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Camera F, Romero-Camarero I, Revell BH, Amaral FM, Sinclair OJ, Simeoni F, Wiseman DH, Stojic L, Somervaille TC. Differentiation block in acute myeloid leukemia regulated by intronic sequences of FTO. iScience 2023; 26:107319. [PMID: 37539037 PMCID: PMC10393733 DOI: 10.1016/j.isci.2023.107319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/23/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023] Open
Abstract
Iroquois transcription factor gene IRX3 is highly expressed in 20-30% of acute myeloid leukemia (AML) and contributes to the pathognomonic differentiation block. Intron 8 FTO sequences ∼220kB downstream of IRX3 exhibit histone acetylation, DNA methylation, and contacts with the IRX3 promoter, which correlate with IRX3 expression. Deletion of these intronic elements confirms a role in positively regulating IRX3. RNAseq revealed long non-coding (lnc) transcripts arising from this locus. FTO-lncAML knockdown (KD) induced differentiation of AML cells, loss of clonogenic activity, and reduced FTO intron 8:IRX3 promoter contacts. While both FTO-lncAML KD and IRX3 KD induced differentiation, FTO-lncAML but not IRX3 KD led to HOXA downregulation suggesting transcript activity in trans. FTO-lncAMLhigh AML samples expressed higher levels of HOXA and lower levels of differentiation genes. Thus, a regulatory module in FTO intron 8 consisting of clustered enhancer elements and a long non-coding RNA is active in human AML, impeding myeloid differentiation.
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Affiliation(s)
- Francesco Camera
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Isabel Romero-Camarero
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Bradley H. Revell
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Fabio M.R. Amaral
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Oliver J. Sinclair
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Fabrizio Simeoni
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Daniel H. Wiseman
- Epigenetics of Haematopoiesis Group, Oglesby Cancer Research Building, The University of Manchester, M20 4GJ Manchester, UK
| | - Lovorka Stojic
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ London, UK
| | - Tim C.P. Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
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2
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Tiana M, Lopez-Jimenez E, de Aja JS, Barral A, Victorino J, Badia-Careaga C, Rollan I, Rouco R, Santos E, Sanchez-Iranzo H, Acemel RD, Torroja C, Adan J, Andres-Leon E, Gomez-Skarmeta JL, Giovinazzo G, Sanchez-Cabo F, Manzanares M. Pluripotency factors regulate the onset of Hox cluster activation in the early embryo. SCIENCE ADVANCES 2022; 8:eabo3583. [PMID: 35857513 PMCID: PMC9286507 DOI: 10.1126/sciadv.abo3583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Pluripotent cells are a transient population of the mammalian embryo dependent on transcription factors, such as OCT4 and NANOG, which maintain pluripotency while suppressing lineage specification. However, these factors are also expressed during early phases of differentiation, and their role in the transition from pluripotency to lineage specification is largely unknown. We found that pluripotency factors play a dual role in regulating key lineage specifiers, initially repressing their expression and later being required for their proper activation. We show that Oct4 is necessary for activation of HoxB genes during differentiation of embryonic stem cells and in the embryo. In addition, we show that the HoxB cluster is coordinately regulated by OCT4 binding sites located at the 3' end of the cluster. Our results show that core pluripotency factors are not limited to maintaining the precommitted epiblast but are also necessary for the proper deployment of subsequent developmental programs.
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Affiliation(s)
- María Tiana
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, 28029 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Elena Lopez-Jimenez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Julio Sainz de Aja
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Antonio Barral
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, 28029 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Jesus Victorino
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Claudio Badia-Careaga
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Isabel Rollan
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Raquel Rouco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Elisa Santos
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Hector Sanchez-Iranzo
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Rafael D. Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO, 41013 Seville, Spain
| | - Carlos Torroja
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Javier Adan
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Eduardo Andres-Leon
- Instituto de Parasitología y Biomedicina López Neyra (IPBL), CSIC, 18100 Granada, Spain
| | | | - Giovanna Giovinazzo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Fatima Sanchez-Cabo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Miguel Manzanares
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, 28029 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
- Corresponding author.
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3
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Bordeira-Carriço R, Teixeira J, Duque M, Galhardo M, Ribeiro D, Acemel RD, Firbas PN, Tena JJ, Eufrásio A, Marques J, Ferreira FJ, Freitas T, Carneiro F, Goméz-Skarmeta JL, Bessa J. Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers. Nat Commun 2022; 13:1945. [PMID: 35410466 PMCID: PMC9001708 DOI: 10.1038/s41467-022-29551-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/17/2022] [Indexed: 11/26/2022] Open
Abstract
The pancreas is a central organ for human diseases. Most alleles uncovered by genome-wide association studies of pancreatic dysfunction traits overlap with non-coding sequences of DNA. Many contain epigenetic marks of cis-regulatory elements active in pancreatic cells, suggesting that alterations in these sequences contribute to pancreatic diseases. Animal models greatly help to understand the role of non-coding alterations in disease. However, interspecies identification of equivalent cis-regulatory elements faces fundamental challenges, including lack of sequence conservation. Here we combine epigenetic assays with reporter assays in zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis-regulatory elements, regardless of sequence conservation. Among other potential disease-relevant enhancers, we identify a zebrafish ptf1a distal-enhancer whose deletion causes pancreatic agenesis, a phenotype previously found to be induced by mutations in a distal-enhancer of PTF1A in humans, further supporting the causality of this condition in vivo. This approach helps to uncover interspecies functionally equivalent cis-regulatory elements and their potential role in human disease. Alterations in cis-regulatory elements (CREs) can contribute to pancreatic diseases. Here the authors combine chromatin profiling and interaction points with in vivo reporter assays in zebrafish to uncover functionally equivalent human CREs, helping to predict disease-relevant enhancers.
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4
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Deforzh E, Uhlmann EJ, Das E, Galitsyna A, Arora R, Saravanan H, Rabinovsky R, Wirawan AD, Teplyuk NM, El Fatimy R, Perumalla S, Jairam A, Wei Z, Mirny L, Krichevsky AM. Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus, and neoplastic transformation in glioma. Mol Cell 2022; 82:1894-1908.e5. [PMID: 35390275 DOI: 10.1016/j.molcel.2022.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/27/2022] [Accepted: 03/10/2022] [Indexed: 01/06/2023]
Abstract
miR-10b is silenced in normal neuroglial cells of the brain but commonly activated in glioma, where it assumes an essential tumor-promoting role. We demonstrate that the entire miR-10b-hosting HOXD locus is activated in glioma via the cis-acting mechanism involving 3D chromatin reorganization and CTCF-cohesin-mediated looping. This mechanism requires two interacting lncRNAs, HOXD-AS2 and LINC01116, one associated with HOXD3/HOXD4/miR-10b promoter and another with the remote enhancer. Knockdown of either lncRNA in glioma cells alters CTCF and cohesin binding, abolishes chromatin looping, inhibits the expression of all genes within HOXD locus, and leads to glioma cell death. Conversely, in cortical astrocytes, enhancer activation is sufficient for HOXD/miR-10b locus reorganization, gene derepression, and neoplastic cell transformation. LINC01116 RNA is essential for this process. Our results demonstrate the interplay of two lncRNAs in the chromatin folding and concordant regulation of miR-10b and multiple HOXD genes normally silenced in astrocytes and triggering the neoplastic glial transformation.
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Affiliation(s)
- Evgeny Deforzh
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Erik J Uhlmann
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eashita Das
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aleksandra Galitsyna
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Ramil Arora
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Harini Saravanan
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rosalia Rabinovsky
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aditya D Wirawan
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nadiya M Teplyuk
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rachid El Fatimy
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sucika Perumalla
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anirudh Jairam
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Leonid Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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5
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Downes DJ, Smith AL, Karpinska MA, Velychko T, Rue-Albrecht K, Sims D, Milne TA, Davies JOJ, Oudelaar AM, Hughes JR. Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nat Protoc 2022; 17:445-475. [PMID: 35121852 PMCID: PMC7613269 DOI: 10.1038/s41596-021-00651-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/27/2021] [Indexed: 12/16/2022]
Abstract
Chromosome conformation capture (3C) methods measure the spatial proximity between DNA elements in the cell nucleus. Many methods have been developed to sample 3C material, including the Capture-C family of protocols. Capture-C methods use oligonucleotides to enrich for interactions of interest from sequencing-ready 3C libraries. This approach is modular and has been adapted and optimized to work for sampling of disperse DNA elements (NuTi Capture-C), including from low cell inputs (LI Capture-C), as well as to generate Hi-C like maps for specific regions of interest (Tiled-C) and to interrogate multiway interactions (Tri-C). We present the design, experimental protocol and analysis pipeline for NuTi Capture-C in addition to the variations for generation of LI Capture-C, Tiled-C and Tri-C data. The entire procedure can be performed in 3 weeks and requires standard molecular biology skills and equipment, access to a next-generation sequencing platform, and basic bioinformatic skills. Implemented with other sequencing technologies, these methods can be used to identify regulatory interactions and to compare the structural organization of the genome in different cell types and genetic models.
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Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Alastair L Smith
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Taras Velychko
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Kevin Rue-Albrecht
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - David Sims
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Haematology Theme, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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6
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Ramirez RN, Chowdhary K, Leon J, Mathis D, Benoist C. FoxP3 associates with enhancer-promoter loops to regulate T reg-specific gene expression. Sci Immunol 2022; 7:eabj9836. [PMID: 35030035 DOI: 10.1126/sciimmunol.abj9836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Gene expression programs are specified by higher-order chromatin structure and enhancer-promoter loops (EPLs). T regulatory cell (Treg) identity is dominantly specified by the transcription factor (TF) FoxP3, whose mechanism of action is unclear. We applied chromatin conformation capture with immunoprecipitation (HiChIP) in Treg and closely related conventional CD4+ T cells (Tconv). EPLs identified by H3K27Ac HiChIP showed a range of connection intensity, with some superconnected genes. TF-specific HiChIP showed that FoxP3 interacts with EPLs at a large number of genes, including some not differentially expressed in Treg versus Tconv, but enriched at the core Treg signature loci that it up-regulates. FoxP3 association correlated with heightened H3K27Ac looping, as ascertained by analysis of FoxP3-deficient Treg-like cells. There was marked asymmetry in the loci where FoxP3 associated at the enhancer- or the promoter-side of EPLs, with enrichment for different transcriptional cofactors. FoxP3 EPL intensity distinguished gene clusters identified by single-cell ATAC-seq as covarying between individual Tregs, supporting a direct transactivation model for FoxP3 in determining Treg identity.
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Affiliation(s)
- Ricardo N Ramirez
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Juliette Leon
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
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7
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Miranda M, Noordermeer D, Moindrot B. Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-seq. Methods Mol Biol 2022; 2532:15-33. [PMID: 35867243 DOI: 10.1007/978-1-0716-2497-5_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chromosome conformation capture techniques are a set of methods used to determine 3D genome organization through the capture and identification of physical contacts between pairs of genomic loci. Among them, 4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing) allows for the identification and quantification of the sequences interacting with a preselected locus of interest. 4C-seq has been widely used in the literature, mainly to study chromatin loops between enhancers and promoters or between CTCF binding sites and to identify chromatin domain boundaries. As 3D-contacts may be established in an allele-specific manner, we describe an up-to-date allele-specific 4C-seq protocol, starting from the selection of allele-specific viewpoints to Illumina sequencing. This protocol has mainly been optimized for cultured mammalian cells, but can be adapted for other cell types with relatively minor changes in initial steps.
