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Lavaud M, Tesfaye R, Lassous L, Brounais B, Baud'huin M, Verrecchia F, Lamoureux F, Georges S, Ory B. Super-enhancers: drivers of cells' identities and cells' debacles. Epigenomics 2024. [PMID: 38587919 DOI: 10.2217/epi-2023-0409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
Precise spatiotemporal regulations of gene expression are essential for determining cells' fates and functions. Enhancers are cis-acting DNA elements that act as periodic transcriptional thrusters and their activities are cell type specific. Clusters of enhancers, called super-enhancers, are more densely occupied by transcriptional activators than enhancers, driving stronger expression of their target genes, which have prominent roles in establishing and maintaining cellular identities. Here we review the current knowledge on the composition and structure of super-enhancers to understand how they robustly stimulate the expression of cellular identity genes. We also review their involvement in the development of various cell types and both noncancerous and cancerous disorders, implying the therapeutic interest of targeting them to fight against various diseases.
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Affiliation(s)
- Mélanie Lavaud
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Robel Tesfaye
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Léa Lassous
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Bénédicte Brounais
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Marc Baud'huin
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Franck Verrecchia
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - François Lamoureux
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Steven Georges
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Benjamin Ory
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
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2
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Vitorakis N, Piperi C. Insights into the Role of Histone Methylation in Brain Aging and Potential Therapeutic Interventions. Int J Mol Sci 2023; 24:17339. [PMID: 38139167 PMCID: PMC10744334 DOI: 10.3390/ijms242417339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Epigenetic mechanisms play a primary role in the cellular damage associated with brain aging. Histone posttranslational modifications represent intrinsic molecular alterations essential for proper physiological functioning, while divergent expression and activity have been detected in several aspects of brain aging. Aberrant histone methylation has been involved in neural stem cell (NSC) quiescence, microglial deficits, inflammatory processes, memory impairment, cognitive decline, neurodegenerative diseases, and schizophrenia. Herein, we provide an overview of recent studies on epigenetic regulation of brain tissue aging, mainly focusing on the role of histone methylation in different cellular and functional aspects of the aging process. Emerging targeting strategies of histone methylation are further explored, including neuroprotective drugs, natural compounds, and lifestyle modifications with therapeutic potential towards the aging process of the brain.
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Affiliation(s)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street, 11527 Athens, Greece;
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3
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Gao Y, Sheng X, Tan D, Kim S, Choi S, Paudel S, Lee T, Yan C, Tan M, Kim KM, Cho SS, Ki SH, Huang H, Zhao Y, Lee S. Identification of Histone Lysine Acetoacetylation as a Dynamic Post-Translational Modification Regulated by HBO1. Adv Sci (Weinh) 2023; 10:e2300032. [PMID: 37382194 PMCID: PMC10477889 DOI: 10.1002/advs.202300032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/29/2023] [Indexed: 06/30/2023]
Abstract
Ketone bodies have long been known as a group of lipid-derived alternative energy sources during glucose shortages. Nevertheless, the molecular mechanisms underlying their non-metabolic functions remain largely elusive. This study identified acetoacetate as the precursor for lysine acetoacetylation (Kacac), a previously uncharacterized and evolutionarily conserved histone post-translational modification. This protein modification is comprehensively validated using chemical and biochemical approaches, including HPLC co-elution and MS/MS analysis using synthetic peptides, Western blot, and isotopic labeling. Histone Kacac can be dynamically regulated by acetoacetate concentration, possibly via acetoacetyl-CoA. Biochemical studies show that HBO1, traditionally known as an acetyltransferase, can also serve as an acetoacetyltransferase. In addition, 33 Kacac sites are identified on mammalian histones, depicting the landscape of histone Kacac marks across species and organs. In summary, this study thus discovers a physiologically relevant and enzymatically regulated histone mark that sheds light on the non-metabolic functions of ketone bodies.
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Affiliation(s)
- Yan Gao
- College of PharmacyKyungpook National UniversityDaegu41566Republic of Korea
| | - Xinlei Sheng
- Ben May Department for Cancer ResearchThe University of ChicagoChicagoIL60637USA
| | - Doudou Tan
- Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - SunJoo Kim
- College of PharmacyKyungpook National UniversityDaegu41566Republic of Korea
- Ben May Department for Cancer ResearchThe University of ChicagoChicagoIL60637USA
| | - Soyoung Choi
- College of PharmacyKyungpook National UniversityDaegu41566Republic of Korea
| | - Sanjita Paudel
- College of PharmacyKyungpook National UniversityDaegu41566Republic of Korea
| | - Taeho Lee
- College of PharmacyKyungpook National UniversityDaegu41566Republic of Korea
| | - Cong Yan
- Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Minjia Tan
- Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Kyu Min Kim
- Department of Biomedical Science, College of Natural ScienceChosun UniversityGwangju61452South Korea
| | - Sam Seok Cho
- College of PharmacyChosun UniversityGwangju61452South Korea
| | - Sung Hwan Ki
- College of PharmacyChosun UniversityGwangju61452South Korea
| | - He Huang
- Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yingming Zhao
- Ben May Department for Cancer ResearchThe University of ChicagoChicagoIL60637USA
| | - Sangkyu Lee
- School of PharmacySungkyunkwan UniversitySuwon16419South Korea
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4
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Herbert A, Pavlov F, Konovalov D, Poptsova M. Conserved microRNAs and Flipons Shape Gene Expression during Development by Altering Promoter Conformations. Int J Mol Sci 2023; 24:ijms24054884. [PMID: 36902315 PMCID: PMC10003719 DOI: 10.3390/ijms24054884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
The classical view of gene regulation draws from prokaryotic models, where responses to environmental changes involve operons regulated by sequence-specific protein interactions with DNA, although it is now known that operons are also modulated by small RNAs. In eukaryotes, pathways based on microRNAs (miR) regulate the readout of genomic information from transcripts, while alternative nucleic acid structures encoded by flipons influence the readout of genetic programs from DNA. Here, we provide evidence that miR- and flipon-based mechanisms are deeply connected. We analyze the connection between flipon conformation and the 211 highly conserved human miR that are shared with other placental and other bilateral species. The direct interaction between conserved miR (c-miR) and flipons is supported by sequence alignments and the engagement of argonaute proteins by experimentally validated flipons as well as their enrichment in promoters of coding transcripts important in multicellular development, cell surface glycosylation and glutamatergic synapse specification with significant enrichments at false discovery rates as low as 10-116. We also identify a second subset of c-miR that targets flipons essential for retrotransposon replication, exploiting that vulnerability to limit their spread. We propose that miR can act in a combinatorial manner to regulate the readout of genetic information by specifying when and where flipons form non-B DNA (NoB) conformations, providing the interactions of the conserved hsa-miR-324-3p with RELA and the conserved hsa-miR-744 with ARHGAP5 genes as examples.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA
- Correspondence:
| | - Fedor Pavlov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
| | - Dmitrii Konovalov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
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5
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Kang Y, Jung WJ, Brent MR. Predicting which genes will respond to transcription factor perturbations. G3 (Bethesda) 2022; 12:jkac144. [PMID: 35666184 PMCID: PMC9339286 DOI: 10.1093/g3journal/jkac144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022]
Abstract
The ability to predict which genes will respond to the perturbation of a transcription factor serves as a benchmark for our systems-level understanding of transcriptional regulatory networks. In previous work, machine learning models have been trained to predict static gene expression levels in a biological sample by using data from the same or similar samples, including data on their transcription factor binding locations, histone marks, or DNA sequence. We report on a different challenge-training machine learning models to predict which genes will respond to the perturbation of a transcription factor without using any data from the perturbed cells. We find that existing transcription factor location data (ChIP-seq) from human cells have very little detectable utility for predicting which genes will respond to perturbation of a transcription factor. Features of genes, including their preperturbation expression level and expression variation, are very useful for predicting responses to perturbation of any transcription factor. This shows that some genes are poised to respond to transcription factor perturbations and others are resistant, shedding light on why it has been so difficult to predict responses from binding locations. Certain histone marks, including H3K4me1 and H3K4me3, have some predictive power when located downstream of the transcription start site. However, the predictive power of histone marks is much less than that of gene expression level and expression variation. Sequence-based or epigenetic properties of genes strongly influence their tendency to respond to direct transcription factor perturbations, partially explaining the oft-noted difficulty of predicting responsiveness from transcription factor binding location data. These molecular features are largely reflected in and summarized by the gene's expression level and expression variation. Code is available at https://github.com/BrentLab/TFPertRespExplainer.
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Affiliation(s)
- Yiming Kang
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Computer Science and Engineering, Washington University, St. Louis, MO 63108, USA
| | - Wooseok J Jung
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Computer Science and Engineering, Washington University, St. Louis, MO 63108, USA
| | - Michael R Brent
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Computer Science and Engineering, Washington University, St. Louis, MO 63108, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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6
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Gladman N, Hufnagel B, Regulski M, Liu Z, Wang X, Chougule K, Kochian L, Magalhães J, Ware D. Sorghum root epigenetic landscape during limiting phosphorus conditions. Plant Direct 2022; 6:e393. [PMID: 35600998 PMCID: PMC9107021 DOI: 10.1002/pld3.393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/07/2022] [Accepted: 02/26/2022] [Indexed: 06/15/2023]
Abstract
Efficient acquisition and use of available phosphorus from the soil is crucial for plant growth, development, and yield. With an ever-increasing acreage of croplands with suboptimal available soil phosphorus, genetic improvement of sorghum germplasm for enhanced phosphorus acquisition from soil is crucial to increasing agricultural output and reducing inputs, while confronted with a growing world population and uncertain climate. Sorghum bicolor is a globally important commodity for food, fodder, and forage. Known for robust tolerance to heat, drought, and other abiotic stresses, its capacity for optimal phosphorus use efficiency (PUE) is still being investigated for optimized root system architectures (RSA). Whilst a few RSA-influencing genes have been identified in sorghum and other grasses, the epigenetic impact on expression and tissue-specific activation of candidate PUE genes remains elusive. Here, we present transcriptomic, epigenetic, and regulatory network profiling of RSA modulation in the BTx623 sorghum background in response to limiting phosphorus (LP) conditions. We show that during LP, sorghum RSA is remodeled to increase root length and surface area, likely enhancing its ability to acquire P. Global DNA 5-methylcytosine and H3K4 and H3K27 trimethylation levels decrease in response to LP, while H3K4me3 peaks and DNA hypomethylated regions contain recognition motifs of numerous developmental and nutrient responsive transcription factors that display disparate expression patterns between different root tissues (primary root apex, elongation zone, and lateral root apex).
