4001
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Chen CW, Koche RP, Sinha AU, Deshpande AJ, Zhu N, Eng R, Doench JG, Xu H, Chu SH, Qi J, Wang X, Delaney C, Bernt KM, Root DE, Hahn WC, Bradner JE, Armstrong SA. DOT1L inhibits SIRT1-mediated epigenetic silencing to maintain leukemic gene expression in MLL-rearranged leukemia. Nat Med 2015; 21:335-43. [PMID: 25822366 PMCID: PMC4390532 DOI: 10.1038/nm.3832] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/02/2015] [Indexed: 12/14/2022]
Abstract
MLL -rearrangements generate MLL-fusion proteins that bind DNA and drive leukemogenic gene expression. This gene expression program is dependent on the histone 3 lysine 79 (H3K79) methyltransferase DOT1L, and small molecule DOT1L inhibitors show promise as therapeutics for these leukemias. However, the mechanisms underlying this dependency are unclear. We conducted a genome-scale RNAi screen and found that the histone deacetylase SIRT1 is required for the establishment of a heterochromatin-like state around MLL-fusion target genes after DOT1L inhibition. DOT1L inhibits chromatin localization of a repressive complex composed of SIRT1 and SUV39H1, thereby maintaining an open chromatin state with elevated H3K9 acetylation and minimal H3K9 methylation at MLL-fusion target genes. Furthermore, the combination of SIRT1 activators and DOT1L inhibitors shows enhanced activity against MLL-rearranged leukemia cells. These results indicate that the dynamic interplay between chromatin regulators controlling activation and repression of gene expression could provide novel opportunities for combination therapy.
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Affiliation(s)
- Chun-Wei Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Richard P Koche
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Amit U Sinha
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Aniruddha J Deshpande
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nan Zhu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rowena Eng
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - John G Doench
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Haiming Xu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Scott H Chu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Xi Wang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christopher Delaney
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kathrin M Bernt
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - William C Hahn
- 1] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - James E Bradner
- 1] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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4002
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Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biol 2015; 16:57. [PMID: 25854118 PMCID: PMC4373242 DOI: 10.1186/s13059-015-0622-4] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.
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4003
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Zerbino DR, Wilder SP, Johnson N, Juettemann T, Flicek PR. The ensembl regulatory build. Genome Biol 2015; 16:56. [PMID: 25887522 PMCID: PMC4407537 DOI: 10.1186/s13059-015-0621-5] [Citation(s) in RCA: 288] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 03/04/2015] [Indexed: 02/07/2023] Open
Abstract
Most genomic variants associated with phenotypic traits or disease do not fall within gene coding regions, but in regulatory regions, rendering their interpretation difficult. We collected public data on epigenetic marks and transcription factor binding in human cell types and used it to construct an intuitive summary of regulatory regions in the human genome. We verified it against independent assays for sensitivity. The Ensembl Regulatory Build will be progressively enriched when more data is made available. It is freely available on the Ensembl browser, from the Ensembl Regulation MySQL database server and in a dedicated track hub.
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Affiliation(s)
- Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Steven P Wilder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Nathan Johnson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Thomas Juettemann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Paul R Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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4004
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Kouwenhoven EN, van Bokhoven H, Zhou H. Gene regulatory mechanisms orchestrated by p63 in epithelial development and related disorders. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:590-600. [PMID: 25797018 DOI: 10.1016/j.bbagrm.2015.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/09/2015] [Accepted: 03/12/2015] [Indexed: 01/30/2023]
Abstract
The transcription factor p63 belongs to the p53 family and is a key regulator in epithelial commitment and development. Mutations in p63 give rise to several epithelial related disorders with defects in skin, limb and orofacial structures. Since the discovery of p63, efforts have been made to identify its target genes using individual gene approaches and to understand p63 function in normal epithelial development and related diseases. Recent genome-wide approaches have identified tens of thousands of potential p63-regulated target genes and regulatory elements, and reshaped the concept of gene regulation orchestrated by p63. These data also provide insights into p63-related disease mechanisms. In this review, we discuss the regulatory role of p63 in normal and diseased epithelial development in light of these novel findings. We also propose future perspectives for dissecting the molecular mechanism of p63-mediated epithelial development and related disorders as well as for potential therapeutic strategies.