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Affiliation(s)
- Mélanie Miranda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
| | - Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
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8
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Marsman J, Day RC, Gimenez G. Circular Chromosome Conformation Capture Sequencing (4C-Seq ) in Primary Adherent Cells. Methods Mol Biol 2022; 2458:301-320. [PMID: 35103974 DOI: 10.1007/978-1-0716-2140-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The three-dimensional structure of the genome is highly organized and is an important aspect of gene regulation. Chromatin interactions can be identified using chromosome conformation capture-based techniques, which rely on proximity ligation. Of these techniques, circular chromosome conformation capture sequencing (4C-seq) is used to identify all chromatin interactions occurring with a single chromosomal location (one versus all). Here we describe a 4C-seq protocol that has been optimized for primary adherent cells, for which the first digestion step is inefficient using standard 4C-seq protocols. It can, however, also be applied to other cell or tissue types. This protocol utilizes a standard DNA library preparation method using a commercial kit, and includes a description of the data processing steps.
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Affiliation(s)
- Judith Marsman
- Department of Cardiology, Division Heart & Lungs, University Medical Centre Utrecht, Utrecht, The Netherlands.
| | - Robert C Day
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Gregory Gimenez
- Department of Cardiology, Division Heart & Lungs, University Medical Centre Utrecht, Utrecht, The Netherlands
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9
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Ramos-Rodríguez M, Subirana-Granés M, Pasquali L. UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C. Bioinformatics 2021; 37:4240-4242. [PMID: 34009302 PMCID: PMC9502148 DOI: 10.1093/bioinformatics/btab392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/30/2021] [Accepted: 05/18/2021] [Indexed: 12/02/2022] Open
Abstract
Motivation UMI-4C, a technique that combines chromosome conformation capture (4C) and unique molecular identifiers (UMI), is widely used to profile and quantitatively compare targeted chromosomal contact profiles. The analysis of UMI-4C experiments presents several computational challenges, including the removal of the PCR duplication bias and the identification of differential chromatin contacts. Results We have developed UMI4Cats (UMI-4C Analysis Turned Simple), an R package that facilitates processing, analyzing and visualizing of data obtained by UMI-4C experiments. Availability and implementation UMI4Cats is implemented as an R package supported on Linux, MacOS and MS Windows. UMI4Cats is available from Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/UMI4Cats.html) and GitHub (https://github.com/Pasquali-lab/UMI4Cats). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mireia Ramos-Rodríguez
- Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra, 08003, Barcelona, Spain
| | - Marc Subirana-Granés
- Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra, 08003, Barcelona, Spain
| | - Lorenzo Pasquali
- Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra, 08003, Barcelona, Spain
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10
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Amorim JP, Gali-Macedo A, Marcelino H, Bordeira-Carriço R, Naranjo S, Rivero-Gil S, Teixeira J, Galhardo M, Marques J, Bessa J. A Conserved Notochord Enhancer Controls Pancreas Development in Vertebrates. Cell Rep 2021; 32:107862. [PMID: 32640228 PMCID: PMC7355232 DOI: 10.1016/j.celrep.2020.107862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 04/06/2020] [Accepted: 06/09/2020] [Indexed: 12/31/2022] Open
Abstract
The notochord is an evolutionary novelty in vertebrates that functions as an important signaling center during development. Notochord ablation in chicken has demonstrated that it is crucial for pancreas development; however, the molecular mechanism has not been fully described. Here, we show that in zebrafish, the loss of function of nog2, a Bmp antagonist expressed in the notochord, impairs β cell differentiation, compatible with the antagonistic role of Bmp in β cell differentiation. In addition, we show that nog2 expression in the notochord is induced by at least one notochord enhancer and its loss of function reduces the number of pancreatic progenitors and impairs β cell differentiation. Tracing Nog2 diffusion, we show that Nog2 emanates from the notochord to the pancreas progenitor domain. Finally, we find a notochord enhancer in human and mice Nog genomic landscapes, suggesting that the acquisition of a Nog notochord enhancer occurred early in the vertebrate phylogeny and contributes to the development of complex organs like the pancreas.
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Affiliation(s)
- João Pedro Amorim
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - Ana Gali-Macedo
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - Hugo Marcelino
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - Renata Bordeira-Carriço
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - Silvia Naranjo
- CABD (Centro Andaluz de Biología del Desarrollo), Universidad Pablo de Olavide, Seville, Spain
| | - Solangel Rivero-Gil
- CABD (Centro Andaluz de Biología del Desarrollo), Universidad Pablo de Olavide, Seville, Spain
| | - Joana Teixeira
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - Mafalda Galhardo
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; CIBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Vairão, Portugal
| | - Joana Marques
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal
| | - José Bessa
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, Porto, Portugal; IBMC (Instituto de Biologia Molecular e Celular), Universidade do Porto, Porto, Portugal.
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11
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Lee BH, Rhie SK. Molecular and computational approaches to map regulatory elements in 3D chromatin structure. Epigenetics Chromatin 2021; 14:14. [PMID: 33741028 PMCID: PMC7980343 DOI: 10.1186/s13072-021-00390-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/08/2021] [Indexed: 12/19/2022] Open
Abstract
Epigenetic marks do not change the sequence of DNA but affect gene expression in a cell-type specific manner by altering the activities of regulatory elements. Development of new molecular biology assays, sequencing technologies, and computational approaches enables us to profile the human epigenome in three-dimensional structure genome-wide. Here we describe various molecular biology techniques and bioinformatic tools that have been developed to measure the activities of regulatory elements and their chromatin interactions. Moreover, we list currently available three-dimensional epigenomic data sets that are generated in various human cell types and tissues to assist in the design and analysis of research projects.
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Affiliation(s)
- Beoung Hun Lee
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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12
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Cajigas I, Chakraborty A, Lynam M, Swyter KR, Bastidas M, Collens L, Luo H, Ay F, Kohtz JD. Sox2- Evf2 lncRNA-mediated mechanisms of chromosome topological control in developing forebrain. Development 2021; 148:dev197202. [PMID: 33593819 PMCID: PMC7990859 DOI: 10.1242/dev.197202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/07/2021] [Indexed: 12/13/2022]
Abstract
The Evf2 long non-coding RNA directs Dlx5/6 ultraconserved enhancer(UCE)-intrachromosomal interactions, regulating genes across a 27 Mb region on chromosome 6 in mouse developing forebrain. Here, we show that Evf2 long-range gene repression occurs through multi-step mechanisms involving the transcription factor Sox2. Evf2 directly interacts with Sox2, antagonizing Sox2 activation of Dlx5/6UCE, and recruits Sox2 to the Dlx5/6eii shadow enhancer and key Dlx5/6UCE interaction sites. Sox2 directly interacts with Dlx1 and Smarca4, as part of the Evf2 ribonucleoprotein complex, forming spherical subnuclear domains (protein pools, PPs). Evf2 targets Sox2 PPs to one long-range repressed target gene (Rbm28), at the expense of another (Akr1b8). Evf2 and Sox2 shift Dlx5/6UCE interactions towards Rbm28, linking Evf2/Sox2 co-regulated topological control and gene repression. We propose a model that distinguishes Evf2 gene repression mechanisms at Rbm28 (Dlx5/6UCE position) and Akr1b8 (limited Sox2 availability). Genome-wide control of RNPs (Sox2, Dlx and Smarca4) shows that co-recruitment influences Sox2 DNA binding. Together, these data suggest that Evf2 organizes a Sox2 PP subnuclear domain and, through Sox2-RNP sequestration and recruitment, regulates chromosome 6 long-range UCE targeting and activity with genome-wide consequences.
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Affiliation(s)
- Ivelisse Cajigas
- Department of Pediatrics, Northwestern University, Feinberg School of Medicine, Department of Human Molecular Genetics, Stanley Manne Children's Research Institute 2430 N Halsted, Chicago, IL 60614, USA
| | - Abhijit Chakraborty
- Centers for Autoimmunity and Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Madison Lynam
- Department of Pediatrics, Northwestern University, Feinberg School of Medicine, Department of Human Molecular Genetics, Stanley Manne Children's Research Institute 2430 N Halsted, Chicago, IL 60614, USA
| | - Kelsey R Swyter
- Department of Pediatrics, Northwestern University, Feinberg School of Medicine, Department of Human Molecular Genetics, Stanley Manne Children's Research Institute 2430 N Halsted, Chicago, IL 60614, USA
| | - Monique Bastidas
- Department of Pediatrics, Northwestern University, Feinberg School of Medicine, Department of Human Molecular Genetics, Stanley Manne Children's Research Institute 2430 N Halsted, Chicago, IL 60614, USA
| | - Linden Collens
- Department of Pediatrics, Northwestern University, Feinberg School of Medicine, Department of Human Molecular Genetics, Stanley Manne Children's Research Institute 2430 N Halsted, Chicago, IL 60614, USA
| | - Hao Luo
- Department of Pediatrics, Northwestern University, Feinberg School of Medicine, Department of Human Molecular Genetics, Stanley Manne Children's Research Institute 2430 N Halsted, Chicago, IL 60614, USA
| | - Ferhat Ay
- Centers for Autoimmunity and Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jhumku D Kohtz
- Department of Pediatrics, Northwestern University, Feinberg School of Medicine, Department of Human Molecular Genetics, Stanley Manne Children's Research Institute 2430 N Halsted, Chicago, IL 60614, USA
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13
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Elmer JL, Hay AD, Kessler NJ, Bertozzi TM, Ainscough EAC, Ferguson-Smith AC. Genomic properties of variably methylated retrotransposons in mouse. Mob DNA 2021; 12:6. [PMID: 33612119 PMCID: PMC7898769 DOI: 10.1186/s13100-021-00235-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs in mice that exhibit inter-individual variability in this methylation (VM-IAPs) with implications for genome function. RESULTS Here we validate these metastable epialleles and discover a novel class that exhibit tissue specificity (tsVM-IAPs) in addition to those with uniform methylation in all tissues (constitutive- or cVM-IAPs); both types have the potential to regulate genes in cis. Screening for variable methylation at other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We identify sequences enriched within cVM-IAPs, but determine that these are not sufficient to confer epigenetic variability. CTCF is enriched at VM-IAPs with binding inversely correlated with DNA methylation. We uncover dynamic physical interactions between cVM-IAPs with low methylation ranges and other genomic loci, suggesting that VM-IAPs have the potential for long-range regulation. CONCLUSION Our findings indicate that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs can result in inter-individual variability in transcriptional outcomes with implications for phenotypic variation.