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Affiliation(s)
| | - Barbara Hufnagel
- Centre National de la Recherche ScientifiqueMontpellierLanguedoc‐RoussillonFrance
| | | | - Zhigang Liu
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonCanada
| | - Xiaofei Wang
- Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | | | - Leon Kochian
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonCanada
| | | | - Doreen Ware
- Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
- U.S. Department of Agriculture‐Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and HealthCornell UniversityIthacaNew YorkUSA
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7
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Le Boiteux E, Guichet PO, Masliantsev K, Montibus B, Vaurs-Barriere C, Gonthier-Gueret C, Chautard E, Verrelle P, Karayan-Tapon L, Fogli A, Court F, Arnaud P. The Long Non-Coding RNA HOXA-AS2 Promotes Proliferation of Glioma Stem Cells and Modulates Their Inflammation Pathway Mainly through Post-Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094743. [PMID: 35563134 PMCID: PMC9102906 DOI: 10.3390/ijms23094743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 12/21/2022] Open
Abstract
Glioblastomas represent approximatively half of all gliomas and are the most deadly and aggressive form. Their therapeutic resistance and tumor relapse rely on a subpopulation of cells that are called Glioma Stem Cells (GSCs). Here, we investigated the role of the long non-coding RNA HOXA-AS2 in GSC biology using descriptive and functional analyses of glioma samples classified according to their isocitrate dehydrogenase (IDH) gene mutation status, and of GSC lines. We found that HOXA-AS2 is overexpressed only in aggressive (IDHwt) glioma and GSC lines. ShRNA-based depletion of HOXA-AS2 in GSCs decreased cell proliferation and altered the expression of several hundreds of genes. Integrative analysis revealed that these expression changes were not associated with changes in DNA methylation or chromatin signatures at the promoter of the majority of genes deregulated following HOXA-AS2 silencing in GSCs, suggesting a post-transcriptional regulation. In addition, transcription factor binding motif enrichment and correlation analyses indicated that HOXA-AS2 affects, directly or indirectly, the expression of key transcription factors implicated in GCS biology, including E2F8, E2F1, STAT1, and ATF3, thus contributing to GCS aggressiveness by promoting their proliferation and modulating the inflammation pathway.
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Affiliation(s)
- Elisa Le Boiteux
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Pierre-Olivier Guichet
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Konstantin Masliantsev
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Bertille Montibus
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Catherine Vaurs-Barriere
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Céline Gonthier-Gueret
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Emmanuel Chautard
- Pathology Department, Jean Perrin Center, F-63000 Clermont-Ferrand, France;
- INSERM, U1240 IMoST, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Pierre Verrelle
- CIMB, INSERM U1196 CNRS UMR9187, Curie Institute, F-91400 Orsay, France;
- Radiotherapy Department, Curie Institute, F-75248 Paris, France
- CNRS UMR 9187, INSERM U1196, Institut Curie, PSL Research University and Paris-Saclay University, F-91405 Orsay, France
| | - Lucie Karayan-Tapon
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Anne Fogli
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Radiation Oncology Department, Institut Curie, F-75005 Paris, France
| | - Franck Court
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Correspondence: (F.C.); (P.A.)
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Correspondence: (F.C.); (P.A.)
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Tutino VM, Kuo CC, Avasthi N, Rai HH, Waqas M, Siddiqui AH, Jarvis JN, Poppenberg KE. Chromatin architecture around stroke haplotypes provides evidence that genetic risk is conferred through vascular cells. Epigenomics 2022; 14:243-259. [PMID: 35184600 DOI: 10.2217/epi-2021-0307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Introduction: Genome-wide association studies (GWAS) have identified numerous stroke-associated SNPs. To understand how SNPs affect gene expression related to increased stroke risk, we studied epigenetic landscapes surrounding 26 common, validated stroke-associated loci. Methods: We mapped the SNPs to linkage disequilibrium (LD) blocks and examined H3K27ac, H3K4me1, H3K9ac, and H3K4me3 histone marks and transcription-factor binding-sites in pathologically relevant cell types (hematopoietic and vascular cells). Hi-C data were used to identify topologically associated domains (TADs) encompassing the LD blocks and overlapping genes. Results: Fibroblasts, smooth muscle, and endothelial cells showed significant enrichment for enhancer-associated marks within stroke-associated LD blocks. Genes within encompassing TADs reflected vessel homeostasis, cellular turnover, and enzymatic activity. Conclusions: Stroke-associated genetic variants confer risk predominantly through vascular cells rather than hematopoietic cell types.
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Affiliation(s)
- Vincent M Tutino
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA.,Department of Pathology & Anatomical Sciences, University at Buffalo, Buffalo, NY 14203, USA.,Department of Mechanical & Aerospace Engineering, University at Buffalo, Buffalo, NY 14203, USA
| | - Cathleen C Kuo
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA
| | - Naval Avasthi
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Biomedical Engineering, University at Buffalo, Buffalo, NY 14203, USA
| | - Hamid H Rai
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Muhammad Waqas
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Adnan H Siddiqui
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA.,Department of Radiology, University at Buffalo, Buffalo, NY 14203, USA
| | - James N Jarvis
- Department of Pediatrics, Department of Pathology & Anatomical Sciences, University at Buffalo, Buffalo, NY 14203, USA.,Genetics, Genomics, & Bioinformatics Program, University at Buffalo, Buffalo, NY 14203, USA
| | - Kerry E Poppenberg
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
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9
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Diab NS, Barish S, Dong W, Zhao S, Allington G, Yu X, Kahle KT, Brueckner M, Jin SC. Molecular Genetics and Complex Inheritance of Congenital Heart Disease. Genes (Basel) 2021; 12:genes12071020. [PMID: 34209044 PMCID: PMC8307500 DOI: 10.3390/genes12071020] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 01/09/2023] Open
Abstract
Congenital heart disease (CHD) is the most common congenital malformation and the leading cause of mortality therein. Genetic etiologies contribute to an estimated 90% of CHD cases, but so far, a molecular diagnosis remains unsolved in up to 55% of patients. Copy number variations and aneuploidy account for ~23% of cases overall, and high-throughput genomic technologies have revealed additional types of genetic variation in CHD. The first CHD risk genotypes identified through high-throughput sequencing were de novo mutations, many of which occur in chromatin modifying genes. Murine models of cardiogenesis further support the damaging nature of chromatin modifying CHD mutations. Transmitted mutations have also been identified through sequencing of population scale CHD cohorts, and many transmitted mutations are enriched in cilia genes and Notch or VEGF pathway genes. While we have come a long way in identifying the causes of CHD, more work is required to end the diagnostic odyssey for all CHD families. Complex genetic explanations of CHD are emerging but will require increasingly sophisticated analysis strategies applied to very large CHD cohorts before they can come to fruition in providing molecular diagnoses to genetically unsolved patients. In this review, we discuss the genetic architecture of CHD and biological pathways involved in its pathogenesis.
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Affiliation(s)
- Nicholas S. Diab
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
| | - Syndi Barish
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Shujuan Zhao
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
| | - Garrett Allington
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA;
| | - Xiaobing Yu
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
- Department of Computer Science & Engineering, Washington University, St. Louis, MO 63130, USA
| | - Kristopher T. Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA;
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Martina Brueckner
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA
- Correspondence: (M.B.); (S.C.J.)
| | - Sheng Chih Jin
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
- Department of Pediatrics, School of Medicine, Washington University, St. Louis, MO 63110, USA
- Correspondence: (M.B.); (S.C.J.)
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10
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Biggar KK, Charih F, Liu H, Ruiz-Blanco YB, Stalker L, Chopra A, Connolly J, Adhikary H, Frensemier K, Hoekstra M, Galka M, Fang Q, Wynder C, Stanford WL, Green JR, Li SS. Proteome-wide Prediction of Lysine Methylation Leads to Identification of H2BK43 Methylation and Outlines the Potential Methyllysine Proteome. Cell Rep 2020; 32:107896. [PMID: 32668242 DOI: 10.1016/j.celrep.2020.107896] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/29/2020] [Accepted: 06/22/2020] [Indexed: 12/15/2022] Open
Abstract
Protein Lys methylation plays a critical role in numerous cellular processes, but it is challenging to identify Lys methylation in a systematic manner. Here we present an approach combining in silico prediction with targeted mass spectrometry (MS) to identify Lys methylation (Kme) sites at the proteome level. We develop MethylSight, a program that predicts Kme events solely on the physicochemical properties of residues surrounding the putative methylation sites, which then requires validation by targeted MS. Using this approach, we identify 70 new histone Kme marks with a 90% validation rate. H2BK43me2, which undergoes dynamic changes during stem cell differentiation, is found to be a substrate of KDM5b. Furthermore, MethylSight predicts that Lys methylation is a prevalent post-translational modification in the human proteome. Our work provides a useful resource for guiding systematic exploration of the role of Lys methylation in human health and disease.
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11
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Abstract
Within the eukaryotic nucleus the genomic DNA is organized into chromatin by stably interacting with the histone proteins as well as with several other nuclear components including non-histone proteins and non-coding RNAs. Together these interactions distribute the genetic material into chromatin subdomains which can exhibit higher and lower compaction levels. This organization contributes to differentially control the access to genomic sequences encoding key regulatory genetic information. In this context, epigenetic mechanisms play a critical role in the regulation of gene expression as they modify the degree of chromatin compaction to facilitate both activation and repression of transcription. Among the most studied epigenetic mechanisms we find the methylation of DNA, ATP-dependent chromatin remodeling, and enzyme-mediated deposition and elimination of post-translational modifications at histone and non-histone proteins. In this mini review, we discuss evidence that supports the role of these epigenetic mechanisms during transcriptional control of osteoblast-related genes. Special attention is dedicated to mechanisms of epigenetic control operating at the Runx2 and Sp7 genes coding for the two principal master regulators of the osteogenic lineage during mesenchymal stem cell commitment.