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Affiliation(s)
- Evelyn N Kouwenhoven
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
| | - Hans van Bokhoven
- Radboud university medical center, Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
| | - Huiqing Zhou
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands; Radboud university medical center, Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
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4005
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Blatti C, Kazemian M, Wolfe S, Brodsky M, Sinha S. Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism. Nucleic Acids Res 2015; 43:3998-4012. [PMID: 25791631 PMCID: PMC4417154 DOI: 10.1093/nar/gkv195] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 02/24/2015] [Indexed: 11/17/2022] Open
Abstract
Characterization of cell type specific regulatory networks and elements is a major challenge in genomics, and emerging strategies frequently employ high-throughput genome-wide assays of transcription factor (TF) to DNA binding, histone modifications or chromatin state. However, these experiments remain too difficult/expensive for many laboratories to apply comprehensively to their system of interest. Here, we explore the potential of elucidating regulatory systems in varied cell types using computational techniques that rely on only data of gene expression, low-resolution chromatin accessibility, and TF–DNA binding specificities (‘motifs’). We show that static computational motif scans overlaid with chromatin accessibility data reasonably approximate experimentally measured TF–DNA binding. We demonstrate that predicted binding profiles and expression patterns of hundreds of TFs are sufficient to identify major regulators of ∼200 spatiotemporal expression domains in the Drosophila embryo. We are then able to learn reliable statistical models of enhancer activity for over 70 expression domains and apply those models to annotate domain specific enhancers genome-wide. Throughout this work, we apply our motif and accessibility based approach to comprehensively characterize the regulatory network of fruitfly embryonic development and show that the accuracy of our computational method compares favorably to approaches that rely on data from many experimental assays.
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Affiliation(s)
- Charles Blatti
- Department of Computer Science, University of Illinois, Urbana, IL 61801, USA
| | - Majid Kazemian
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scot Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01655, USA Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Michael Brodsky
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01655, USA Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois, Urbana, IL 61801, USA Institute of Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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4006
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Farré M, Robinson TJ, Ruiz-Herrera A. An Integrative Breakage Model of genome architecture, reshuffling and evolution: The Integrative Breakage Model of genome evolution, a novel multidisciplinary hypothesis for the study of genome plasticity. Bioessays 2015; 37:479-88. [PMID: 25739389 DOI: 10.1002/bies.201400174] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 12/23/2022]
Abstract
Our understanding of genomic reorganization, the mechanics of genomic transmission to offspring during germ line formation, and how these structural changes contribute to the speciation process, and genetic disease is far from complete. Earlier attempts to understand the mechanism(s) and constraints that govern genome remodeling suffered from being too narrowly focused, and failed to provide a unified and encompassing view of how genomes are organized and regulated inside cells. Here, we propose a new multidisciplinary Integrative Breakage Model for the study of genome evolution. The analysis of the high-level structural organization of genomes (nucleome), together with the functional constrains that accompany genome reshuffling, provide insights into the origin and plasticity of genome organization that may assist with the detection and isolation of therapeutic targets for the treatment of complex human disorders.