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Affiliation(s)
- Jessica L. Elmer
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Amir D. Hay
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Noah J. Kessler
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Tessa M. Bertozzi
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
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14
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Arnould C, Rocher V, Finoux AL, Clouaire T, Li K, Zhou F, Caron P, Mangeot PE, Ricci EP, Mourad R, Haber JE, Noordermeer D, Legube G. Loop extrusion as a mechanism for formation of DNA damage repair foci. Nature 2021; 590:660-665. [PMID: 33597753 PMCID: PMC7116834 DOI: 10.1038/s41586-021-03193-z] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 01/06/2021] [Indexed: 12/26/2022]
Abstract
The repair of DNA double-strand breaks (DSBs) is essential for safeguarding genome integrity. When a DSB forms, the PI3K-related ATM kinase rapidly triggers the establishment of megabase-sized, chromatin domains decorated with phosphorylated histone H2AX (γH2AX), which act as seeds for the formation of DNA-damage response foci1. It is unclear how these foci are rapidly assembled to establish a 'repair-prone' environment within the nucleus. Topologically associating domains are a key feature of 3D genome organization that compartmentalize transcription and replication, but little is known about their contribution to DNA repair processes2,3. Here we show that topologically associating domains are functional units of the DNA damage response, and are instrumental for the correct establishment of γH2AX-53BP1 chromatin domains in a manner that involves one-sided cohesin-mediated loop extrusion on both sides of the DSB. We propose a model in which H2AX-containing nucleosomes are rapidly phosphorylated as they actively pass by DSB-anchored cohesin. Our work highlights the importance of chromosome conformation in the maintenance of genome integrity and demonstrates the establishment of a chromatin modification by loop extrusion.
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Affiliation(s)
- Coline Arnould
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Vincent Rocher
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Anne-Laure Finoux
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Thomas Clouaire
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Kevin Li
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Felix Zhou
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Pierre Caron
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - Philippe E Mangeot
- CIRI - International Center for Infectiology Research, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, INSERM U1293, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Raphaël Mourad
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - James E Haber
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Gaëlle Legube
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France.
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15
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Downes DJ, Beagrie RA, Gosden ME, Telenius J, Carpenter SJ, Nussbaum L, De Ornellas S, Sergeant M, Eijsbouts CQ, Schwessinger R, Kerry J, Roberts N, Shivalingam A, El-Sagheer A, Oudelaar AM, Brown T, Buckle VJ, Davies JOJ, Hughes JR. High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale. Nat Commun 2021; 12:531. [PMID: 33483495 PMCID: PMC7822813 DOI: 10.1038/s41467-020-20809-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023] Open
Abstract
Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods generally provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at limited numbers of loci. Due to technical limitations, generation of reproducible high-resolution interaction profiles has not been achieved at genome-wide scale. Here, to overcome this barrier, we systematically test each step of 3C and report two improvements over current methods. We show that up to 30% of reporter events generated using the popular in situ 3C method arise from ligations between two individual nuclei, but this noise can be almost entirely eliminated by isolating intact nuclei after ligation. Using Nuclear-Titrated Capture-C, we generate reproducible high-resolution genome-wide 3C interaction profiles by targeting 8055 gene promoters in erythroid cells. By pairing high-resolution 3C interaction calls with nascent gene expression we interrogate the role of promoter hubs and super-enhancers in gene regulation.
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Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Matthew E Gosden
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jelena Telenius
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stephanie J Carpenter
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Lea Nussbaum
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sara De Ornellas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Martin Sergeant
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chris Q Eijsbouts
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jon Kerry
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Arun Shivalingam
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Afaf El-Sagheer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tom Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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16
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Abstract
Chromosome conformation capture and its variants have allowed chromatin topology to be interrogated at a superior resolution and throughput than by microscopic methods. Among the method derivatives, 4C-seq (circular chromosome conformation capture, coupled to high-throughput sequencing) is a versatile, cost-effective means of assessing all chromatin interactions with a specific genomic region of interest, making it particularly suitable for interrogating chromatin looping events. We present the principles and procedures for designing and implementing successful 4C-seq experiments.
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17
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Martínez-Gil N, Roca-Ayats N, Atalay N, Pineda-Moncusí M, Garcia-Giralt N, Van Hul W, Boudin E, Ovejero D, Mellibovsky L, Nogués X, Díez-Pérez A, Grinberg D, Balcells S. Functional Assessment of Coding and Regulatory Variants From the DKK1 Locus. JBMR Plus 2020; 4:e10423. [PMID: 33354644 PMCID: PMC7745885 DOI: 10.1002/jbm4.10423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/03/2020] [Indexed: 12/17/2022] Open
Abstract
The DKK1 gene encodes an extracellular inhibitor of the Wnt pathway with an important role in bone tissue development, bone homeostasis, and different critical aspects of bone biology. Several BMD genome‐wide association studies (GWASs) have consistently found association with SNPs in the DKK1 genomic region. For these reasons, it is important to assess the functionality of coding and regulatory variants in the gene. Here, we have studied the functionality of putative regulatory variants, previously found associated with BMD in different studies by others and ourselves, and also six missense variants present in the general population. Using a Wnt‐pathway‐specific luciferase reporter assay, we have determined that the variants p.Ala41Thr, p.Tyr74Phe, p.Arg120Leu, and p.Ser157Ile display a reduced DKK1 inhibitory capacity as compared with WT. This result agrees with the high‐bone‐mass (HBM) phenotype of two women from our cohort who carried mutations p.Tyr74Phe or p.Arg120Leu. On the other hand, by means of a circularized chromosome conformation capture‐ (4C‐) sequencing experiment, we have detected that the region containing 24 BMD‐GWA variants, located 350‐kb downstream of DKK1, interacts both with DKK1 and the LNCAROD (LncRNA‐activating regulator of DKK1, AKA LINC0148) in osteoblastic cells. In conclusion, we have shown that some rare coding variants are partial loss‐of‐function mutations that may lead to a HBM phenotype, whereas the common SNPs associated with BMD in GWASs belong to a putative long‐range regulatory region, through a yet unknown mechanism involving LNCAROD. © 2020 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Núria Martínez-Gil
- Department of Genetics, Microbiology and Statistics, Faculty of Biology Universitat de Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Institut de Biomedicina de la Universitat de Barcelona (IBUB), Institut de Recerca Sant Joan de Déu (IRSJD) Barcelona Spain
| | - Neus Roca-Ayats
- Department of Genetics, Microbiology and Statistics, Faculty of Biology Universitat de Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Institut de Biomedicina de la Universitat de Barcelona (IBUB), Institut de Recerca Sant Joan de Déu (IRSJD) Barcelona Spain
| | - Nurgül Atalay
- Department of Genetics, Microbiology and Statistics, Faculty of Biology Universitat de Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Institut de Biomedicina de la Universitat de Barcelona (IBUB), Institut de Recerca Sant Joan de Déu (IRSJD) Barcelona Spain
| | - Marta Pineda-Moncusí
- Musculoskeletal Research Group, Hospital del Mar Medical Research Institute Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable, ISCIII Barcelona Spain
| | - Natàlia Garcia-Giralt
- Musculoskeletal Research Group, Hospital del Mar Medical Research Institute Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable, ISCIII Barcelona Spain
| | - Wim Van Hul
- Center of Medical Genetics University of Antwerp & University Hospital Antwerp Antwerp Belgium
| | - Eveline Boudin
- Center of Medical Genetics University of Antwerp & University Hospital Antwerp Antwerp Belgium
| | - Diana Ovejero
- Musculoskeletal Research Group, Hospital del Mar Medical Research Institute Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable, ISCIII Barcelona Spain
| | - Leonardo Mellibovsky
- Musculoskeletal Research Group, Hospital del Mar Medical Research Institute Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable, ISCIII Barcelona Spain
| | - Xavier Nogués
- Musculoskeletal Research Group, Hospital del Mar Medical Research Institute Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable, ISCIII Barcelona Spain
| | - Adolfo Díez-Pérez
- Musculoskeletal Research Group, Hospital del Mar Medical Research Institute Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable, ISCIII Barcelona Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology Universitat de Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Institut de Biomedicina de la Universitat de Barcelona (IBUB), Institut de Recerca Sant Joan de Déu (IRSJD) Barcelona Spain
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology Universitat de Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Institut de Biomedicina de la Universitat de Barcelona (IBUB), Institut de Recerca Sant Joan de Déu (IRSJD) Barcelona Spain
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18
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Matthews BJ, Waxman DJ. Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver. Epigenetics Chromatin 2020; 13:30. [PMID: 32680543 PMCID: PMC7368777 DOI: 10.1186/s13072-020-00350-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Several thousand sex-differential distal enhancers have been identified in mouse liver; however, their links to sex-biased genes and the impact of any sex-differences in nuclear organization and chromatin interactions are unknown. To address these issues, we first characterized 1847 mouse liver genomic regions showing significant sex differential occupancy by cohesin and CTCF, two key 3D nuclear organizing factors. These sex-differential binding sites were primarily distal to sex-biased genes but rarely generated sex-differential TAD (topologically associating domain) or intra-TAD loop anchors, and were sometimes found in TADs without sex-biased genes. A substantial subset of sex-biased cohesin-non-CTCF binding sites, but not sex-biased cohesin-and-CTCF binding sites, overlapped sex-biased enhancers. Cohesin depletion reduced the expression of male-biased genes with distal, but not proximal, sex-biased enhancers by >10-fold, implicating cohesin in long-range enhancer interactions regulating sex-biased genes. Using circularized chromosome conformation capture-based sequencing (4C-seq), we showed that sex differences in distal sex-biased enhancer-promoter interactions are common. Intra-TAD loops with sex-independent cohesin-and-CTCF anchors conferred sex specificity to chromatin interactions indirectly, by insulating sex-biased enhancer-promoter contacts and by bringing sex-biased genes into closer proximity to sex-biased enhancers. Furthermore, sex-differential chromatin interactions involving sex-biased gene promoters, enhancers, and lncRNAs were associated with sex-biased binding of cohesin and/or CTCF. These studies elucidate how 3D genome organization impacts sex-biased gene expression in a non-reproductive tissue through both direct and indirect effects of cohesin and CTCF looping on distal enhancer interactions with sex-differentially expressed genes.