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Affiliation(s)
- Martin Montecino
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - Margarita E Carrasco
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - Gino Nardocci
- Faculty of Medicine, Universidad de los Andes, Santiago, Chile.,Molecular Biology and Bioinformatic Lab, Program in Molecular Biology and Bioinformatics, Center for Biomedical Research and Innovation (CIIB), Universidad de los Andes, Santiago, Chile
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12
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Fal K, Tomkova D, Vachon G, Chabouté ME, Berr A, Carles CC. Chromatin Manipulation and Editing: Challenges, New Technologies and Their Use in Plants. Int J Mol Sci 2021; 22:E512. [PMID: 33419220 PMCID: PMC7825600 DOI: 10.3390/ijms22020512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/25/2022] Open
Abstract
An ongoing challenge in functional epigenomics is to develop tools for precise manipulation of epigenetic marks. These tools would allow moving from correlation-based to causal-based findings, a necessary step to reach conclusions on mechanistic principles. In this review, we describe and discuss the advantages and limits of tools and technologies developed to impact epigenetic marks, and which could be employed to study their direct effect on nuclear and chromatin structure, on transcription, and their further genuine role in plant cell fate and development. On one hand, epigenome-wide approaches include drug inhibitors for chromatin modifiers or readers, nanobodies against histone marks or lines expressing modified histones or mutant chromatin effectors. On the other hand, locus-specific approaches consist in targeting precise regions on the chromatin, with engineered proteins able to modify epigenetic marks. Early systems use effectors in fusion with protein domains that recognize a specific DNA sequence (Zinc Finger or TALEs), while the more recent dCas9 approach operates through RNA-DNA interaction, thereby providing more flexibility and modularity for tool designs. Current developments of "second generation", chimeric dCas9 systems, aiming at better targeting efficiency and modifier capacity have recently been tested in plants and provided promising results. Finally, recent proof-of-concept studies forecast even finer tools, such as inducible/switchable systems, that will allow temporal analyses of the molecular events that follow a change in a specific chromatin mark.
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Affiliation(s)
- Kateryna Fal
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
| | - Denisa Tomkova
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Gilles Vachon
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Cristel C. Carles
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
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13
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Paraiso KD, Blitz IL, Coley M, Cheung J, Sudou N, Taira M, Cho KWY. Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation. Cell Rep 2020; 27:2962-2977.e5. [PMID: 31167141 PMCID: PMC6610736 DOI: 10.1016/j.celrep.2019.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/30/2019] [Accepted: 05/01/2019] [Indexed: 01/06/2023] Open
Abstract
Elucidation of the sequence of events underlying the dynamic interaction
between transcription factors and chromatin states is essential. Maternal
transcription factors function at the top of the regulatory hierarchy to specify
the primary germ layers at the onset of zygotic genome activation (ZGA). We
focus on the formation of endoderm progenitor cells and examine the interactions
between maternal transcription factors and chromatin state changes underlying
the cell specification process. Endoderm-specific factors Otx1 and Vegt together
with Foxh1 orchestrate endoderm formation by coordinated binding to select
regulatory regions. These interactions occur before the deposition of enhancer
histone marks around the regulatory regions, and these TFs recruit RNA
polymerase II, regulate enhancer activity, and establish super-enhancers
associated with important endodermal genes. Therefore, maternal transcription
factors Otx1, Vegt, and Foxh1 combinatorially regulate the activity of
super-enhancers, which in turn activate key lineage-specifying genes during
ZGA. How do maternal transcription factors interact with chromatin regions to
coordinate the endodermal gene regulatory program? Paraiso et al. demonstrate
that combinatorial binding of maternal Otx1, Vegt, and Foxh1 to select enhancers
and super-enhancers in the genome controls endodermal cell fate specification
during zygotic gene activation.
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Affiliation(s)
- Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Masani Coley
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jessica Cheung
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Norihiro Sudou
- Department of Anatomy, Tokyo Women's Medical University, Tokyo, Japan
| | - Masanori Taira
- Department of Biological Sciences, Chuo University, Tokyo, Japan
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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14
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Behera V, Stonestrom AJ, Hamagami N, Hsiung CC, Keller CA, Giardine B, Sidoli S, Yuan ZF, Bhanu NV, Werner MT, Wang H, Garcia BA, Hardison RC, Blobel GA. Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription. Cell Rep 2019; 27:400-415.e5. [PMID: 30970245 DOI: 10.1016/j.celrep.2019.03.057] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/30/2018] [Accepted: 03/14/2019] [Indexed: 12/12/2022] Open
Abstract
Chromatin reader protein BRD4 is thought to bookmark mitotic chromatin to propagate transcriptional states across mitosis. Behera et al. profiled and perturbed mitotic BRD4 chromatin occupancy to show that BRD4 is dispensable for this process. Instead, BRD4 mitotic chromatin association is likely a mere reflection of mitotically stable histone marks. Global changes in chromatin organization and the cessation of transcription during mitosis are thought to challenge the resumption of appropriate transcription patterns after mitosis. The acetyl-lysine binding protein BRD4 has been previously suggested to function as a transcriptional “bookmark” on mitotic chromatin. Here, genome-wide location analysis of BRD4 in erythroid cells, combined with data normalization and peak characterization approaches, reveals that BRD4 widely occupies mitotic chromatin. However, removal of BRD4 from mitotic chromatin does not impair post-mitotic activation of transcription. Additionally, histone mass spectrometry reveals global preservation of most posttranslational modifications (PTMs) during mitosis. In particular, H3K14ac, H3K27ac, H3K122ac, and H4K16ac widely mark mitotic chromatin, especially at lineagespecific genes, and predict BRD4 mitotic binding genome wide. Therefore, BRD4 is likely not a mitotic bookmark but only a “passenger.” Instead, mitotic histone acetylation patterns may constitute the actual bookmarks that restore lineage-specific transcription patterns after mitosis.
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15
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Linhares ND, Pereira DA, Conceição IM, Franco GR, Eckalbar WL, Ahituv N, Luizon MR. Noncoding SNPs associated with increased GDF15 levels located in a metformin-activated enhancer region upstream of GDF15. Pharmacogenomics 2020; 21:509-520. [PMID: 32427048 DOI: 10.2217/pgs-2020-0010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: GDF15 levels are a biomarker for metformin use. We performed the functional annotation of noncoding genome-wide association study (GWAS) SNPs for GDF15 levels and the Genotype-Tissue Expression (GTEx)-expression quantitative trait loci (eQTLs) for GDF15 expression within metformin-activated enhancers around GDF15. Materials & methods: These enhancers were identified using chromatin immunoprecipitation followed by sequencing data for active (H3K27ac) and silenced (H3K27me3) histone marks on human hepatocytes treated with metformin, Encyclopedia of DNA Elements data and cis-regulatory elements assignment tools. Results: The GWAS lead SNP rs888663, the SNP rs62122429 associated with GDF15 levels in the Outcome Reduction with Initial Glargine Intervention trial, and the GTEx-expression quantitative trait locus rs4808791 for GDF15 expression in whole blood are located in a metformin-activated enhancer upstream of GDF15 and tightly linked in Europeans and East Asians. Conclusion: Noncoding variation within a metformin-activated enhancer may increase GDF15 expression and help to predict GDF15 levels.
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Affiliation(s)
- Natália D Linhares
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Daniela A Pereira
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Izabela McA Conceição
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Glória R Franco
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Walter L Eckalbar
- Institute for Human Genetics, The University of California, San Francisco, CA 94143, USA.,Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nadav Ahituv
- Institute for Human Genetics, The University of California, San Francisco, CA 94143, USA.,Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marcelo R Luizon
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.,Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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16
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Garsuault D, Bouyer C, Nguyen E, Kandhari R, Prochazkova-Carlotti M, Chevret E, Forgez P, Ségal-Bendirdjian E. Complex context relationships between DNA methylation and accessibility, histone marks, and hTERT gene expression in acute promyelocytic leukemia cells: perspectives for all-trans retinoic acid in cancer therapy. Mol Oncol 2020; 14:1310-1326. [PMID: 32239597 PMCID: PMC7266276 DOI: 10.1002/1878-0261.12681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/19/2020] [Accepted: 03/28/2020] [Indexed: 02/06/2023] Open
Abstract
Telomerase (hTERT) reactivation and sustained expression is a key event in the process of cellular transformation. Therefore, the identification of the mechanisms regulating hTERT expression is of great interest for the development of new anticancer therapies. Although the epigenetic state of hTERT gene promoter is important, we still lack a clear understanding of the mechanisms by which epigenetic changes affect hTERT expression. Retinoids are well-known inducers of granulocytic maturation in acute promyelocytic leukemia (APL). We have previously shown that retinoids repressed hTERT expression in the absence of maturation leading to growth arrest and cell death. Exploring the mechanisms of this repression, we showed that transcription factor binding was dependent on the epigenetic status of hTERT promoter. In the present study, we used APL cells lines and publicly available datasets from APL patients to further investigate the integrated epigenetic events that promote hTERT promoter transition from its silent to its active state, and inversely. We showed, in APL patients, that the methylation of the distal domain of hTERT core promoter was altered and correlated with the outcome of the disease. Further studies combining complementary approaches carried out on APL cell lines highlighted the significance of a domain outside the minimal promoter, localized around 5 kb upstream from the transcription start site, in activating hTERT. This domain is characterized by DNA hypomethylation and H3K4Me3 deposition. Our findings suggest a cooperative interplay between hTERT promoter methylation, chromatin accessibility, and histone modifications that force the revisiting of previously proposed concepts regarding hTERT epigenetic regulation. They represent, therefore, a major advance in predicting sensitivity to retinoid-induced hTERT repression and, more generally, in the potential development of therapies targeting hTERT expression in cancers.