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Affiliation(s)
- Marta Farré
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB, Barcelona, Spain
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4007
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Suryamohan K, Halfon MS. Identifying transcriptional cis-regulatory modules in animal genomes. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2015; 4:59-84. [PMID: 25704908 PMCID: PMC4339228 DOI: 10.1002/wdev.168] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/04/2014] [Accepted: 11/16/2014] [Indexed: 11/08/2022]
Abstract
UNLABELLED Gene expression is regulated through the activity of transcription factors (TFs) and chromatin-modifying proteins acting on specific DNA sequences, referred to as cis-regulatory elements. These include promoters, located at the transcription initiation sites of genes, and a variety of distal cis-regulatory modules (CRMs), the most common of which are transcriptional enhancers. Because regulated gene expression is fundamental to cell differentiation and acquisition of new cell fates, identifying, characterizing, and understanding the mechanisms of action of CRMs is critical for understanding development. CRM discovery has historically been challenging, as CRMs can be located far from the genes they regulate, have few readily identifiable sequence characteristics, and for many years were not amenable to high-throughput discovery methods. However, the recent availability of complete genome sequences and the development of next-generation sequencing methods have led to an explosion of both computational and empirical methods for CRM discovery in model and nonmodel organisms alike. Experimentally, CRMs can be identified through chromatin immunoprecipitation directed against TFs or histone post-translational modifications, identification of nucleosome-depleted 'open' chromatin regions, or sequencing-based high-throughput functional screening. Computational methods include comparative genomics, clustering of known or predicted TF-binding sites, and supervised machine-learning approaches trained on known CRMs. All of these methods have proven effective for CRM discovery, but each has its own considerations and limitations, and each is subject to a greater or lesser number of false-positive identifications. Experimental confirmation of predictions is essential, although shortcomings in current methods suggest that additional means of validation need to be developed. For further resources related to this article, please visit the WIREs website. CONFLICT OF INTEREST The authors have declared no conflicts of interest for this article.
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Affiliation(s)
- Kushal Suryamohan
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| | - Marc S. Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
- Molecular and Cellular Biology Department and Program in Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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4008
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Tomazou EM, Sheffield NC, Schmidl C, Schuster M, Schönegger A, Datlinger P, Kubicek S, Bock C, Kovar H. Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1. Cell Rep 2015; 10:1082-95. [PMID: 25704812 PMCID: PMC4542316 DOI: 10.1016/j.celrep.2015.01.042] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 11/17/2014] [Accepted: 01/15/2015] [Indexed: 01/13/2023] Open
Abstract
Transcription factor fusion proteins can transform cells by inducing global changes of the transcriptome, often creating a state of oncogene addiction. Here, we investigate the role of epigenetic mechanisms in this process, focusing on Ewing sarcoma cells that are dependent on the EWS-FLI1 fusion protein. We established reference epigenome maps comprising DNA methylation, seven histone marks, open chromatin states, and RNA levels, and we analyzed the epigenome dynamics upon downregulation of the driving oncogene. Reduced EWS-FLI1 expression led to widespread epigenetic changes in promoters, enhancers, and super-enhancers, and we identified histone H3K27 acetylation as the most strongly affected mark. Clustering of epigenetic promoter signatures defined classes of EWS-FLI1-regulated genes that responded differently to low-dose treatment with histone deacetylase inhibitors. Furthermore, we observed strong and opposing enrichment patterns for E2F and AP-1 among EWS-FLI1-correlated and anticorrelated genes. Our data describe extensive genome-wide rewiring of epigenetic cell states driven by an oncogenic fusion protein. Reference epigenome maps identify widespread epigenetic change in Ewing sarcoma cells EWS-FLI1-regulated genes fall into clusters with characteristic chromatin signatures Transcriptome response to HDAC inhibitors depends on promoter-specific histone marks EWS-FLI1 induces global changes in H3K27ac and genome-wide enhancer reprogramming
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Affiliation(s)
- Eleni M Tomazou
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090 Vienna, Austria
| | - Nathan C Sheffield
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Christian Schmidl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andreas Schönegger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.
| | - Heinrich Kovar
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090 Vienna, Austria; Department of Pediatrics, Medical University of Vienna, 1090 Vienna, Austria.