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Affiliation(s)
- Bryan J Matthews
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
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19
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Walter C, Schuetzmann D, Rosenbauer F, Dugas M. Benchmarking of 4C-seq pipelines based on real and simulated data. Bioinformatics 2020; 35:4938-4945. [PMID: 31134276 PMCID: PMC6901067 DOI: 10.1093/bioinformatics/btz426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/24/2019] [Accepted: 05/23/2019] [Indexed: 12/15/2022] Open
Abstract
Motivation With its capacity for high-resolution data output in one region of interest, chromosome conformation capture combined with high-throughput sequencing (4C-seq) is a state-of-the-art next-generation sequencing technique that provides epigenetic insights, and regularly advances current medical research. However, 4C-seq data are complex and prone to biases, and while specialized programs exist, an unbiased, extensive benchmarking is still lacking. Furthermore, neither substantial datasets with fully characterized ground truth, nor simulation programs for realistic 4C-seq data have been published. Results We conducted a benchmarking study on 66 4C-seq samples from 20 datasets, and developed a novel 4C-seq simulation software, Basic4CSim, to allow for detailed comparisons of 4C-seq algorithms on 50 simulated datasets with 10–120 samples each. Simulations and benchmarking were adapted to address different characteristics of 4C-seq data. Simulated data were compared with published samples to validate simulation settings. We identified differences between 4C-seq algorithms in terms of precision, recall, interaction structure, and run time, and observed general trends. Novel differential pipeline versions of single-sample based 4C-seq algorithms were included in the benchmarking. While no single tool was optimally suited for both near-cis and far-cis, and both single-sample and differential analyses, choosing a high-performing algorithm variant did improve results considerably. For near-cis scenarios, r3Cseq, peakC and FourCSeq offered high precision, while fourSig demonstrated high overall F1 scores in far-cis analyses. Finally, 4C-seq simulations may aid in the development of improved analysis algorithms. Availability and implementation Basic4CSim is available at https://github.com/walter–ca/Basic4CSim. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Carolin Walter
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Daniel Schuetzmann
- Institute of Molecular Tumorbiology, University of Münster, Münster, Germany
| | - Frank Rosenbauer
- Institute of Molecular Tumorbiology, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
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20
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Ruiz Buendía GA, Leleu M, Marzetta F, Vanzan L, Tan JY, Ythier V, Randall EL, Marques AC, Baubec T, Murr R, Xenarios I, Dion V. Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion. SCIENCE ADVANCES 2020; 6:eaaz4012. [PMID: 32656337 PMCID: PMC7334000 DOI: 10.1126/sciadv.aaz4012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Expanded CAG/CTG repeats underlie 13 neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Upon expansion, disease loci acquire heterochromatic characteristics, which may provoke changes to chromatin conformation and thereby affect both gene expression and repeat instability. Here, we tested this hypothesis by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD-derived cells. We find that allele sizes ranging from 15 to 1700 repeats displayed similar chromatin interaction profiles. This was true for both loci and for alleles with different DNA methylation levels and CTCF binding. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the conformation of the surrounding chromatin. We conclude that CAG/CTG repeat expansions are not enough to alter chromatin conformation in cis. Therefore, it is unlikely that changes in chromatin interactions drive repeat instability or changes in gene expression in these disorders.
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Affiliation(s)
- Gustavo A. Ruiz Buendía
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marion Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Flavia Marzetta
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ludovica Vanzan
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Jennifer Y. Tan
- Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Victor Ythier
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Emma L. Randall
- UK Dementia Research Institute at Cardiff University at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK
| | - Ana C. Marques
- Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Rabih Murr
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland
| | - Ioannis Xenarios
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vincent Dion
- UK Dementia Research Institute at Cardiff University at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK
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21
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Dong K, Zhang S. Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data. Brief Bioinform 2020; 22:5860691. [PMID: 32578841 PMCID: PMC8138825 DOI: 10.1093/bib/bbaa120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
The rapid accumulation of single-cell chromatin accessibility data offers a unique opportunity to investigate common and specific regulatory mechanisms across different cell types. However, existing methods for cis-regulatory network reconstruction using single-cell chromatin accessibility data were only designed for cells belonging to one cell type, and resulting networks may be incomparable directly due to diverse cell numbers of different cell types. Here, we adopt a computational method to jointly reconstruct cis-regulatory interaction maps (JRIM) of multiple cell populations based on patterns of co-accessibility in single-cell data. We applied JRIM to explore common and specific regulatory interactions across multiple tissues from single-cell ATAC-seq dataset containing ~80 000 cells across 13 mouse tissues. Reconstructed common interactions among 13 tissues indeed relate to basic biological functions, and individual cis-regulatory networks show strong tissue specificity and functional relevance. More importantly, tissue-specific regulatory interactions are mediated by coordination of histone modifications and tissue-related TFs, and many of them may reveal novel regulatory mechanisms.
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Affiliation(s)
- Kangning Dong
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences
| | - Shihua Zhang
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences
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22
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Tsujimura T, Takase O, Yoshikawa M, Sano E, Hayashi M, Hoshi K, Takato T, Toyoda A, Okano H, Hishikawa K. Controlling gene activation by enhancers through a drug-inducible topological insulator. eLife 2020; 9:47980. [PMID: 32369019 PMCID: PMC7200164 DOI: 10.7554/elife.47980] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
While regulation of gene-enhancer interaction is intensively studied, its application remains limited. Here, we reconstituted arrays of CTCF-binding sites and devised a synthetic topological insulator with tetO for chromatin-engineering (STITCH). By coupling STITCH with tetR linked to the KRAB domain to induce heterochromatin and disable the insulation, we developed a drug-inducible system to control gene activation by enhancers. In human induced pluripotent stem cells, STITCH inserted between MYC and the enhancer down-regulated MYC. Progressive mutagenesis of STITCH led to a preferential escalation of the gene-enhancer interaction, corroborating the strong insulation ability of STITCH. STITCH also altered epigenetic states around MYC. Time-course analysis by drug induction uncovered deposition and removal of H3K27me3 repressive marks follows and reflects, but does not precede and determine, the expression change. Finally, STITCH inserted near NEUROG2 impaired the gene activation in differentiating neural progenitor cells. Thus, STITCH should be broadly useful for functional genetic studies.
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Affiliation(s)
- Taro Tsujimura
- Department of iPS Cell Research & Epigenetic Medicine, Keio University School of Medicine, Tokyo, Japan.,Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Osamu Takase
- Department of iPS Cell Research & Epigenetic Medicine, Keio University School of Medicine, Tokyo, Japan.,Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Masahiro Yoshikawa
- Department of iPS Cell Research & Epigenetic Medicine, Keio University School of Medicine, Tokyo, Japan.,Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Etsuko Sano
- Department of iPS Cell Research & Epigenetic Medicine, Keio University School of Medicine, Tokyo, Japan.,Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Matsuhiko Hayashi
- Apheresis and Dialysis Center, Keio University School of Medicine, Tokyo, Japan
| | - Kazuto Hoshi
- Division of Tissue Engineering, University of Tokyo Hospital, Tokyo, Japan.,Department of Oral and Maxillofacial Surgery, University of Tokyo Hospital, Tokyo, Japan
| | - Tsuyoshi Takato
- Division of Tissue Engineering, University of Tokyo Hospital, Tokyo, Japan.,Department of Oral and Maxillofacial Surgery, University of Tokyo Hospital, Tokyo, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Keiichi Hishikawa
- Department of iPS Cell Research & Epigenetic Medicine, Keio University School of Medicine, Tokyo, Japan.,Department of Physiology, Keio University School of Medicine, Tokyo, Japan
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23
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Zisis D, Krajewski P, Stam M, Weber B, Hövel I. Analysis of 4C-seq data: A comparison of methods. J Bioinform Comput Biol 2020; 18:2050001. [PMID: 32336253 DOI: 10.1142/s0219720020500018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The circular chromosome conformation capture technique followed by sequencing (4C-seq) has been used in a number of studies to investigate chromosomal interactions between DNA fragments. Computational pipelines have been developed and published that offer various possibilities of 4C-seq data processing and statistical analysis. Here, we present an overview of four of such pipelines (fourSig, FourCSeq, 4C-ker and w4Cseq) taking into account the most important stages of computations. We provide comparisons of the methods and discuss their advantages and possible weaknesses. We illustrate the results with the use of data obtained for two different species, in a study devoted to vernalization control in Arabidopsis thaliana by the FLOWERING LOCUS C (FLC) gene and to long-range chromatin interactions in mouse embryonic stem cells.
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Affiliation(s)
- Dimitrios Zisis
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 61-479 Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 61-479 Poznań, Poland
| | - Maike Stam
- Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
| | - Blaise Weber
- Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
| | - Iris Hövel
- Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
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24
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de Anda-Jáuregui G, Hernández-Lemus E. Computational Oncology in the Multi-Omics Era: State of the Art. Front Oncol 2020; 10:423. [PMID: 32318338 PMCID: PMC7154096 DOI: 10.3389/fonc.2020.00423] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/10/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is the quintessential complex disease. As technologies evolve faster each day, we are able to quantify the different layers of biological elements that contribute to the emergence and development of malignancies. In this multi-omics context, the use of integrative approaches is mandatory in order to gain further insights on oncological phenomena, and to move forward toward the precision medicine paradigm. In this review, we will focus on computational oncology as an integrative discipline that incorporates knowledge from the mathematical, physical, and computational fields to further the biomedical understanding of cancer. We will discuss the current roles of computation in oncology in the context of multi-omic technologies, which include: data acquisition and processing; data management in the clinical and research settings; classification, diagnosis, and prognosis; and the development of models in the research setting, including their use for therapeutic target identification. We will discuss the machine learning and network approaches as two of the most promising emerging paradigms, in computational oncology. These approaches provide a foundation on how to integrate different layers of biological description into coherent frameworks that allow advances both in the basic and clinical settings.
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Affiliation(s)
- Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Cátedras Conacyt Para Jóvenes Investigadores, National Council on Science and Technology, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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25
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Zhang W, Chronis C, Chen X, Zhang H, Spalinskas R, Pardo M, Chen L, Wu G, Zhu Z, Yu Y, Yu L, Choudhary J, Nichols J, Parast MM, Greber B, Sahlén P, Plath K. The BAF and PRC2 Complex Subunits Dpf2 and Eed Antagonistically Converge on Tbx3 to Control ESC Differentiation. Cell Stem Cell 2020; 24:138-152.e8. [PMID: 30609396 PMCID: PMC6486830 DOI: 10.1016/j.stem.2018.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 06/21/2018] [Accepted: 12/05/2018] [Indexed: 01/01/2023]
Abstract
BAF complexes are composed of different subunits with varying functional and developmental roles, although many subunits have not been examined in depth. Here we show that the Baf45 subunit Dpf2 maintains pluripotency and ESC differentiation potential. Dpf2 co-occupies enhancers with Oct4, Sox2, p300, and the BAF subunit Brg1, and deleting Dpf2 perturbs ESC self-renewal, induces repression of Tbx3, and impairs mesendodermal differentiation without dramatically altering Brg1 localization. Mesendodermal differentiation can be rescued by restoring Tbx3 expression, whose distal enhancer is positively regulated by Dpf2-dependent H3K27ac maintenance and recruitment of pluripotency TFs and Brg1. In contrast, the PRC2 subunit Eed binds an intragenic Tbx3 enhancer to oppose Dpf2-dependent Tbx3 expression and mesendodermal differentiation. The PRC2 subunit Ezh2 likewise opposes Dpf2-dependent differentiation through a distinct mechanism involving Nanog repression. Together, these findings delineate distinct mechanistic roles for specific BAF and PRC2 subunits during ESC differentiation. Dpf2 and Eed antagonistically regulate mesendodermal differentiation of ESCs via Tbx3 Dpf2 and Eed bind different Tbx3 enhancers to control its expression Dpf2 controls H3K27ac and the access of pluripotency TFs at critical target sites Ezh2 and Eed counteract Dpf2 function in differentiation through distinct mechanisms
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Affiliation(s)
- Wensheng Zhang
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China; Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA; Bioinformatics Program, Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Xi Chen
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Heyao Zhang
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Rapolas Spalinskas
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Mercedes Pardo
- The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Liangliang Chen
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Zhexin Zhu
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Yong Yu
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Lu Yu
- The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Jyoti Choudhary
- The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Mana M Parast
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Boris Greber
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Pelin Sahlén
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA; Bioinformatics Program, Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
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26
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Ben Zouari Y, Platania A, Molitor AM, Sexton T. 4See: A Flexible Browser to Explore 4C Data. Front Genet 2020; 10:1372. [PMID: 32038719 PMCID: PMC6985583 DOI: 10.3389/fgene.2019.01372] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/16/2019] [Indexed: 01/01/2023] Open
Abstract
It is established that transcription of many metazoan genes is regulated by distal regulatory sequences beyond the promoter. Enhancers have been identified at up to megabase distances from their regulated genes, and/or proximal to or within the introns of unregulated genes. The unambiguous identification of the target genes of newly identified regulatory elements can thus be challenging. Well-studied enhancers have been found to come into direct physical proximity with regulated genes, presumably by the formation of chromatin loops. Chromosome conformation capture (3C) derivatives that assess the frequency of proximity between different genetic elements is thus a popular method for exploring gene regulation by distal regulatory elements. For studies of chromatin loops and promoter-enhancer communication, 4C (circular chromosome conformation capture) is one of the methods of choice, optimizing cost (required sequencing depth), throughput, and resolution. For ease of visual inspection of 4C data we present 4See, a versatile and user-friendly browser. 4See allows 4C profiles from the same bait to be flexibly plotted together, allowing biological replicates to either be compared, or pooled for comparisons between different cell types or experimental conditions. 4C profiles can be integrated with gene tracks, linear epigenomic profiles, and annotated regions of interest, such as called significant interactions, allowing rapid data exploration with limited computational resources or bioinformatics expertise.