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Affiliation(s)
- Delphine Garsuault
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Université de Paris, Paris Sorbonne Cité, France.,Paris-Sud University, Paris-Saclay University, Orsay, France
| | - Claire Bouyer
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Université de Paris, Paris Sorbonne Cité, France
| | - Eric Nguyen
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Université de Paris, Paris Sorbonne Cité, France
| | - Rohan Kandhari
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Indian Institute of Technology, BHU, Varanasi, India
| | | | - Edith Chevret
- Team Cutaneous Lymphoma Oncogenesis, INSERM U1053, Bordeaux, France
| | - Patricia Forgez
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Université de Paris, Paris Sorbonne Cité, France
| | - Evelyne Ségal-Bendirdjian
- Team: Cellular Homeostasis, Cancer, and Therapies, INSERM UMR-S 1124, Université de Paris, France.,Université de Paris, Paris Sorbonne Cité, France.,BioMedTech Facilities, CNRS UMS2009/INSERM US36, Université de Paris, France
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17
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Yi G, Wierenga ATJ, Petraglia F, Narang P, Janssen-Megens EM, Mandoli A, Merkel A, Berentsen K, Kim B, Matarese F, Singh AA, Habibi E, Prange KHM, Mulder AB, Jansen JH, Clarke L, Heath S, van der Reijden BA, Flicek P, Yaspo ML, Gut I, Bock C, Schuringa JJ, Altucci L, Vellenga E, Stunnenberg HG, Martens JHA. Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes. Cell Rep 2020; 26:1059-1069.e6. [PMID: 30673601 PMCID: PMC6363099 DOI: 10.1016/j.celrep.2018.12.098] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/27/2018] [Accepted: 12/21/2018] [Indexed: 12/19/2022] Open
Abstract
Global investigation of histone marks in acute myeloid leukemia (AML) remains limited. Analyses of 38 AML samples through integrated transcriptional and chromatin mark analysis exposes 2 major subtypes. One subtype is dominated by patients with NPM1 mutations or MLL-fusion genes, shows activation of the regulatory pathways involving HOX-family genes as targets, and displays high self-renewal capacity and stemness. The second subtype is enriched for RUNX1 or spliceosome mutations, suggesting potential interplay between the 2 aberrations, and mainly depends on IRF family regulators. Cellular consequences in prognosis predict a relatively worse outcome for the first subtype. Our integrated profiling establishes a rich resource to probe AML subtypes on the basis of expression and chromatin data.
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MESH Headings
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin/pathology
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Humans
- Leukemia, Myeloid, Acute/classification
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mutation
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
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Affiliation(s)
- Guoqiang Yi
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Albertus T J Wierenga
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands; Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Francesca Petraglia
- Dipartimento di Biochimica, Biofisica e Patologia generale, Università degli Studi della Campania "Luigi Vanvitelli," Vico L. De Crecchio 7, 80138 Napoli, Italy
| | - Pankaj Narang
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Eva M Janssen-Megens
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Amit Mandoli
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Angelika Merkel
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, Spain
| | - Kim Berentsen
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bowon Kim
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Filomena Matarese
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Abhishek A Singh
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Ehsan Habibi
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Koen H M Prange
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - André B Mulder
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Heath
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, Spain
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ivo Gut
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, Spain
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Jan Jacob Schuringa
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Lucia Altucci
- Dipartimento di Biochimica, Biofisica e Patologia generale, Università degli Studi della Campania "Luigi Vanvitelli," Vico L. De Crecchio 7, 80138 Napoli, Italy
| | - Edo Vellenga
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands.
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18
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Martín B, Pappa S, Díez-Villanueva A, Mallona I, Custodio J, Barrero MJ, Peinado MA, Jordà M. Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. Epigenetics 2020; 15:765-779. [PMID: 32041475 DOI: 10.1080/15592294.2020.1722398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Alu repeats constitute a major fraction of human genome and for a small subset of them a role in gene regulation has been described. The number of studies focused on the functional characterization of particular Alu elements is very limited. Most Alu elements are DNA methylated and then assumed to lie in repressed chromatin domains. We hypothesize that Alu elements with low or variable DNA methylation are candidates for a functional role. In a genome-wide study in normal and cancer tissues, we pinpointed an Alu repeat (AluSq2) with differential methylation located upstream of the promoter region of the DIEXF gene. DIEXF encodes a highly conserved factor essential for the development of zebrafish digestive tract. To characterize the contribution of the Alu element to the regulation of DIEXF we analysed the epigenetic landscapes of the gene promoter and flanking regions in different cell types and cancers. Alternate epigenetic profiles (DNA methylation and histone modifications) of the AluSq2 element were associated with DIEXF transcript diversity as well as protein levels, while the epigenetic profile of the CpG island associated with the DIEXF promoter remained unchanged. These results suggest that AluSq2 might directly contribute to the regulation of DIEXF transcription and protein expression. Moreover, AluSq2 was DNA hypomethylated in different cancer types, pointing out its putative contribution to DIEXF alteration in cancer and its potential as tumoural biomarker.
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Affiliation(s)
- Berta Martín
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Stella Pappa
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Anna Díez-Villanueva
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Izaskun Mallona
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Joaquín Custodio
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - María José Barrero
- Center for Regenerative Medicine in Barcelona (CMRB), Avinguda de la Granvia de l'Hospitalet , Barcelona, Spain
| | - Miguel A Peinado
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Mireia Jordà
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
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19
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Zhu H, Wei T, Cai Y, Jin J. Small Molecules Targeting the Specific Domains of Histone-Mark Readers in Cancer Therapy. Molecules 2020; 25:E578. [PMID: 32013155 DOI: 10.3390/molecules25030578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
Epigenetic modifications (or epigenetic tags) on DNA and histones not only alter the chromatin structure, but also provide a recognition platform for subsequent protein recruitment and enable them to acquire executive instructions to carry out specific intracellular biological processes. In cells, different epigenetic-tags on DNA and histones are often recognized by the specific domains in proteins (readers), such as bromodomain (BRD), chromodomain (CHD), plant homeodomain (PHD), Tudor domain, Pro-Trp-Trp-Pro (PWWP) domain and malignant brain tumor (MBT) domain. Recent accumulating data reveal that abnormal intracellular histone modifications (histone marks) caused by tumors can be modulated by small molecule-mediated changes in the activity of the above domains, suggesting that small molecules targeting histone-mark reader domains may be the trend of new anticancer drug development. Here, we summarize the protein domains involved in histone-mark recognition, and introduce recent research findings about small molecules targeting histone-mark readers in cancer therapy.
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20
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Blanco E, González-Ramírez M, Alcaine-Colet A, Aranda S, Di Croce L. The Bivalent Genome: Characterization, Structure, and Regulation. Trends Genet 2019; 36:118-131. [PMID: 31818514 DOI: 10.1016/j.tig.2019.11.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/28/2019] [Accepted: 11/08/2019] [Indexed: 02/05/2023]
Abstract
An intricate molecular machinery is at the core of gene expression regulation in every cell. During the initial stages of organismal development, the coordinated activation of diverse transcriptional programs is crucial and must be carefully executed to shape every organ and tissue. Bivalent promoters and poised enhancers are regulatory regions decorated with histone marks that are associated with both positive and negative transcriptional outcomes. These apparently contradictory signals are important for setting bivalent genes in a poised state, which is subsequently resolved during differentiation into either active or repressive states. We discuss the origins of bivalent promoters and the mechanisms implicated in their acquisition and maintenance. We further review how the presence of bivalent marks influences genome architecture. Finally, we highlight the potential link between bivalency and cancer which could drive biomedical research in disease etiology and treatment.
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Affiliation(s)
- Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Mar González-Ramírez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Anna Alcaine-Colet
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain.
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21
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Matyášek R, Krumpolcová A, Lunerová J, Mikulášková E, Rosselló JA, Kovařík A. Unique Epigenetic Features of Ribosomal RNA Genes (rDNA) in Early Diverging Plants (Bryophytes). Front Plant Sci 2019; 10:1066. [PMID: 31543890 PMCID: PMC6739443 DOI: 10.3389/fpls.2019.01066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/06/2019] [Indexed: 05/03/2023]
Abstract
Introduction: In plants, the multicopy genes encoding ribosomal RNA (rDNA) typically exhibit heterochromatic features and high level of DNA methylation. Here, we explored rDNA methylation in early diverging land plants from Bryophyta (15 species, 14 families) and Marchantiophyta (4 species, 4 families). DNA methylation was investigated by methylation-sensitive Southern blot hybridization in all species. We also carried out whole genomic bisulfite sequencing in Polytrichum formosum (Polytrichaceae) and Dicranum scoparium (Dicranaceae) and used available model plant methyloms (Physcomitrella patents and Marchantia polymorpha) to determine rDNA unit-wide methylation patterns. Chromatin structure was analyzed using fluorescence in situ hybridization (FISH) and immunoprecipitation (CHIP) assays. Results: In contrast to seed plants, bryophyte rDNAs were efficiently digested with methylation-sensitive enzymes indicating no or low levels of CG and CHG methylation in these loci. The rDNA methylom analyses revealed variation between species ranging from negligible (<3%, P. formosum, P. patens) to moderate (7 and 17% in M. polymorpha and D. scoparium, respectively) methylation levels. There were no differences between coding and noncoding parts of rDNA units and between gametophyte and sporophyte tissues. However, major satellite repeat and transposable elements were heavily methylated in P. formosum and D. scoparium. In P. formosum rDNA, the euchromatic H3K4m3 and heterochromatic H3K9m2 histone marks were nearly balanced contrasting the angiosperms data where H3K9m2 typically dominates rDNA chromatin. In moss interphase nuclei, rDNA was localized at the nucleolar periphery and its condensation level was high. Conclusions: Unlike seed plants, the rRNA genes seem to escape global methylation machinery in bryophytes. Distinct epigenetic features may be related to rDNA expression and the physiology of these early diverging plants that exist in haploid state for most of their life cycles.