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4009
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Lavin Y, Winter D, Blecher-Gonen R, David E, Keren-Shaul H, Merad M, Jung S, Amit I. Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment. Cell 2015; 159:1312-26. [PMID: 25480296 DOI: 10.1016/j.cell.2014.11.018] [Citation(s) in RCA: 1534] [Impact Index Per Article: 170.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/11/2014] [Accepted: 11/11/2014] [Indexed: 02/09/2023]
Abstract
Macrophages are critical for innate immune defense and also control organ homeostasis in a tissue-specific manner. They provide a fitting model to study the impact of ontogeny and microenvironment on chromatin state and whether chromatin modifications contribute to macrophage identity. Here, we profile the dynamics of four histone modifications across seven tissue-resident macrophage populations. We identify 12,743 macrophage-specific enhancers and establish that tissue-resident macrophages have distinct enhancer landscapes beyond what can be explained by developmental origin. Combining our enhancer catalog with gene expression profiles and open chromatin regions, we show that a combination of tissue- and lineage-specific transcription factors form the regulatory networks controlling chromatin specification in tissue-resident macrophages. The environment is capable of shaping the chromatin landscape of transplanted bone marrow precursors, and even differentiated macrophages can be reprogrammed when transferred into a new microenvironment. These results provide a comprehensive view of macrophage regulatory landscape and highlight the importance of the microenvironment, along with pioneer factors in orchestrating identity and plasticity.
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Affiliation(s)
- Yonit Lavin
- Department of Oncological Sciences, Immunology Institute and the Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deborah Winter
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miriam Merad
- Department of Oncological Sciences, Immunology Institute and the Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Steffen Jung
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
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4010
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Mathelier A, Shi W, Wasserman WW. Identification of altered cis-regulatory elements in human disease. Trends Genet 2015; 31:67-76. [DOI: 10.1016/j.tig.2014.12.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 02/01/2023]
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4011
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Davie K, Jacobs J, Atkins M, Potier D, Christiaens V, Halder G, Aerts S. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet 2015; 11:e1004994. [PMID: 25679813 PMCID: PMC4334524 DOI: 10.1371/journal.pgen.1004994] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/08/2015] [Indexed: 01/24/2023] Open
Abstract
Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-)activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling, combined with motif discovery, is a straightforward approach to identify functional genomic regulatory regions, master regulators, and gene regulatory networks controlling complex in vivo processes.
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Affiliation(s)
- Kristofer Davie
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Jelle Jacobs
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Mardelle Atkins
- Laboratory of Growth Control and Cancer Research, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for the Biology of Disease, Laboratory for Molecular Cancer Biology, Leuven, Belgium
| | - Delphine Potier
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Valerie Christiaens
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Georg Halder
- Laboratory of Growth Control and Cancer Research, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for the Biology of Disease, Laboratory for Molecular Cancer Biology, Leuven, Belgium
| | - Stein Aerts
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
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4012
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Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JMA, Bertelsen MF, Murchison EP, Flicek P, Odom DT. Enhancer evolution across 20 mammalian species. Cell 2015; 160:554-66. [PMID: 25635462 PMCID: PMC4313353 DOI: 10.1016/j.cell.2015.01.006] [Citation(s) in RCA: 467] [Impact Index Per Article: 51.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/31/2014] [Accepted: 12/15/2014] [Indexed: 12/21/2022]
Abstract
The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements. In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences. These results provide important insight into the functional genetics underpinning mammalian regulatory evolution.