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Affiliation(s)
- Yousra Ben Zouari
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France.,CNRS UMR7104, Illkirch, France.,INSERM U1258, Illkirch, France.,University of Strasbourg, Illkirch, France
| | - Angeliki Platania
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France.,CNRS UMR7104, Illkirch, France.,INSERM U1258, Illkirch, France.,University of Strasbourg, Illkirch, France
| | - Anne M Molitor
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France.,CNRS UMR7104, Illkirch, France.,INSERM U1258, Illkirch, France.,University of Strasbourg, Illkirch, France
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France.,CNRS UMR7104, Illkirch, France.,INSERM U1258, Illkirch, France.,University of Strasbourg, Illkirch, France
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27
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Schilit SL, Menon S, Friedrich C, Kammin T, Wilch E, Hanscom C, Jiang S, Kliesch S, Talkowski ME, Tüttelmann F, MacQueen AJ, Morton CC. SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility. Am J Hum Genet 2020; 106:41-57. [PMID: 31866047 DOI: 10.1016/j.ajhg.2019.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 11/21/2019] [Indexed: 12/28/2022] Open
Abstract
Unexplained infertility affects 2%-3% of reproductive-aged couples. One approach to identifying genes involved in infertility is to study subjects with this clinical phenotype and a de novo balanced chromosomal aberration (BCA). While BCAs may reduce fertility by production of unbalanced gametes, a chromosomal rearrangement may also disrupt or dysregulate genes important in fertility. One such subject, DGAP230, has severe oligozoospermia and 46,XY,t(20;22)(q13.3;q11.2). We identified exclusive overexpression of SYCP2 from the der(20) allele that is hypothesized to result from enhancer adoption. Modeling the dysregulation in budding yeast resulted in disrupted structural integrity of the synaptonemal complex, a common cause of defective spermatogenesis in mammals. Exome sequencing of infertile males revealed three heterozygous SYCP2 frameshift variants in additional subjects with cryptozoospermia and azoospermia. In sum, this investigation illustrates the power of precision cytogenetics for annotation of the infertile genome, suggests that these mechanisms should be considered as an alternative etiology to that of segregation of unbalanced gametes in infertile men harboring a BCA, and provides evidence of SYCP2-mediated male infertility in humans.
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28
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Llères D, Moindrot B, Pathak R, Piras V, Matelot M, Pignard B, Marchand A, Poncelet M, Perrin A, Tellier V, Feil R, Noordermeer D. CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains. Genome Biol 2019; 20:272. [PMID: 31831055 PMCID: PMC6909504 DOI: 10.1186/s13059-019-1896-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genomic imprinting is essential for mammalian development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. So far, the detailed allele-specific chromatin organization of imprinted gene domains has mostly been lacking. Here, we explored the chromatin structure of the two conserved imprinted domains controlled by paternal DNA methylation imprints-the Igf2-H19 and Dlk1-Dio3 domains-and assessed the involvement of the insulator protein CTCF in mouse cells. RESULTS Both imprinted domains are located within overarching topologically associating domains (TADs) that are similar on both parental chromosomes. At each domain, a single differentially methylated region is bound by CTCF on the maternal chromosome only, in addition to multiple instances of bi-allelic CTCF binding. Combinations of allelic 4C-seq and DNA-FISH revealed that bi-allelic CTCF binding alone, on the paternal chromosome, correlates with a first level of sub-TAD structure. On the maternal chromosome, additional CTCF binding at the differentially methylated region adds a further layer of sub-TAD organization, which essentially hijacks the existing paternal-specific sub-TAD organization. Perturbation of maternal-specific CTCF binding site at the Dlk1-Dio3 locus, using genome editing, results in perturbed sub-TAD organization and bi-allelic Dlk1 activation during differentiation. CONCLUSIONS Maternal allele-specific CTCF binding at the imprinted Igf2-H19 and the Dlk1-Dio3 domains adds an additional layer of sub-TAD organization, on top of an existing three-dimensional configuration and prior to imprinted activation of protein-coding genes. We speculate that this allele-specific sub-TAD organization provides an instructive or permissive context for imprinted gene activation during development.
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Affiliation(s)
- David Llères
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Benoît Moindrot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Rakesh Pathak
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Vincent Piras
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Mélody Matelot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Benoît Pignard
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Alice Marchand
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Mallory Poncelet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélien Perrin
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Virgile Tellier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France.
| | - Daan Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France.
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29
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rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock Treatment. Cells 2019; 8:cells8111393. [PMID: 31694324 PMCID: PMC6912461 DOI: 10.3390/cells8111393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 12/29/2022] Open
Abstract
Human rDNA clusters form numerous contacts with different chromosomal regions as evidenced by chromosome conformation capture data. Heterochromatization of rDNA genes leads to heterochromatization in different chromosomal regions coupled with the activation of the transcription of genes related to differentiation. These data suggest a role for rDNA clusters in the regulation of many human genes. However, the genes that reside within the rDNA-contacting regions have not been identified. The purpose of this study was to detect and characterize the regions where rDNA clusters make frequent contacts and to identify and categorize genes located in these regions. We analyzed the regions that contact rDNA using 4C data and show that these regions are enriched with genes specifying transcription factors and non-coding RNAs involved in differentiation and development. The rDNA-contacting genes are involved in neuronal development and are associated with different cancers. Heat shock treatment led to dramatic changes in the pattern of rDNA-contacting sites, especially in the regions possessing long stretches of H3K27ac marks. Whole-genome analysis of rDNA-contacting sites revealed specific epigenetic marks and the transcription sites of 20–100 nt non-coding RNAs in these regions. The rDNA-contacting genes jointly regulate many genes that are involved in the control of transcription by RNA polymerase II and the development of neurons. Our data suggest a role for rDNA clusters in the differentiation of human cells and carcinogenesis.
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30
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Man JCK, Mohan RA, Boogaard MVD, Hilvering CRE, Jenkins C, Wakker V, Bianchi V, Laat WD, Barnett P, Boukens BJ, Christoffels VM. An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo. Nat Commun 2019; 10:4943. [PMID: 31666509 PMCID: PMC6821807 DOI: 10.1038/s41467-019-12856-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 10/03/2019] [Indexed: 12/19/2022] Open
Abstract
Mutations and variations in and around SCN5A, encoding the major cardiac sodium channel, influence impulse conduction and are associated with a broad spectrum of arrhythmia disorders. Here, we identify an evolutionary conserved regulatory cluster with super enhancer characteristics downstream of SCN5A, which drives localized cardiac expression and contains conduction velocity-associated variants. We use genome editing to create a series of deletions in the mouse genome and show that the enhancer cluster controls the conformation of a >0.5 Mb genomic region harboring multiple interacting gene promoters and enhancers. We find that this cluster and its individual components are selectively required for cardiac Scn5a expression, normal cardiac conduction and normal embryonic development. Our studies reveal physiological roles of an enhancer cluster in the SCN5A-SCN10A locus, show that it controls the chromatin architecture of the locus and Scn5a expression, and suggest that genetic variants affecting its activity may influence cardiac function.
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Affiliation(s)
- Joyce C K Man
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Rajiv A Mohan
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Malou van den Boogaard
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Catharina R E Hilvering
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Catherine Jenkins
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Vincent Wakker
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Valerio Bianchi
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Phil Barnett
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Bastiaan J Boukens
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands.
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31
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Geeven G, Teunissen H, de Laat W, de Wit E. peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data. Nucleic Acids Res 2019; 46:e91. [PMID: 29800273 PMCID: PMC6125690 DOI: 10.1093/nar/gky443] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/13/2018] [Indexed: 11/14/2022] Open
Abstract
It is becoming increasingly clear that chromosome organization plays an important role in gene regulation. High-resolution methods such as 4C, Capture-C and promoter capture Hi-C (PCHiC) enable the study of chromatin loops such as those formed between promoters and enhancers or CTCF/cohesin binding sites. An important aspect of 4C/Capture-C/PCHiC analyses is the reliable identification of chromatin loops, preferably not based on visual inspection of a DNA contact profile, but on reproducible statistical analysis that robustly scores interaction peaks in the non-uniform contact background. Here, we present peakC, an R package for the analysis of 4C/Capture-C/PCHiC data. We generated 4C data for 13 viewpoints in two tissues in at least triplicate to test our methods. We developed a non-parametric peak caller based on rank-products. Sampling analysis shows that not read depth but template quality is the most important determinant of success in 4C experiments. By performing peak calling on single experiments we show that the peak calling results are similar to the replicate experiments, but that false positive rates are significantly reduced by performing replicates. Our software is user-friendly and enables robust peak calling for one-vs-all chromosome capture experiments. peakC is available at: https://github.com/deWitLab/peakC.
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Affiliation(s)
- Geert Geeven
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Hans Teunissen
- Oncode Institute and Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Elzo de Wit
- Oncode Institute and Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
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Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. Nat Cell Biol 2019; 21:568-578. [PMID: 31036938 DOI: 10.1038/s41556-019-0310-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 03/11/2019] [Indexed: 01/09/2023]
Abstract
The mechanisms underlying enhancer activation and the extent to which enhancer-promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time-resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between 'serum' and '2i' states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer-promoter rewiring that becomes more evident in primed-state pluripotency. Instead, differential gene expression is strongly linked to enhancer activation via H3K27ac. Conditional depletion of transcription factors and allele-specific enhancer analysis reveal an essential role for Esrrb in H3K27 acetylation and activation of 2i-specific enhancers. Restoration of a polymorphic ESRRB motif using CRISPR-Cas9 in a hybrid ESC line restores ESRRB binding and enhancer H3K27ac in an allele-specific manner but has no effect on chromatin interactions. Our study shows that enhancer activation in serum- and 2i-ESCs is largely driven by transcription factor binding and epigenetic marking in a hardwired network of chromatin interactions.
