becskei
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel 4056, Switzerland.
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48
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Lhoumaud P, Sethia G, Izzo F, Sakellaropoulos T, Snetkova V, Vidal S, Badri S, Cornwell M, Di Giammartino DC, Kim KT, Apostolou E, Stadtfeld M, Landau DA, Skok J. EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation. Genome Biol 2019; 20:248. [PMID: 31752933 PMCID: PMC6868874 DOI: 10.1186/s13059-019-1853-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/04/2019] [Indexed: 11/10/2022] Open
Abstract
Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or transcription factor (TF) binding if assays are performed separately. We developed a fast, low-input, low sequencing depth method, EpiMethylTag, that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA. Here we demonstrate that EpiMethylTag can be used to study the functional interplay between chromatin accessibility and TF binding (CTCF and KLF4) at methylated sites.
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Affiliation(s)
| | - Gunjan Sethia
- New York University Langone Health, New York, NY USA
| | - Franco Izzo
- New York Genome Center, New York, NY USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY USA
| | - Theodore Sakellaropoulos
- New York University Langone Health, New York, NY USA
- Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY USA
| | | | - Simon Vidal
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Helen L. and Martin S. Kimmel Center for Biology and Medicine, Laura and Isaac Perlmutter Cancer Center, New York, NY USA
| | - Sana Badri
- New York University Langone Health, New York, NY USA
| | | | - Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY USA
| | - Kyu-Tae Kim
- New York Genome Center, New York, NY USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY USA
| | - Matthias Stadtfeld
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Helen L. and Martin S. Kimmel Center for Biology and Medicine, Laura and Isaac Perlmutter Cancer Center, New York, NY USA
| | - Dan Avi Landau
- New York Genome Center, New York, NY USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY USA
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY USA
| | - Jane Skok
- New York University Langone Health, New York, NY USA
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Helen L. and Martin S. Kimmel Center for Biology and Medicine, Laura and Isaac Perlmutter Cancer Center, New York, NY USA
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49
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Bazov I, Sarkisyan D, Kononenko O, Watanabe H, Taqi MM, Stålhandske L, Verbeek DS, Mulder J, Rajkowska G, Sheedy D, Kril J, Sun X, Syvänen AC, Yakovleva T, Bakalkin G. Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain. Cereb Cortex 2019; 28:3129-3142. [PMID: 28968778 DOI: 10.1093/cercor/bhx181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Indexed: 12/13/2022] Open
Abstract
Molecular mechanisms that define patterns of neuropeptide expression are essential for the formation and rewiring of neural circuits. The prodynorphin gene (PDYN) gives rise to dynorphin opioid peptides mediating depression and substance dependence. We here demonstrated that PDYN is expressed in neurons in human dorsolateral prefrontal cortex (dlPFC), and identified neuronal differentially methylated region in PDYN locus framed by CCCTC-binding factor binding sites. A short, nucleosome size human-specific promoter CpG island (CGI), a core of this region may serve as a regulatory module, which is hypomethylated in neurons, enriched in 5-hydroxymethylcytosine, and targeted by USF2, a methylation-sensitive E-box transcription factor (TF). USF2 activates PDYN transcription in model systems, and binds to nonmethylated CGI in dlPFC. USF2 and PDYN expression is correlated, and USF2 and PDYN proteins are co-localized in dlPFC. Segregation of activatory TF and repressive CGI methylation may ensure contrasting PDYN expression in neurons and glia in human brain.
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Affiliation(s)
- Igor Bazov
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Daniil Sarkisyan
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Olga Kononenko
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Hiroyuki Watanabe
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Mumtaz Malik Taqi
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden.,Faculty of Medicine, NORMENT, University of Oslo, Oslo, Norway
| | - Lada Stålhandske
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Jan Mulder
- Department of Neuroscience, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Grazyna Rajkowska
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Donna Sheedy
- Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Jillian Kril
- Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Xueguang Sun
- Zymo Research Corporation, 17062 Murphy Avenue, Irvine, CA, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tatiana Yakovleva
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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50
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de Mendoza A, Lister R, Bogdanovic O. Evolution of DNA Methylome Diversity in Eukaryotes. J Mol Biol 2019:S0022-2836(19)30659-X. [PMID: 31726061 DOI: 10.1016/j.jmb.2019.11.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022]
Abstract
Cytosine DNA methylation (5mC) is a widespread base modification in eukaryotic genomes with critical roles in transcriptional regulation. In recent years, our understanding of 5mC has changed because of advances in 5mC detection techniques that allow mapping of this mark on the whole genome scale. Profiling DNA methylomes from organisms across the eukaryotic tree of life has reshaped our views on the evolution of 5mC. In this review, we explore the macroevolution of 5mC in major eukaryotic groups, and then focus on recent advances made in animals. Genomic 5mC patterns as well as the mechanisms of 5mC deposition tend to be evolutionary labile across large phylogenetic distances; however, some common patterns are starting to emerge. Within the animal kingdom, 5mC diversity has proven to be much greater than anticipated. For example, a previously held common view that genome hypermethylation is a trait exclusive to vertebrates has recently been challenged. Also, data from genome-wide studies are starting to yield insights into the potential roles of 5mC in invertebrate cis regulation. Here we provide an evolutionary perspective of both the well-known and enigmatic roles of 5mC across the eukaryotic tree of life.
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Affiliation(s)
- Alex de Mendoza
- ARC CoE Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia.
| | - Ryan Lister
- ARC CoE Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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