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Affiliation(s)
- Roman Matyášek
- Department of Molecular Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - Alice Krumpolcová
- Department of Molecular Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - Eva Mikulášková
- Department of Botany and Zoology, Masaryk University, Brno, Czechia
| | - Josep A. Rosselló
- Jardín Botánico, ICBiBE-Unidad Asociada CSIC, Universidad de Valencia, Valencia, Spain
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
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22
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Rifaï K, Judes G, Idrissou M, Daures M, Bignon YJ, Penault-Llorca F, Bernard-Gallon D. SIRT1-dependent epigenetic regulation of H3 and H4 histone acetylation in human breast cancer. Oncotarget 2018; 9:30661-30678. [PMID: 30093977 PMCID: PMC6078139 DOI: 10.18632/oncotarget.25771] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the most frequently diagnosed malignancy in women worldwide. It is well established that the complexity of carcinogenesis involves profound epigenetic deregulations that contribute to the tumorigenesis process. Deregulated H3 and H4 acetylated histone marks are amongst those alterations. Sirtuin-1 (SIRT1) is a class-III histone deacetylase deeply involved in apoptosis, genomic stability, gene expression regulation and breast tumorigenesis. However, the underlying molecular mechanism by which SIRT1 regulates H3 and H4 acetylated marks, and consequently cancer-related gene expression in breast cancer, remains uncharacterized. In this study, we elucidated SIRT1 epigenetic role and analyzed the link between the latter and histones H3 and H4 epigenetic marks in all 5 molecular subtypes of breast cancer. Using a cohort of 135 human breast tumors and their matched normal tissues, as well as 5 human-derived cell lines, we identified H3k4ac as a new prime target of SIRT1 in breast cancer. We also uncovered an inverse correlation between SIRT1 and the 3 epigenetic marks H3k4ac, H3k9ac and H4k16ac expression patterns. We showed that SIRT1 modulates the acetylation patterns of histones H3 and H4 in breast cancer. Moreover, SIRT1 regulates its H3 acetylated targets in a subtype-specific manner. Furthermore, SIRT1 siRNA-mediated knockdown increases histone acetylation levels at 6 breast cancer-related gene promoters: AR, BRCA1, ERS1, ERS2, EZH2 and EP300. In summary, this report characterizes for the first time the epigenetic behavior of SIRT1 in human breast carcinoma. These novel findings point to a potential use of SIRT1 as an epigenetic therapeutic target in breast cancer.
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Affiliation(s)
- Khaldoun Rifaï
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
| | - Gaëlle Judes
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
| | - Mouhamed Idrissou
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
| | - Marine Daures
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
| | - Yves-Jean Bignon
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
| | - Frédérique Penault-Llorca
- INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France.,Department of Biopathology, Centre Jean Perrin, Clermont-Ferrand 63011, France
| | - Dominique Bernard-Gallon
- Department of Oncogenetics, Centre Jean Perrin, CBRV, Clermont-Ferrand 63001, France.,INSERM, UMR 1240, IMoST Imagerie Moléculaire et Stratégies Théranostiques, Clermont-Ferrand 63005, France
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23
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Zhang X, Biagini Myers JM, Burleson JD, Ulm A, Bryan KS, Chen X, Weirauch MT, Baker TA, Butsch Kovacic MS, Ji H. Nasal DNA methylation is associated with childhood asthma. Epigenomics 2018; 10:629-641. [PMID: 29692198 DOI: 10.2217/epi-2017-0127] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
AIM We aim to study DNA methylation (DNAm) variations associated with childhood asthma. METHODS Nasal DNAm was compared between sibling pairs discordant for asthma, 29 sib pairs for genome-wide association studies and 54 sib pairs for verification by pyrosequencing. Associations of methylation with asthma symptoms, allergy and environmental exposures were evaluated. In vitro experiments and functional genomic analyses were performed to explore biologic relevance. RESULTS Three CpGs were associated with asthma. cg14830002 was associated with allergies in nonasthmatics. cg23602092 was associated with asthma symptoms. cg14830002 and cg23602092 were associated with traffic-related air pollution exposure. Nearby genes were transcriptionally regulated by diesel exhaust, house dust mite and 5-aza-2'-deoxycytidine. Active chromatin marks and transcription factor binding were found around these sites. CONCLUSION We identified novel DNAm variations associated with childhood asthma and suggested new disease-contributing epigenetic mechanisms.
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Affiliation(s)
- Xue Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jocelyn M Biagini Myers
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - J D Burleson
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ashley Ulm
- Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kelly S Bryan
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoting Chen
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA.,Center for Autoimmune Genomics & Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Divisions of Biomedical Informatics & Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Theresa A Baker
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Melinda S Butsch Kovacic
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA.,Division of Biostatistics & Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Hong Ji
- Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
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24
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Liu Y, Pelham-Webb B, Di Giammartino DC, Li J, Kim D, Kita K, Saiz N, Garg V, Doane A, Giannakakou P, Hadjantonakis AK, Elemento O, Apostolou E. Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells. Cell Rep 2018; 19:1283-1293. [PMID: 28514649 DOI: 10.1016/j.celrep.2017.04.067] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/17/2017] [Accepted: 04/24/2017] [Indexed: 10/19/2022] Open
Abstract
During mitosis, transcription is halted and many chromatin features are lost, posing a challenge for the continuity of cell identity, particularly in fast cycling stem cells, which constantly balance self-renewal with differentiation. Here we show that, in pluripotent stem cells, certain histone marks and stem cell regulators remain associated with specific genomic regions of mitotic chromatin, a phenomenon known as mitotic bookmarking. Enhancers of stem cell-related genes are bookmarked by both H3K27ac and the master regulators OCT4, SOX2, and KLF4, while promoters of housekeeping genes retain high levels of mitotic H3K27ac in a cell-type invariant manner. Temporal degradation of OCT4 during mitotic exit compromises its ability both to maintain and induce pluripotency, suggesting that its regulatory function partly depends on its bookmarking activity. Together, our data document a widespread yet specific bookmarking by histone modifications and transcription factors promoting faithful and efficient propagation of stemness after cell division.
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Affiliation(s)
- Yiyuan Liu
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Bobbie Pelham-Webb
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Dafne Campigli Di Giammartino
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jiexi Li
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Daleum Kim
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Katsuhiro Kita
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Nestor Saiz
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ashley Doane
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Paraskevi Giannakakou
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Effie Apostolou
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
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25
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Lee E, Wang J, Jung Y, Cackowski FC, Taichman RS. Reduction of two histone marks, H3k9me3 and H3k27me3 by epidrug induces neuroendocrine differentiation in prostate cancer. J Cell Biochem 2018; 119:3697-3705. [PMID: 29236331 DOI: 10.1002/jcb.26586] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/06/2017] [Indexed: 12/21/2022]
Abstract
Neuroendocrine prostate cancer (NE PCa) is an aggressive malignancy, often presenting with advanced metastasis. We previously reported that reduction of histone marks regulated by DNMT1 following epidrug (5-Azacitidine, 5-Aza) treatment controls induction of epithelial to mesenchymal (EMT) and a cancer stem cell (CSC) phenotype, which facilitates tumorigenesis in PCa cells. Here, we use the epidrug 5-Aza as a model for how histone marks may regulate the reprogramming of prostate adenocarcinoma into NE phenotypic cells. First, we observed that 5-Aza treatment of PCa cells in vitro induces a neuron-like phenotype. In addition, significant increases in the expression of the NE markers N-Myc downstream regulated gene 1 (NDRG1), enolase-2 (ENO2), and synaptophysin were observed. Critically, a high density of NE cells with synaptophysin expression was found in tumors generated by 5-Aza pretreatment of PCa cells. Importantly, induction of NE differentiation of PCa cells was associated with an enhancement of NDRG1 expression by reduction of two histone marks, H3K9me3 and H3K27me3. Further, more NDRG1 expression was detected in the subset of PCa cells with reduced expression of H3K9me3 or H3K27me3 in the tumors generated by 5-Aza pretreated PCa cells and critically, these biological differences are also observed in small cell carcinoma in advanced stage of human primary PCa tumors. Our results suggest that reduction of histone marks regulated by the epidrug 5-Aza may control induction of a NE phenotype, which facilitates PCa progression. These studies suggest a strong rationale for developing therapeutics, which target epigenetic regulation.