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Greenberg M, Teissandier A, Walter M, Noordermeer D, Bourc'his D. Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency. eLife 2019; 8:44057. [PMID: 30990414 PMCID: PMC6488298 DOI: 10.7554/elife.44057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/15/2019] [Indexed: 12/29/2022] Open
Abstract
During early mammalian development, the chromatin landscape undergoes profound transitions. The Zdbf2 gene—involved in growth control—provides a valuable model to study this window: upon exit from naïve pluripotency and prior to tissue differentiation, it undergoes a switch from a distal to a proximal promoter usage, accompanied by a switch from polycomb to DNA methylation occupancy. Using a mouse embryonic stem cell (ESC) system to mimic this period, we show here that four enhancers contribute to the Zdbf2 promoter switch, concomitantly with dynamic changes in chromatin architecture. In ESCs, the locus is partitioned to facilitate enhancer contacts with the distal Zdbf2 promoter. Relieving the partition enhances proximal Zdbf2 promoter activity, as observed during differentiation or with genetic mutants. Importantly, we show that 3D regulation occurs upstream of the polycomb and DNA methylation pathways. Our study reveals the importance of multi-layered regulatory frameworks to ensure proper spatio-temporal activation of developmentally important genes.
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Affiliation(s)
- Maxim Greenberg
- Institut Curie, PSL Research University, INSERM, CNRS, Paris, France
| | | | - Marius Walter
- Institut Curie, PSL Research University, INSERM, CNRS, Paris, France
| | - Daan Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), Université Paris Sud, Université Paris-Saclay, CEA, CNRS, Paris, France
| | - Deborah Bourc'his
- Institut Curie, PSL Research University, INSERM, CNRS, Paris, France
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Evolutionary Loss of Genomic Proximity to Conserved Noncoding Elements Impacted the Gene Expression Dynamics During Mammalian Brain Development. Genetics 2019; 211:1239-1254. [PMID: 30796012 DOI: 10.1534/genetics.119.301973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/14/2019] [Indexed: 01/05/2023] Open
Abstract
Conserved noncoding elements (CNEs) have a significant regulatory influence on their neighboring genes. Loss of proximity to CNEs through genomic rearrangements can, therefore, impact the transcriptional states of the cognate genes. Yet, the evolutionary implications of such chromosomal alterations have not been studied. Through genome-wide analysis of CNEs and the cognate genes of representative species from five different mammalian orders, we observed a significant loss of genes' linear proximity to CNEs in the rat lineage. The CNEs and the genes losing proximity had a significant association with fetal, but not postnatal, brain development as assessed through ontology terms, developmental gene expression, chromatin marks, and genetic mutations. The loss of proximity to CNEs correlated with the independent evolutionary loss of fetus-specific upregulation of nearby genes in the rat brain. DNA breakpoints implicated in brain abnormalities of germline origin had significant representation between a CNE and the gene that exhibited loss of proximity, signifying the underlying developmental tolerance of genomic rearrangements that allowed the evolutionary splits of CNEs and the cognate genes in the rodent lineage. Our observations highlighted a nontrivial impact of chromosomal rearrangements in shaping the evolutionary dynamics of mammalian brain development and might explain the loss of brain traits, like cerebral folding of the cortex, in the rodent lineage.
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35
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LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice. Nature 2019; 565:448-453. [PMID: 30626972 PMCID: PMC6436840 DOI: 10.1038/s41586-018-0845-0] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 12/06/2018] [Indexed: 01/28/2023]
Abstract
The genome is partitioned into topologically associated domains (TADs) and genomic compartments of shared chromatin valance. This architecture is constrained by the DNA polymer, which precludes genic interactions between chromosomes. Here, we report a dramatic divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons (OSNs). In situ HiC on FAC-sorted OSNs and their progenitors shows that olfactory receptor (OR) gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation. These contacts are orchestrated by intergenic OR enhancers, the Greek Islands, which first contribute to the formation of OR compartments and then form a multi-chromosomal super-enhancer that associates with the single active OR. Greek Island-bound transcription factor Lhx2 and adaptor protein Ldb1 regulate the assembly and maintenance of OR compartments, Greek Island hubs, and OR transcription, providing mechanistic insight and functional support for the role of trans interactions in gene expression.
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36
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TBX2 is a neuroblastoma core regulatory circuitry component enhancing MYCN/FOXM1 reactivation of DREAM targets. Nat Commun 2018; 9:4866. [PMID: 30451831 PMCID: PMC6242972 DOI: 10.1038/s41467-018-06699-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022] Open
Abstract
Chromosome 17q gains are almost invariably present in high-risk neuroblastoma cases. Here, we perform an integrative epigenomics search for dosage-sensitive transcription factors on 17q marked by H3K27ac defined super-enhancers and identify TBX2 as top candidate gene. We show that TBX2 is a constituent of the recently established core regulatory circuitry in neuroblastoma with features of a cell identity transcription factor, driving proliferation through activation of p21-DREAM repressed FOXM1 target genes. Combined MYCN/TBX2 knockdown enforces cell growth arrest suggesting that TBX2 enhances MYCN sustained activation of FOXM1 targets. Targeting transcriptional addiction by combined CDK7 and BET bromodomain inhibition shows synergistic effects on cell viability with strong repressive effects on CRC gene expression and p53 pathway response as well as several genes implicated in transcriptional regulation. In conclusion, we provide insight into the role of the TBX2 CRC gene in transcriptional dependency of neuroblastoma cells warranting clinical trials using BET and CDK7 inhibitors. In high-risk neuroblastoma cases, gains in chromosome 17q are common. Here, the authors investigate the epigenomics and transcriptomics of neuroblastoma, identifying TBX2 as a core regulatory circuitry component enhancing the reactivation of DREAM targets by MYCN/FOXM1.
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37
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Brettmann EA, Oh IY, de Guzman Strong C. High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq). J Vis Exp 2018. [PMID: 30346381 DOI: 10.3791/58030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The identification of regulatory elements for a given target gene poses a significant technical challenge owing to the variability in the positioning and effect sizes of regulatory elements to a target gene. Some progress has been made with the bioinformatic prediction of the existence and function of proximal epigenetic modifications associated with activated gene expression using conserved transcription factor binding sites. Chromatin conformation capture studies have revolutionized our ability to discover physical chromatin contacts between sequences and even within an entire genome. Circular chromatin conformation capture coupled with next-generation sequencing (4C-seq), in particular, is designed to discover all possible physical chromatin interactions for a given sequence of interest (viewpoint), such as a target gene or a regulatory enhancer. Current 4C-seq strategies directly sequence from within the viewpoint but require numerous and diverse viewpoints to be simultaneously sequenced to avoid the technical challenges of uniform base calling (imaging) with next generation sequencing platforms. This volume of experiments may not be practical for many laboratories. Here, we report a modified approach to the 4C-seq protocol that incorporates both an additional restriction enzyme digest and qPCR-based amplification steps that are designed to facilitate a greater capture of diverse sequence reads and mitigate the potential for PCR bias, respectively. Our modified 4C method is amenable to the standard molecular biology lab for assessing chromatin architecture.
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Affiliation(s)
- Erin A Brettmann
- Division of Dermatology, Center for Pharmacogenomics, Center for the Study of Itch, Department of Medicine, Washington University School of Medicine
| | - Inez Y Oh
- Division of Dermatology, Center for Pharmacogenomics, Center for the Study of Itch, Department of Medicine, Washington University School of Medicine
| | - Cristina de Guzman Strong
- Division of Dermatology, Center for Pharmacogenomics, Center for the Study of Itch, Department of Medicine, Washington University School of Medicine;
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38
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Cajigas I, Chakraborty A, Swyter KR, Luo H, Bastidas M, Nigro M, Morris ER, Chen S, VanGompel MJW, Leib D, Kohtz SJ, Martina M, Koh S, Ay F, Kohtz JD. The Evf2 Ultraconserved Enhancer lncRNA Functionally and Spatially Organizes Megabase Distant Genes in the Developing Forebrain. Mol Cell 2018; 71:956-972.e9. [PMID: 30146317 PMCID: PMC6428050 DOI: 10.1016/j.molcel.2018.07.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/30/2018] [Accepted: 07/20/2018] [Indexed: 02/06/2023]
Abstract
Gene regulation requires selective targeting of DNA regulatory enhancers over megabase distances. Here we show that Evf2, a cloud-forming Dlx5/6 ultraconserved enhancer (UCE) lncRNA, simultaneously localizes to activated (Umad1, 1.6 Mb distant) and repressed (Akr1b8, 27 Mb distant) chr6 target genes, precisely regulating UCE-gene distances and cohesin binding in mouse embryonic forebrain GABAergic interneurons (INs). Transgene expression of Evf2 activates Lsm8 (12 Mb distant) but fails to repress Akr1b8, supporting trans activation and long-range cis repression. Through both short-range (Dlx6 antisense) and long-range (Akr1b8) repression, the Evf2-5'UCE links homeodomain and mevalonate pathway-regulated enhancers to IN diversity. The Evf2-3' end is required for long-range activation but dispensable for RNA cloud localization, functionally dividing the RNA into 3'-activator and 5'UCE repressor and targeting regions. Together, these results support that Evf2 selectively regulates UCE interactions with multi-megabase distant genes through complex effects on chromosome topology, linking lncRNA-dependent topological and transcriptional control with interneuron diversity and seizure susceptibility.
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Affiliation(s)
- Ivelisse Cajigas
- Department of Pediatrics and Developmental Biology, Feinberg School of Medicine, Northwestern University and Stanley Manne Children's Research Institute, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Abhijit Chakraborty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Kelsey R Swyter
- Department of Pediatrics and Developmental Biology, Feinberg School of Medicine, Northwestern University and Stanley Manne Children's Research Institute, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Hao Luo
- Department of Pediatrics and Developmental Biology, Feinberg School of Medicine, Northwestern University and Stanley Manne Children's Research Institute, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Monique Bastidas
- Department of Pediatrics and Developmental Biology, Feinberg School of Medicine, Northwestern University and Stanley Manne Children's Research Institute, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Maximilliano Nigro
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Elizabeth R Morris
- Department of Pediatrics and Developmental Biology, Feinberg School of Medicine, Northwestern University and Stanley Manne Children's Research Institute, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Sean Chen
- Department of Pediatrics and Developmental Biology, Feinberg School of Medicine, Northwestern University and Stanley Manne Children's Research Institute, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Michael J W VanGompel
- Department of Pediatrics and Developmental Biology, Feinberg School of Medicine, Northwestern University and Stanley Manne Children's Research Institute, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - David Leib
- Department of Pediatrics and Developmental Biology, Feinberg School of Medicine, Northwestern University and Stanley Manne Children's Research Institute, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Sara J Kohtz
- Department of Pediatrics and Developmental Biology, Feinberg School of Medicine, Northwestern University and Stanley Manne Children's Research Institute, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Marco Martina
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Sooky Koh
- Department of Pediatrics, Emory University, Atlanta, GA 30307, USA
| | - Ferhat Ay
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA; School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jhumku D Kohtz
- Department of Pediatrics and Developmental Biology, Feinberg School of Medicine, Northwestern University and Stanley Manne Children's Research Institute, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA.
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Tsujimura T, Takase O, Yoshikawa M, Sano E, Hayashi M, Takato T, Toyoda A, Okano H, Hishikawa K. Control of directionality of chromatin folding for the inter- and intra-domain contacts at the Tfap2c-Bmp7 locus. Epigenetics Chromatin 2018; 11:51. [PMID: 30213272 PMCID: PMC6137755 DOI: 10.1186/s13072-018-0221-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/27/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Contact domains of chromatin serve as a fundamental unit to regulate action of enhancers for target genes. Looping between a pair of CCCTC-binding factor (CTCF)-binding sites in convergent orientations underlies the formation of contact domains, while those in divergent orientations establish domain boundaries. However, every CTCF site is not necessarily engaged in loop or boundary structures, leaving functions of CTCF in varied genomic contexts still elusive. The locus containing Tfap2c and Bmp7 encompasses two contact domains separated by a region between the two genes, termed transition zone (TZ), characterized by two arrays of CTCF sites in divergent configuration. In this study, we created deletion and inversion alleles of these and other regions across the locus and investigated how they impinge on the conformation. RESULTS Deletion of the whole two CTCF arrays with the CRISPR/Cas9 system resulted in impairment of blocking of chromatin contacts by the TZ, as assessed by the circular chromatin conformation capture assay (4C-seq). Deletion and inversion of either of the two arrays similarly, but less pronouncedly, led to reduction in the blocking activity. Thus, the divergent configuration provides the TZ with the strong boundary activity. Uniquely, we show the TZ harbors a 50-kb region within one of the two arrays that contacts broadly with the both flanking intervals, regardless of the presence or orientation of the other CTCF array. Further, we show the boundary CTCF array has little impact on intra-domain folding; instead, locally associating CTCF sites greatly affect it. CONCLUSIONS Our results show that the TZ not only separates the two domains, but also bears a wide interval that shows isotropic behavior of chromatin folding, indicating a potentially complex nature of actual boundaries in the genome. We also show that CTCF-binding sites inside a domain greatly contribute to the intra-domain folding of chromatin. Thus, the study reveals diverse and context-dependent roles of CTCF in organizing chromatin conformation at different levels.
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Affiliation(s)
- Taro Tsujimura
- Department of iPS Cell Research and Epigenetic Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
| | - Osamu Takase
- Department of iPS Cell Research and Epigenetic Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
| | - Masahiro Yoshikawa
- Department of iPS Cell Research and Epigenetic Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
| | - Etsuko Sano
- Department of iPS Cell Research and Epigenetic Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
| | - Matsuhiko Hayashi
- Apheresis and Dialysis Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
| | - Tsuyoshi Takato
- Department of Tissue Engineering, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 Japan
- Department of Oral-Maxillofacial Surgery and Orthodontics, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540 Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
| | - Keiichi Hishikawa
- Department of iPS Cell Research and Epigenetic Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 Japan
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Sarro R, Kocher AA, Emera D, Uebbing S, Dutrow EV, Weatherbee SD, Nottoli T, Noonan JP. Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development. Development 2018; 145:dev.158550. [PMID: 29549111 DOI: 10.1242/dev.158550] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/09/2018] [Indexed: 12/28/2022]
Abstract
Developmental gene expression patterns are orchestrated by thousands of distant-acting transcriptional enhancers. However, identifying enhancers essential for the expression of their target genes has proven challenging. Maps of long-range regulatory interactions may provide the means to identify enhancers crucial for developmental gene expression. To investigate this hypothesis, we used circular chromosome conformation capture coupled with interaction maps in the mouse limb to characterize the regulatory topology of Pitx1, which is essential for hindlimb development. We identified a robust hindlimb-specific interaction between Pitx1 and a putative hindlimb-specific enhancer. To interrogate the role of this interaction in Pitx1 regulation, we used genome editing to delete this enhancer in mouse. Although deletion of the enhancer completely disrupts the interaction, Pitx1 expression in the hindlimb is only mildly affected, without any detectable compensatory interactions between the Pitx1 promoter and potentially redundant enhancers. Pitx1 enhancer null mice did not exhibit any of the characteristic morphological defects of the Pitx1-/- mutant. Our results suggest that robust, tissue-specific physical interactions at essential developmental genes have limited predictive value for identifying enhancer mutations with strong loss-of-function phenotypes.
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Affiliation(s)
- Richard Sarro
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Deena Emera
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Emily V Dutrow
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Scott D Weatherbee
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06520, USA.,Yale Genome Editing Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
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41
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Chang P, Gohain M, Yen MR, Chen PY. Computational Methods for Assessing Chromatin Hierarchy. Comput Struct Biotechnol J 2018; 16:43-53. [PMID: 29686798 PMCID: PMC5910504 DOI: 10.1016/j.csbj.2018.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/29/2018] [Accepted: 02/11/2018] [Indexed: 12/27/2022] Open
Abstract
The hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling "higher-order" and "primary-order" chromatin structures from both experimental and computational aspects. Experimental requirements and considerations specific for each method were highlighted. For computational analysis, we summarized a common analysis strategy for both levels of chromatin assessment, focusing on the characteristic computing steps and the tools. The recently developed single-cell level techniques based on Hi-C and ATAC-seq present great potential to reveal cell-to-cell variability in chromosome architecture. A brief discussion on these methods in terms of experimental and data analysis features is included. We also touch upon the biological relevance of chromatin organization and how the combination with other techniques uncovers the underlying mechanisms. We conclude with a summary and our prospects on necessary improvements of currently available methods in order to advance understanding of chromatin hierarchy. Our review brings together the analyses of both higher- and primary-order chromatin structures, and serves as a roadmap when choosing appropriate experimental and computational methods for assessing chromatin hierarchy.
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Affiliation(s)
- Pearl Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Moloya Gohain
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion GJ, Beato M, Marti-Renom MA, Graf T. Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming. Nat Genet 2018; 50:238-249. [PMID: 29335546 PMCID: PMC5810905 DOI: 10.1038/s41588-017-0030-7] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 12/01/2017] [Indexed: 01/28/2023]
Abstract
Chromosomal architecture is known to influence gene expression, yet its role in controlling cell fate remains poorly understood. Reprogramming of somatic cells into pluripotent stem cells (PSCs) by the transcription factors (TFs) OCT4, SOX2, KLF4 and MYC offers an opportunity to address this question but is severely limited by the low proportion of responding cells. We have recently developed a highly efficient reprogramming protocol that synchronously converts somatic into pluripotent stem cells. Here, we used this system to integrate time-resolved changes in genome topology with gene expression, TF binding and chromatin-state dynamics. The results showed that TFs drive topological genome reorganization at multiple architectural levels, often before changes in gene expression. Removal of locus-specific topological barriers can explain why pluripotency genes are activated sequentially, instead of simultaneously, during reprogramming. Together, our results implicate genome topology as an instructive force for implementing transcriptional programs and cell fate in mammals.
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Affiliation(s)
- Ralph Stadhouders
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands.
| | - Enrique Vidal
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - François Serra
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Bruno Di Stefano
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University and Harvard Medical School, Cambridge, MA, USA
| | - François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Antonio Gomez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Samuel Collombet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, Paris, France
| | - Clara Berenguer
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Yasmina Cuartero
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Jochen Hecht
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Genomics Unit, CRG, BIST, Barcelona, Spain
| | - Guillaume J Filion
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc A Marti-Renom
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Thomas Graf
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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Grob S, Cavalli G. Technical Review: A Hitchhiker's Guide to Chromosome Conformation Capture. Methods Mol Biol 2018; 1675:233-246. [PMID: 29052195 DOI: 10.1007/978-1-4939-7318-7_14] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The introduction of chromosome conformation capture (3C) technologies boosted the field of 3D-genome research and significantly enhanced the available toolset to study chromosomal architecture. 3C technologies not only offer increased resolution compared to the previously dominant cytological approaches but also allow the simultaneous study of genome-wide 3D chromatin contacts, thereby enabling a candidate-free perspective on 3D-genome architecture. Since its introduction in 2002, 3C technologies evolved rapidly and now constitute a collection of tools, each with their strengths and pitfalls with respect to specific research questions. This chapter aims at guiding 3C novices through the labyrinth of potential applications of the various family members, hopefully providing a valuable basis for choosing the appropriate strategy for different research questions.
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Affiliation(s)
- Stefan Grob
- Institute of Human Genetics, Centre National de la Recherche UMR9002, Montpellier, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, Centre National de la Recherche UMR9002, Montpellier, France
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44
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Schauer T, Ghavi‐Helm Y, Sexton T, Albig C, Regnard C, Cavalli G, Furlong EEM, Becker PB. Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation. EMBO Rep 2017; 18:1854-1868. [PMID: 28794204 PMCID: PMC5623837 DOI: 10.15252/embr.201744292] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 11/09/2022] Open
Abstract
X chromosome dosage compensation in Drosophila requires chromosome-wide coordination of gene activation. The male-specific lethal dosage compensation complex (DCC) identifies and binds to X-chromosomal high-affinity sites (HAS) from which it boosts transcription. A sub-class of HAS, PionX sites, represent first contacts on the X. Here, we explored the chromosomal interactions of representative PionX sites by high-resolution 4C and determined the global chromosome conformation by Hi-C in sex-sorted embryos. Male and female X chromosomes display similar nuclear architecture, concordant with clustered, constitutively active genes. PionX sites, like HAS, are evenly distributed in the active compartment and engage in short- and long-range interactions beyond compartment boundaries. Long-range, inter-domain interactions between DCC binding sites are stronger in males, suggesting that the complex refines chromatin organization. By de novo induction of DCC in female cells, we monitored the extent of activation surrounding PionX sites. This revealed a remarkable range of DCC action not only in linear proximity, but also at megabase distance if close in space, suggesting that DCC profits from pre-existing chromosome folding to activate genes.