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Affiliation(s)
- Eunsohl Lee
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor,, Michigan
| | - Jingcheng Wang
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor,, Michigan
| | - Younghun Jung
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor,, Michigan
| | - Frank C Cackowski
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor,, Michigan.,Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Russell S Taichman
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor,, Michigan
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26
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Savitsky P, Krojer T, Fujisawa T, Lambert JP, Picaud S, Wang CY, Shanle EK, Krajewski K, Friedrichsen H, Kanapin A, Goding C, Schapira M, Samsonova A, Strahl BD, Gingras AC, Filippakopoulos P. Multivalent Histone and DNA Engagement by a PHD/BRD/PWWP Triple Reader Cassette Recruits ZMYND8 to K14ac-Rich Chromatin. Cell Rep 2016; 17:2724-37. [PMID: 27926874 DOI: 10.1016/j.celrep.2016.11.014] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/27/2016] [Accepted: 10/31/2016] [Indexed: 12/12/2022] Open
Abstract
Elucidation of interactions involving DNA and histone post-translational-modifications (PTMs) is essential for providing insights into complex biological functions. Reader assemblies connected by flexible linkages facilitate avidity and increase affinity; however, little is known about the contribution to the recognition process of multiple PTMs because of rigidity in the absence of conformational flexibility. Here, we resolve the crystal structure of the triple reader module (PHD-BRD-PWWP) of ZMYND8, which forms a stable unit capable of simultaneously recognizing multiple histone PTMs while presenting a charged platform for association with DNA. Single domain disruptions destroy the functional network of interactions initiated by ZMYND8, impairing recruitment to sites of DNA damage. Our data establish a proof of principle that rigidity can be compensated by concomitant DNA and histone PTM interactions, maintaining multivalent engagement of transient chromatin states. Thus, our findings demonstrate an important role for rigid multivalent reader modules in nucleosome binding and chromatin function. The ZMYND8 PHD/BRD/PWW cassette forms a stable structural reader ensemble The reader ensemble binds chromatin via simultaneous engagement of histones and DNA Each module of the ZMYND8 reader ensemble contributes to chromatin interactions Genome-wide distribution of ZMYND8 at enhancers is mediated by K14ac interactions
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27
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Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JHA, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Rep 2017; 17:2137-2150. [PMID: 27851974 PMCID: PMC5120369 DOI: 10.1016/j.celrep.2016.10.059] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 08/25/2016] [Accepted: 09/30/2016] [Indexed: 12/14/2022] Open
Abstract
Epigenome-wide association studies (EWAS) provide an alternative approach for studying human disease through consideration of non-genetic variants such as altered DNA methylation. To advance the complex interpretation of EWAS, we developed eFORGE (http://eforge.cs.ucl.ac.uk/), a new standalone and web-based tool for the analysis and interpretation of EWAS data. eFORGE determines the cell type-specific regulatory component of a set of EWAS-identified differentially methylated positions. This is achieved by detecting enrichment of overlap with DNase I hypersensitive sites across 454 samples (tissues, primary cell types, and cell lines) from the ENCODE, Roadmap Epigenomics, and BLUEPRINT projects. Application of eFORGE to 20 publicly available EWAS datasets identified disease-relevant cell types for several common diseases, a stem cell-like signature in cancer, and demonstrated the ability to detect cell-composition effects for EWAS performed on heterogeneous tissues. Our approach bridges the gap between large-scale epigenomics data and EWAS-derived target selection to yield insight into disease etiology.
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Affiliation(s)
- Charles E Breeze
- UCL Cancer Institute, University College London, London WC1E 6BT, UK.
| | - Dirk S Paul
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081BT Amsterdam, the Netherlands
| | - Lee M Butcher
- UCL Cancer Institute, University College London, London WC1E 6BT, UK; Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - John C Ambrose
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - James E Barrett
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Robert Lowe
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT London, UK
| | - Vardhman K Rakyan
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT London, UK
| | - Valentina Iotchkova
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0QQ, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Willem H Ouwehand
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0QQ, UK
| | - Jonathan Laperle
- Département d'Informatique, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Pierre-Étienne Jacques
- Département d'Informatique, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC H3G 1Y6, Canada; Génome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Anke K Bergmann
- Institute of Human Genetics, Christian Albrechts University, 24105 Kiel, Germany; Department of Pediatrics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian Albrechts University, 24105 Kiel, Germany; Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Edo Vellenga
- Department of Hematology, University of Groningen and University Medical Center Groningen, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Sadia Saeed
- Department of Biochemistry, PMAS Arid Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan; Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands
| | - Filomena Matarese
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands
| | | | - Javier Herrero
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, London WC1E 6BT, UK.
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Gates LA, Foulds CE, O'Malley BW. Histone Marks in the 'Driver's Seat': Functional Roles in Steering the Transcription Cycle. Trends Biochem Sci 2017; 42:977-989. [PMID: 29122461 DOI: 10.1016/j.tibs.2017.10.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/16/2017] [Indexed: 12/27/2022]
Abstract
Particular chromatin modifications are associated with different states of gene transcription, yet our understanding of which modifications are causal 'drivers' in promoting transcription is incomplete. Here, we discuss new developments describing the ordered, mechanistic role of select histone marks occurring during distinct steps in the RNA polymerase II (Pol II) transcription cycle. In particular, we highlight the interplay between histone marks in specifying the 'next step' of transcription. While many studies have described correlative relationships between histone marks and their occupancy at distinct gene regions, we focus on studies that elucidate clear functional consequences of specific histone marks during different stages of transcription. These recent discoveries have refined our current mechanistic understanding of how histone marks promote Pol II transcriptional progression.
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Affiliation(s)
- Leah A Gates
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Current address: Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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Stadler J, Richly H. Regulation of DNA Repair Mechanisms: How the Chromatin Environment Regulates the DNA Damage Response. Int J Mol Sci 2017; 18:E1715. [PMID: 28783053 DOI: 10.3390/ijms18081715] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/17/2017] [Accepted: 08/02/2017] [Indexed: 01/21/2023] Open
Abstract
Cellular DNA is constantly challenged by damage-inducing factors derived from exogenous or endogenous sources. In order to maintain genome stability and integrity, cells have evolved a wide variety of DNA repair pathways which counteract different types of DNA lesions, also referred to as the DNA damage response (DDR). However, DNA in eukaryotes is highly organized and compacted into chromatin representing major constraints for all cellular pathways, including DNA repair pathways, which require DNA as their substrate. Therefore, the chromatin configuration surrounding the lesion site undergoes dramatic remodeling to facilitate access of DNA repair factors and subsequent removal of the DNA lesion. In this review, we focus on the question of how the cellular DNA repair pathways overcome the chromatin barrier, how the chromatin environment is rearranged to facilitate efficient DNA repair, which proteins mediate this re-organization process and, consequently, how the altered chromatin landscape is involved in the regulation of DNA damage responses.
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Abstract
Aberrations in the epigenetic landscape are a hallmark of cancer. Alterations in enzymes that are “writers,” “erasers,” or “readers” of histone modification marks are common. Bromodomains are “readers” that bind acetylated lysines in histone tails. Their most important function is the regulation of gene transcription by the recruitment of different molecular partners. Moreover, proteins containing bromodomains are also epigenetic regulators, although little is known about the specific function of these domains. In recent years, there has been increasing interest in developing small molecules that can target specific bromodomains. First, this has helped clarify biological functions of bromodomain-containing proteins. Secondly, it opens a new front for combatting cancer. In this review we will describe the structures and mechanisms associated with Bromodomain and Extra-Terminal motif (BET) inhibitors and non-BET inhibitors, their current status of development, and their promising role as anti-cancer agents.
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Affiliation(s)
- Montserrat Pérez-Salvia
- a Cancer Epigenetics and Biology Program (PEBC) , Bellvitge Biomedical Research Institute (IDIBELL) , Barcelona , Catalonia , Spain
| | - Manel Esteller
- a Cancer Epigenetics and Biology Program (PEBC) , Bellvitge Biomedical Research Institute (IDIBELL) , Barcelona , Catalonia , Spain.,b Department of Physiological Sciences II, School of Medicine , University of Barcelona , Barcelona , Catalonia , Spain.,c Institució Catalana de Recerca i Estudis Avançats (ICREA) , Barcelona , Catalonia , Spain
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31
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Laczik M, Hendrickx J, Veillard AC, Tammoh M, Marzi S, Poncelet D. Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks. Bioinform Biol Insights 2016; 10:209-224. [PMID: 27812282 PMCID: PMC5081244 DOI: 10.4137/bbi.s40628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/23/2016] [Accepted: 08/28/2016] [Indexed: 01/18/2023] Open
Abstract
As chromatin immunoprecipitation (ChIP) sequencing is becoming the dominant technique for studying chromatin modifications, new protocols surface to improve the method. Bioinformatics is also essential to analyze and understand the results, and precise analysis helps us to identify the effects of protocol optimizations. We applied iterative sonication – sending the fragmented DNA after ChIP through additional round(s) of shearing – to a number of samples, testing the effects on different histone marks, aiming to uncover potential benefits of inactive histone marks specifically. We developed an analysis pipeline that utilizes our unique, enrichment-type specific approach to peak calling. With the help of this pipeline, we managed to accurately describe the advantages and disadvantages of the iterative refragmentation technique, and we successfully identified possible fields for its applications, where it enhances the results greatly. In addition to the resonication protocol description, we provide guidelines for peak calling optimization and a freely implementable pipeline for data analysis.
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Affiliation(s)
- Miklós Laczik
- Doctorate Student, Doctoral College of Agronomy and Bioengineering, Gembloux Agro-Biotech, University of Liège, Liège, Belgium.; Researcher, R&D Epigenetics Department of Diagenode SA, Liège, Belgium
| | - Jan Hendrickx
- Researcher, R&D Epigenetics Department of Diagenode SA, Liège, Belgium
| | | | - Mustafa Tammoh
- Researcher, R&D Epigenetics Department of Diagenode SA, Liège, Belgium
| | - Sarah Marzi
- Doctorate Student, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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Abstract
Stromal cells of the tumor microenvironment have been shown to play important roles in both supporting and limiting cancer growth. The altered phenotype of tumor-associated stromal cells (fibroblasts, immune cells, endothelial cells etc.) is proposed to be mainly due to epigenetic dysregulation of gene expression; however, only limited studies have probed the roles of epigenetic mechanisms in the regulation of stromal cell function. We review recent studies demonstrating how specific epigenetic mechanisms (DNA methylation and histone post-translational modification-based gene expression regulation, and miRNA-mediated translational regulation) drive aspects of stromal cell phenotype, and discuss the implications of these findings for treatment of malignancies. We also summarize the effects of epigenetic mechanism-targeted drugs on stromal cells and discuss the consideration of the microenvironment response in attempts to use these drugs for cancer treatment.