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Affiliation(s)
- Tamás Schauer
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
| | - Yad Ghavi‐Helm
- European Molecular Biology LaboratoryGenome Biology UnitHeidelbergGermany
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular BiologyIllkirchFrance
| | - Christian Albig
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
| | - Catherine Regnard
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
| | - Giacomo Cavalli
- Institute of Human GeneticsCNRSMontpellierFrance
- University of MontpellierMontpellierFrance
| | - Eileen EM Furlong
- European Molecular Biology LaboratoryGenome Biology UnitHeidelbergGermany
| | - Peter B Becker
- Molecular Biology DivisionBiomedical Center and Center for Integrated Protein Science Ludwig‐Maximilians‐UniversityMunichGermany
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45
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Mishra A, Hawkins RD. Three-dimensional genome architecture and emerging technologies: looping in disease. Genome Med 2017; 9:87. [PMID: 28964259 PMCID: PMC5623062 DOI: 10.1186/s13073-017-0477-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genome compaction is a universal feature of cells and has emerged as a global regulator of gene expression. Compaction is maintained by a multitude of architectural proteins, long non-coding RNAs (lncRNAs), and regulatory DNA. Each component comprises interlinked regulatory circuits that organize the genome in three-dimensional (3D) space to manage gene expression. In this review, we update the current state of 3D genome catalogues and focus on how recent technological advances in 3D genomics are leading to an enhanced understanding of disease mechanisms. We highlight the use of genome-wide chromatin conformation capture (Hi-C) coupled with oligonucleotide capture technology (capture Hi-C) to map interactions between gene promoters and distal regulatory elements such as enhancers that are enriched for disease variants from genome-wide association studies (GWASs). We discuss how aberrations in architectural units are associated with various pathological outcomes, and explore how recent advances in genome and epigenome editing show great promise for a systematic understanding of complex genetic disorders. Our growing understanding of 3D genome architecture—coupled with the ability to engineer changes in it—may create novel therapeutic opportunities.
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Affiliation(s)
- Arpit Mishra
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98195-5065, USA
| | - R David Hawkins
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98195-5065, USA.
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46
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Gomez-Velazquez M, Badia-Careaga C, Lechuga-Vieco AV, Nieto-Arellano R, Tena JJ, Rollan I, Alvarez A, Torroja C, Caceres EF, Roy AR, Galjart N, Delgado-Olguin P, Sanchez-Cabo F, Enriquez JA, Gomez-Skarmeta JL, Manzanares M. CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart. PLoS Genet 2017; 13:e1006985. [PMID: 28846746 PMCID: PMC5591014 DOI: 10.1371/journal.pgen.1006985] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/08/2017] [Accepted: 08/17/2017] [Indexed: 11/27/2022] Open
Abstract
Cardiac progenitors are specified early in development and progressively differentiate and mature into fully functional cardiomyocytes. This process is controlled by an extensively studied transcriptional program. However, the regulatory events coordinating the progression of such program from development to maturation are largely unknown. Here, we show that the genome organizer CTCF is essential for cardiogenesis and that it mediates genomic interactions to coordinate cardiomyocyte differentiation and maturation in the developing heart. Inactivation of Ctcf in cardiac progenitor cells and their derivatives in vivo during development caused severe cardiac defects and death at embryonic day 12.5. Genome wide expression analysis in Ctcf mutant hearts revealed that genes controlling mitochondrial function and protein production, required for cardiomyocyte maturation, were upregulated. However, mitochondria from mutant cardiomyocytes do not mature properly. In contrast, multiple development regulatory genes near predicted heart enhancers, including genes in the IrxA cluster, were downregulated in Ctcf mutants, suggesting that CTCF promotes cardiomyocyte differentiation by facilitating enhancer-promoter interactions. Accordingly, loss of CTCF disrupts gene expression and chromatin interactions as shown by chromatin conformation capture followed by deep sequencing. Furthermore, CRISPR-mediated deletion of an intergenic CTCF site within the IrxA cluster alters gene expression in the developing heart. Thus, CTCF mediates local regulatory interactions to coordinate transcriptional programs controlling transitions in morphology and function during heart development. Properly regulated gene expression in time and space during development and differentiation requires not only transcriptional inputs, but also specific structuring of the chromatin. CTCF is a DNA binding factor that is believed to be critical for this process through binding to tens of thousands of sites across the genome. Despite the knowledge gained in recent years on the role of CTCF in genome organization, its functions in vivo are poorly understood. To address this issue, we studied the effect of genetically deleting CTCF in differentiating cardiomyocytes at early stages of mouse development. Surprisingly only a fraction of genes change their expression when CTCF is removed. Importantly, misregulated genes control opposing genetic programs in charge of development and patterning on one hand, and cardiomyocyte maturation on the other. This imbalance leads to faulty mitochondria and incorrect expression of cardiac patterning genes, and subsequent embryonic lethality. Our results suggest that CTCF is not necessary for maintenance of global genome structure, but coordinates dynamic genetic programs controlling phenotypic transitions in developing cells and tissues.
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Affiliation(s)
| | | | - Ana Victoria Lechuga-Vieco
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | | | - Juan J. Tena
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Isabel Rollan
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Alba Alvarez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Carlos Torroja
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Eva F. Caceres
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Anna R. Roy
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Niels Galjart
- Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Paul Delgado-Olguin
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Heart and Stroke Richard Lewar Centre of Excellence, Toronto, Ontario, Canada
| | | | | | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Miguel Manzanares
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- * E-mail:
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47
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Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, Snyder M, Chang HY, Fraser P, Khavari PA. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nat Genet 2017; 49:1522-1528. [PMID: 28805829 PMCID: PMC5715812 DOI: 10.1038/ng.3935] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/21/2017] [Indexed: 12/16/2022]
Abstract
Chromosome conformation is an important feature of metazoan gene regulation; however, enhancer-promoter contact remodeling during cellular differentiation remains poorly understood. To address this, genome-wide promoter capture Hi-C (CHi-C) was performed during epidermal differentiation. Two classes of enhancer-promoter contacts associated with differentiation-induced genes were identified. The first class ('gained') increased in contact strength during differentiation in concert with enhancer acquisition of the H3K27ac activation mark. The second class ('stable') were pre-established in undifferentiated cells, with enhancers constitutively marked by H3K27ac. The stable class was associated with the canonical conformation regulator cohesin, whereas the gained class was not, implying distinct mechanisms of contact formation and regulation. Analysis of stable enhancers identified a new, essential role for a constitutively expressed, lineage-restricted ETS-family transcription factor, EHF, in epidermal differentiation. Furthermore, neither class of contacts was observed in pluripotent cells, suggesting that lineage-specific chromatin structure is established in tissue progenitor cells and is further remodeled in terminal differentiation.
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Affiliation(s)
- Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Brook C Barajas
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Mayra Furlan-Magaril
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.,Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Vanessa Lopez-Pajares
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Maxwell R Mumbach
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Imani Howard
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Daniel S Kim
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Lisa D Boxer
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Jonathan Cairns
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Minyi Shi
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Zhixin Zhao
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Howard Y Chang
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.,Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.,Veterans Affairs Palo Alto Healthcare System, Palo Alto, California, USA
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48
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Gupta RM, Hadaya J, Trehan A, Zekavat SM, Roselli C, Klarin D, Emdin CA, Hilvering CRE, Bianchi V, Mueller C, Khera AV, Ryan RJH, Engreitz JM, Issner R, Shoresh N, Epstein CB, de Laat W, Brown JD, Schnabel RB, Bernstein BE, Kathiresan S. A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression. Cell 2017; 170:522-533.e15. [PMID: 28753427 PMCID: PMC5785707 DOI: 10.1016/j.cell.2017.06.049] [Citation(s) in RCA: 286] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/13/2017] [Accepted: 06/29/2017] [Indexed: 01/20/2023]
Abstract
Genome-wide association studies (GWASs) implicate the PHACTR1 locus (6p24) in risk for five vascular diseases, including coronary artery disease, migraine headache, cervical artery dissection, fibromuscular dysplasia, and hypertension. Through genetic fine mapping, we prioritized rs9349379, a common SNP in the third intron of the PHACTR1 gene, as the putative causal variant. Epigenomic data from human tissue revealed an enhancer signature at rs9349379 exclusively in aorta, suggesting a regulatory function for this SNP in the vasculature. CRISPR-edited stem cell-derived endothelial cells demonstrate rs9349379 regulates expression of endothelin 1 (EDN1), a gene located 600 kb upstream of PHACTR1. The known physiologic effects of EDN1 on the vasculature may explain the pattern of risk for the five associated diseases. Overall, these data illustrate the integration of genetic, phenotypic, and epigenetic analysis to identify the biologic mechanism by which a common, non-coding variant can distally regulate a gene and contribute to the pathogenesis of multiple vascular diseases.
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Affiliation(s)
- Rajat M Gupta
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Joseph Hadaya
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Aditi Trehan
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | | | - Carolina Roselli
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Derek Klarin
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Connor A Emdin
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | | | - Valerio Bianchi
- Hubrecht Institute, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Christian Mueller
- Department of General and Interventional Cardiology, University Heart Center Hamburg-Eppendorf, Hamburg, Germany
| | - Amit V Khera
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Russell J H Ryan
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Robbyn Issner
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Noam Shoresh
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | | | - Wouter de Laat
- Hubrecht Institute, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jonathan D Brown
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Renate B Schnabel
- Department of General and Interventional Cardiology, University Heart Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bradley E Bernstein
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sekar Kathiresan
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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49
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Genome-wide characterization of mammalian promoters with distal enhancer functions. Nat Genet 2017; 49:1073-1081. [PMID: 28581502 DOI: 10.1038/ng.3884] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/01/2017] [Indexed: 12/15/2022]
Abstract
Gene expression in mammals is precisely regulated by the combination of promoters and gene-distal regulatory regions, known as enhancers. Several studies have suggested that some promoters might have enhancer functions. However, the extent of this type of promoters and whether they actually function to regulate the expression of distal genes have remained elusive. Here, by exploiting a high-throughput enhancer reporter assay, we unravel a set of mammalian promoters displaying enhancer activity. These promoters have distinct genomic and epigenomic features and frequently interact with other gene promoters. Extensive CRISPR-Cas9 genomic manipulation demonstrated the involvement of these promoters in the cis regulation of expression of distal genes in their natural loci. Our results have important implications for the understanding of complex gene regulation in normal development and disease.
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50
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Carty M, Zamparo L, Sahin M, González A, Pelossof R, Elemento O, Leslie CS. An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data. Nat Commun 2017; 8:15454. [PMID: 28513628 PMCID: PMC5442359 DOI: 10.1038/ncomms15454] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 03/29/2017] [Indexed: 01/03/2023] Open
Abstract
Here we present HiC-DC, a principled method to estimate the statistical significance (P values) of chromatin interactions from Hi-C experiments. HiC-DC uses hurdle negative binomial regression account for systematic sources of variation in Hi-C read counts—for example, distance-dependent random polymer ligation and GC content and mappability bias—and model zero inflation and overdispersion. Applied to high-resolution Hi-C data in a lymphoblastoid cell line, HiC-DC detects significant interactions at the sub-topologically associating domain level, identifying potential structural and regulatory interactions supported by CTCF binding sites, DNase accessibility, and/or active histone marks. CTCF-associated interactions are most strongly enriched in the middle genomic distance range (∼700 kb–1.5 Mb), while interactions involving actively marked DNase accessible elements are enriched both at short (<500 kb) and longer (>1.5 Mb) genomic distances. There is a striking enrichment of longer-range interactions connecting replication-dependent histone genes on chromosome 6, potentially representing the chromatin architecture at the histone locus body. Genome-wide chromosome conformation capture has helped us identify features of genome topology influencing biology but requires careful statistical analysis. Here the authors present HiC-DC, a bioinformatics method that can detect statistically significant regulatory interactions.
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Affiliation(s)
- Mark Carty
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York 10065, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA
| | - Lee Zamparo
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Merve Sahin
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA
| | - Alvaro González
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Raphael Pelossof
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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