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Affiliation(s)
- David L Marks
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Rachel Lo Olson
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,University of Minnesota Rochester, Rochester, MN 55904, USA
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Fang Y, Wang L, Wang X, You Q, Pan X, Xiao J, Wang XE, Wu Y, Su Z, Zhang W. Histone modifications facilitate the coexpression of bidirectional promoters in rice. BMC Genomics 2016; 17:768. [PMID: 27716056 PMCID: PMC5045660 DOI: 10.1186/s12864-016-3125-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/26/2016] [Indexed: 12/27/2022] Open
Abstract
Background Bidirectional gene pairs are highly abundant and mostly co-regulated in eukaryotic genomes. The structural features of bidirectional promoters (BDPs) have been well studied in yeast, humans and plants. However, the underlying mechanisms responsible for the coexpression of BDPs remain understudied, especially in plants. Results Here, we characterized chromatin features associated with rice BDPs. Several unique chromatin features were present in rice BDPs but were missing from unidirectional promoters (UDPs), including overrepresented active histone marks, canonical nucleosomes and underrepresented H3K27me3. In particular, overrepresented active marks (H3K4ac, H4K12ac, H4K16ac, H3K4me2 and H3K36me3) were truly overrepresented in type I BDPs but not in the other two BDPs, based on a Kolmogorov-Smirnov test. Conclusions Our analyses indicate that active marks (H3K4ac, H4K12ac, H4K16ac, H3K4me3, H3K9ac and H3K27ac) may coordinate with repressive marks (H3K27me3 and H3K9me1/3) to build a unique chromatin structure that favors the coregulation of bidirectional gene pairs. Thus, our findings help to enhance the understanding of unique epigenetic mechanisms that regulate bidirectional gene pairs and may improve the manipulation of gene pairs for crop bioengineering. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3125-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuan Fang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Lei Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Ximeng Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, CBS, China Agricultural University, Beijing, 100193, China
| | - Xiucai Pan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Jin Xiao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Xiu-E Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, CBS, China Agricultural University, Beijing, 100193, China.
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China. .,JiangSu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China.
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Lutz L, Fitzner IC, Ahrens T, Geißler AL, Makowiec F, Hopt UT, Bogatyreva L, Hauschke D, Werner M, Lassmann S. Histone modifiers and marks define heterogeneous groups of colorectal carcinomas and affect responses to HDAC inhibitors in vitro. Am J Cancer Res 2016; 6:664-676. [PMID: 27152243 PMCID: PMC4851845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/01/2016] [Indexed: 06/05/2023] Open
Abstract
Little is known about histone modifiers and histone marks in colorectal cancers (CRC). The present study therefore addressed the role of histone acetylation and histone deacetylases (HDAC) in CRCs in situ and in vitro. Immunohistochemistry of primary CRCs (n=47) revealed that selected histone marks were frequently present (H3K4me3: 100%; H3K9me3: 77%; H3K9ac: 75%), partially displayed intratumoral heterogeneity (H3K9me3; H3K9ac) and were significantly linked to higher pT category (H3K9me3: p=0.023; H3K9ac: p=0.028). Furthermore, also HDAC1 (62%), HDAC2 (100%) and HDAC3 (72%) expression was frequent, revealing four CRC types: cases expressing 1) HDAC1, HDAC2 and HDAC3 (49%), 2) HDAC2 and HDAC3 (30%), 3) HDAC1 and HDAC2 (10.5%) and 4) exclusively HDAC2 (10.5%). Correlation to clinico-pathological parameters (pT, pN, G, MSI status) revealed that heterogeneous HDAC1 expression correlated with lymph node status (p=0.012). HDAC expression in situ was partially reflected by six CRC cell lines, with similar expression of all three HDACs (DLD1, LS174T), preferential HDAC2 and HDAC3 expression (SW480, Caco2) or lower HDAC2 and HDAC3 expression (HCT116, HT29). HDAC activity was variably higher in HCT116, HT29, DLD1 and SW480 compared to LS174T and Caco2 cells. Treatment with broad (SAHA) and specific (MS-275; FK228) HDAC inhibitors (HDACi) caused loss of cell viability in predominantly MSIpositive CRC cells (HCT116, LS174T, DLD1; SAHA, MS-275 and in part FK228). In contrast, MSI-negative CRC cells (Caco2, HT29, SW480) were resistant, except for high doses of FK228 (Caco2, HT29). Cell viability patterns were not linked to different efficacies of HDACi on reduction of HDAC activity or histone acetylation, p21 expression and/or induction of DNA damage (γH2A-X levels). In summary, this study reveals inter- and intra-tumoral heterogeneity of histone marks and HDAC expression in CRCs. This is reflected by diverse HDACi responses in vitro, which do not follow known modes of action. Together, this implies further exploitation of histone alterations in CRC for molecular classification and/or novel treatment options.
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Affiliation(s)
- Lisa Lutz
- Department of Pathology, All University Medical CenterFreiburg, Germany
| | - Ingrid Coutiño Fitzner
- Department of Pathology, All University Medical CenterFreiburg, Germany
- Faculty of Biology, University of FreiburgFreiburg, Germany
| | - Theresa Ahrens
- Department of Pathology, All University Medical CenterFreiburg, Germany
- Faculty of Biology, University of FreiburgFreiburg, Germany
| | - Anna-Lena Geißler
- Department of Pathology, All University Medical CenterFreiburg, Germany
- Faculty of Biology, University of FreiburgFreiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)Heidelberg, Germany
| | - Frank Makowiec
- Department of Surgery, All University Medical CenterFreiburg, Germany
| | - Ulrich T Hopt
- Department of Surgery, All University Medical CenterFreiburg, Germany
| | - Lioudmila Bogatyreva
- Institute of Medical Biometry and Medical Informatics, All University Medical CenterFreiburg, Germany
| | - Dieter Hauschke
- Institute of Medical Biometry and Medical Informatics, All University Medical CenterFreiburg, Germany
| | - Martin Werner
- Department of Pathology, All University Medical CenterFreiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)Heidelberg, Germany
- Comprehensive Cancer Center Freiburg, All University Medical CenterFreiburg, Germany
| | - Silke Lassmann
- Department of Pathology, All University Medical CenterFreiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)Heidelberg, Germany
- Comprehensive Cancer Center Freiburg, All University Medical CenterFreiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of FreiburgGermany
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McCuaig RD, Dunn J, Li J, Masch A, Knaute T, Schutkowski M, Zerweck J, Rao S. PKC-Theta is a Novel SC35 Splicing Factor Regulator in Response to T Cell Activation. Front Immunol 2015; 6:562. [PMID: 26594212 PMCID: PMC4633479 DOI: 10.3389/fimmu.2015.00562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/21/2015] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing of nuclear pre-mRNA is essential for generating protein diversity and regulating gene expression. While many immunologically relevant genes undergo alternative splicing, the role of regulated splicing in T cell immune responses is largely unexplored, and the signaling pathways and splicing factors that regulate alternative splicing in T cells are poorly defined. Here, we show using a combination of Jurkat T cells, human primary T cells, and ex vivo naïve and effector virus-specific T cells isolated after influenza A virus infection that SC35 phosphorylation is induced in response to stimulatory signals. We show that SC35 colocalizes with RNA polymerase II in activated T cells and spatially overlaps with H3K27ac and H3K4me3, which mark transcriptionally active genes. Interestingly, SC35 remains coupled to the active histone marks in the absence of continuing stimulatory signals. We show for the first time that nuclear PKC-θ co-exists with SC35 in the context of the chromatin template and is a key regulator of SC35 in T cells, directly phosphorylating SC35 peptide residues at RNA recognition motif and RS domains. Collectively, our findings suggest that nuclear PKC-θ is a novel regulator of the key splicing factor SC35 in T cells.
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Affiliation(s)
- Robert Duncan McCuaig
- Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Maths, University of Canberra , Canberra, ACT , Australia
| | - Jennifer Dunn
- Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Maths, University of Canberra , Canberra, ACT , Australia
| | - Jasmine Li
- Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne, VIC , Australia
| | - Antonia Masch
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University , Halle , Germany
| | | | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University , Halle , Germany
| | | | - Sudha Rao
- Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Maths, University of Canberra , Canberra, ACT , Australia
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Li X, Ghezzi A, Krishnan HR, Pohl JB, Bohm AY, Atkinson NS. A histone modification identifies a DNA element controlling slo BK channel gene expression in muscle. J Neurogenet 2015; 29:124-34. [PMID: 25967280 DOI: 10.3109/01677063.2015.1050097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The slo gene encodes the BK-type Ca(2+)-activated K(+) channels. In Drosophila, expression of slo is induced by organic solvent sedation (benzyl alcohol and ethanol), and this increase in neural slo expression contributes to the production of functional behavioral tolerance (inducible resistance) to these drugs. Within the slo promoter region, we observed that benzyl alcohol sedation produces a localized spike of histone acetylation over a 65-nucleotide (65-n) conserved DNA element called 55b. Changes in histone acetylation are commonly the consequence of transcription factor activity, and previously, a localized histone acetylation spike was used to successfully map a DNA element involved in benzyl alcohol-induced slo expression. To determine whether the 55b element was also involved in benzyl alcohol-induced neural expression of slo, we deleted it from the endogenous slo gene by homologous recombination. Flies lacking the 55b element were normal with respect to basal and benzyl alcohol-induced neural slo expression, the capacity to acquire and maintain functional tolerance, their threshold for electrically-induced seizures, and most slo-related behaviors. Removal of the 55b element did however increase the level of basal expression from the muscle/tracheal cell-specific slo core promoter and produced a slight increase in overall locomotor activity. We conclude that the 55b element is involved in control of slo expression from the muscle and tracheal-cell promoter but is not involved in the production of functional benzyl alcohol tolerance.
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Affiliation(s)
- Xiaolei Li
- a School of Biological Sciences, Nanyang Technological University , Singapore
| | - Alfredo Ghezzi
- b Department of Neuroscience and The Waggoner Center for Alcohol and Addiction Research , The University of Texas at Austin , Austin, Texas , USA
| | - Harish R Krishnan
- c Department of Psychiatry , University of Illinois at Chicago and Jesse Brown VA Medical Center , Chicago , IL , USA
| | - Jascha B Pohl
- b Department of Neuroscience and The Waggoner Center for Alcohol and Addiction Research , The University of Texas at Austin , Austin, Texas , USA
| | - Arun Y Bohm
- b Department of Neuroscience and The Waggoner Center for Alcohol and Addiction Research , The University of Texas at Austin , Austin, Texas , USA
| | - Nigel S Atkinson
- b Department of Neuroscience and The Waggoner Center for Alcohol and Addiction Research , The University of Texas at Austin , Austin, Texas , USA
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Tetzlaff MT, Torres-Cabala CA, Pattanaprichakul P, Rapini RP, Prieto VG, Curry JL. Emerging clinical applications of selected biomarkers in melanoma. Clin Cosmet Investig Dermatol 2015; 8:35-46. [PMID: 25674009 PMCID: PMC4321413 DOI: 10.2147/ccid.s49578] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Melanoma is a lethal skin disease with a mostly predictable clinical course according to a known constellation of clinical and pathologic features. The distinction of melanoma from benign melanocytic nevus is typically unequivocol; however, there is a subset of tumors known for its diagnostic challenges, development of late metastases, and difficulties in treatment. Several melanocytic tissue biomarkers are available that can facilitate the histopathologic interpretation of melanoma as well as provide insight into the biologic potential and mutational status of this disease. This review describes the clinical application of some of these established and emerging tissue biomarkers available to assess melanocytic differentiation, vascular invasion, mitotic capacity, and mutation status. The selected tissue biomarkers in this review include MiTF, Sox10, D2-40, PHH3, H3KT (anti-H3K79me3T80ph), anti-BRAFV600E, and anti-BAP-1.
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Affiliation(s)
- Michael T Tetzlaff
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carlos A Torres-Cabala
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Penvadee Pattanaprichakul
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Dermatology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ronald P Rapini
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Victor G Prieto
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan L Curry
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Abstract
We present a modified approach of chromatin immuno-precipitation followed by sequencing (ChIP-Seq), which relies on the direct ligation of molecular barcodes to chromatin fragments, thereby permitting experimental scale-up. With Bar-ChIP now enabling the concurrent profiling of multiple DNA–protein interactions, we report the simultaneous generation of 90 ChIP-Seq datasets without any robotic instrumentation. We demonstrate that application of Bar-ChIP to a panel of Saccharomyces cerevisiae chromatin-associated mutants provides a rapid and accurate genome-wide overview of their chromatin status. Additionally, we validate the utility of this technology to derive novel biological insights by identifying a role for the Rpd3S complex in maintaining H3K14 hypo-acetylation in gene bodies. We also report an association between the presence of intragenic H3K4 tri-methylation and the emergence of cryptic transcription in a Set2 mutant. Finally, we uncover a crosstalk between H3K14 acetylation and H3K4 methylation in this mutant. These results show that Bar-ChIP enables biological discovery through rapid chromatin profiling at single-nucleosome resolution for various conditions and protein modifications at once.
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Affiliation(s)
| | - Sophie H Adjalley
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Bernd Klaus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Emilie S Fritsch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Ishaan Gupta
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Vicent Pelechano
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany Stanford Genome Technology Center, Palo Alto, CA, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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Hunter RG, Gagnidze K, McEwen BS, Pfaff DW. Stress and the dynamic genome: Steroids, epigenetics, and the transposome. Proc Natl Acad Sci U S A 2015; 112:6828-33. [PMID: 25385609 DOI: 10.1073/pnas.1411260111] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Stress plays a substantial role in shaping behavior and brain function, often with lasting effects. How these lasting effects occur in the context of a fixed postmitotic neuronal genome has been an enduring question for the field. Synaptic plasticity and neurogenesis have provided some of the answers to this question, and more recently epigenetic mechanisms have come to the fore. The exploration of epigenetic mechanisms recently led us to discover that a single acute stress can regulate the expression of retrotransposons in the rat hippocampus via an epigenetic mechanism. We propose that this response may represent a genomic stress response aimed at maintaining genomic and transcriptional stability in vulnerable brain regions such as the hippocampus. This finding and those of other researchers have made clear that retrotransposons and the genomic plasticity they permit play a significant role in brain function during stress and disease. These observations also raise the possibility that the transposome might have adaptive functions at the level of both evolution and the individual organism.
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40
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Goldowitz D, Lussier AA, Boyle JK, Wong K, Lattimer SL, Dubose C, Lu L, Kobor MS, Hamre KM. Molecular pathways underpinning ethanol-induced neurodegeneration. Front Genet 2014; 5:203. [PMID: 25076964 PMCID: PMC4097813 DOI: 10.3389/fgene.2014.00203] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/17/2014] [Indexed: 11/29/2022] Open
Abstract
While genetics impacts the type and severity of damage following developmental ethanol exposure, little is currently known about the molecular pathways that mediate these effects. Traditionally, research in this area has used a candidate gene approach and evaluated effects on a gene-by-gene basis. Recent studies, however, have begun to use unbiased approaches and genetic reference populations to evaluate the roles of genotype and epigenetic modifications in phenotypic changes following developmental ethanol exposure, similar to studies that evaluated numerous alcohol-related phenotypes in adults. Here, we present work assessing the role of genetics and chromatin-based alterations in mediating ethanol-induced apoptosis in the developing nervous system. Utilizing the expanded family of BXD recombinant inbred mice, animals were exposed to ethanol at postnatal day 7 via subcutaneous injection (5.0 g/kg in 2 doses). Tissue was collected 7 h after the initial ethanol treatment and analyzed by activated caspase-3 immunostaining to visualize dying cells in the cerebral cortex and hippocampus. In parallel, the levels of two histone modifications relevant to apoptosis, γH2AX and H3K14 acetylation, were examined in the cerebral cortex using protein blot analysis. Activated caspase-3 staining identified marked differences in cell death across brain regions between different mouse strains. Genetic analysis of ethanol susceptibility in the hippocampus led to the identification of a quantitative trait locus on chromosome 12, which mediates, at least in part, strain-specific differential vulnerability to ethanol-induced apoptosis. Furthermore, analysis of chromatin modifications in the cerebral cortex revealed a global increase in γH2AX levels following ethanol exposure, but did not show any change in H3K14 acetylation levels. Together, these findings provide new insights into the molecular mechanisms and genetic contributions underlying ethanol-induced neurodegeneration.
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Affiliation(s)
- Dan Goldowitz
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute - Department of Medical Genetics, University of British Columbia Vancouver, BC, Canada
| | - Alexandre A Lussier
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute - Department of Medical Genetics, University of British Columbia Vancouver, BC, Canada
| | - Julia K Boyle
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute - Department of Medical Genetics, University of British Columbia Vancouver, BC, Canada
| | - Kaelan Wong
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute - Department of Medical Genetics, University of British Columbia Vancouver, BC, Canada
| | - Scott L Lattimer
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center Memphis, TN, USA
| | - Candis Dubose
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center Memphis, TN, USA
| | - Lu Lu
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center Memphis, TN, USA
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute - Department of Medical Genetics, University of British Columbia Vancouver, BC, Canada ; Human Early Learning Partnership, School of Population and Public Health, University of British Columbia Vancouver, BC, Canada
| | - Kristin M Hamre
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center Memphis, TN, USA
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41
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Abstract
We recently analyzed the functional roles of UTX-1 during development. utx-1 is an essential gene required for the correct embryonic and post-embryonic development of C. elegans, and it displays an H3K27me3 demethylase activity. Rescue experiments demonstrated that the enzymatic activity of UTX-1 is not relevant for its role in development. The phenotypes associated with loss of UTX-1 might, instead, be a result of compromised functions of an UTX-1-containing complex. Here we discuss the possible mechanisms by which UTX-1 contributes to normal development.
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Affiliation(s)
- Julien Vandamme
- Biotech Research and Innovation Centre (BRIC); University of Copenhagen; Copenhagen, Denmark
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42
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Abstract
It is almost ten years since senescence associated heterochromatic foci (SAHFs) were first described in human diploid fibroblasts (HDFs). Since then, a number of factors have been identified that affect SAHF formation, including HMGA proteins, structural components of SAHFs. However, the involvement of epigenetic marks in SAHF formation remains unclear. Our recent study, combining microscopy and ChIP-seq approaches, revealed that SAHFs are formed through spatial repositioning of the genome. This occurs according to certain chromatin features that are correlated with, but do not require, the repressive marks histone H3 trimethylated on lysine 9 (H3K9me3) and H3K27me3. These repressive marks are segregated from each other within SAHFs, forming layered high-order chromatin structures (HOCS). During the dynamic change in HOCS as SAHFs form, the linear epigenomic profiles of these repressive marks are highly static. This is in marked contrast to the spreading of repressive marks occurring during embryonic cell differentiation. Thus the layered HOCS of SAHFs is likely achieved mainly through the spatial rearrangement of pre-existing heterochromatin, rather than spreading of heterochromatin. Evidence for the co-association of similar types of chromatin is emerging and SAHFs may provide a unique model system to study the correlation between HOCS and chromatin types, which are readily visible and regulable.
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Affiliation(s)
- Tamir Chandra
- Epigenetics and Nuclear Dynamics; The Babraham Institute; Cambridge, UK
| | - Masashi Narita
- Cancer Research UK; Cambridge Research Institute; Cambridge, UK
- Department of Oncology; University of Cambridge; Cambridge, UK
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43
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Abstract
Asthma is heritable, influenced by the environment, and modified by in utero exposures and aging; all of these features are also common to epigenetic regulation. Furthermore, the transcription factors that are involved in the development of mature T cells that are critical to the T(H)2 immune phenotype in asthmatic patients are regulated by epigenetic mechanisms. Epigenetic marks (DNA methylation, modifications of histone tails, and noncoding RNAs) work in concert with other components of the cellular regulatory machinery to control the spatial and temporal levels of expressed genes. Technology to measure epigenetic marks on a genomic scale and comprehensive approaches to data analysis have recently emerged and continue to improve. Alterations in epigenetic marks have been associated with exposures relevant to asthma, particularly air pollution and tobacco smoke, as well as asthma phenotypes, in a few population-based studies. On the other hand, animal studies have begun to decipher the role of epigenetic regulation of gene expression associated with the development of allergic airway disease. Epigenetic mechanisms represent a promising line of inquiry that might, in part, explain the inheritance and immunobiology of asthma.
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Affiliation(s)
- Ivana V Yang
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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