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Affiliation(s)
- Diego Villar
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Camille Berthelot
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sarah Aldridge
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Tim F Rayner
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Margus Lukk
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Thomas J Park
- Department of Biological Sciences, University of Illinois at Chicago (UIC), 845 West Taylor Street, Chicago, IL 60607, USA
| | - Robert Deaville
- UK Cetacean Strandings Investigation Programme (CSIP) and Institute of Zoology, Zoological Society of London, Outer Circle, Regent's Park, London NW1 4RY, UK
| | - Jonathan T Erichsen
- School of Optometry and Vision Sciences, Cardiff University, Maindy Road, Cardiff CF24 4HQ, UK
| | - Anna J Jasinska
- UCLA Center for Neurobehavioral Genetics, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - James M A Turner
- Division of Stem Cell Biology and Developmental Genetics, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Mads F Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - Elizabeth P Murchison
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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4013
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Spencer DH, Young MA, Lamprecht TL, Helton NM, Fulton R, O'Laughlin M, Fronick C, Magrini V, Demeter RT, Miller CA, Klco JM, Wilson RK, Ley TJ. Epigenomic analysis of the HOX gene loci reveals mechanisms that may control canonical expression patterns in AML and normal hematopoietic cells. Leukemia 2015; 29:1279-89. [PMID: 25600023 DOI: 10.1038/leu.2015.6] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/19/2014] [Accepted: 12/16/2014] [Indexed: 01/05/2023]
Abstract
HOX genes are highly expressed in many acute myeloid leukemia (AML) samples, but the patterns of expression and associated regulatory mechanisms are not clearly understood. We analyzed RNA sequencing data from 179 primary AML samples and normal hematopoietic cells to understand the range of expression patterns in normal versus leukemic cells. HOX expression in AML was restricted to specific genes in the HOXA or HOXB loci, and was highly correlated with recurrent cytogenetic abnormalities. However, the majority of samples expressed a canonical set of HOXA and HOXB genes that was nearly identical to the expression signature of normal hematopoietic stem/progenitor cells. Transcriptional profiles at the HOX loci were similar between normal cells and AML samples, and involved bidirectional transcription at the center of each gene cluster. Epigenetic analysis of a subset of AML samples also identified common regions of chromatin accessibility in AML samples and normal CD34(+) cells that displayed differences in methylation depending on HOX expression patterns. These data provide an integrated epigenetic view of the HOX gene loci in primary AML samples, and suggest that HOX expression in most AML samples represents a normal stem cell program that is controlled by epigenetic mechanisms at specific regulatory elements.
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Affiliation(s)
- D H Spencer
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - M A Young
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - T L Lamprecht
- Department of Internal Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St Louis, MO, USA
| | - N M Helton
- Department of Internal Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St Louis, MO, USA
| | - R Fulton
- The Genome Institute, Washington University, St Louis, MO, USA
| | - M O'Laughlin
- The Genome Institute, Washington University, St Louis, MO, USA
| | - C Fronick
- The Genome Institute, Washington University, St Louis, MO, USA
| | - V Magrini
- The Genome Institute, Washington University, St Louis, MO, USA
| | - R T Demeter
- The Genome Institute, Washington University, St Louis, MO, USA
| | - C A Miller
- The Genome Institute, Washington University, St Louis, MO, USA
| | - J M Klco
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - R K Wilson
- The Genome Institute, Washington University, St Louis, MO, USA
| | - T J Ley
- 1] Department of Internal Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St Louis, MO, USA [2] The Genome Institute, Washington University, St Louis, MO, USA
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4014
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Siggens L, Cordeddu L, Rönnerblad M, Lennartsson A, Ekwall K. Transcription-coupled recruitment of human CHD1 and CHD2 influences chromatin accessibility and histone H3 and H3.3 occupancy at active chromatin regions. Epigenetics Chromatin 2015; 8:4. [PMID: 25621013 PMCID: PMC4305392 DOI: 10.1186/1756-8935-8-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/23/2014] [Indexed: 01/31/2023] Open
Abstract
Background CHD1 and CHD2 chromatin remodeling enzymes play important roles in development, cancer and differentiation. At a molecular level, the mechanisms are not fully understood but include transcriptional regulation, nucleosome organization and turnover. Results Here we show human CHD1 and CHD2 enzymes co-occupy active chromatin regions associated with transcription start sites (TSS), enhancer like regions and active tRNA genes. We demonstrate that their recruitment is transcription-coupled. CHD1 and CHD2 show distinct binding profiles across active TSS regions. Depletion of CHD1 influences chromatin accessibility at TSS and enhancer-like chromatin regions. CHD2 depletion causes increased histone H3 and reduced histone variant H3.3 occupancy. Conclusions We conclude that transcription-coupled recruitment of CHD1 and CHD2 occurs at transcribed gene TSSs and at intragenic and intergenic enhancer-like sites. The recruitment of CHD1 and CHD2 regulates the architecture of active chromatin regions through chromatin accessibility and nucleosome disassembly. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-8-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lee Siggens
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden
| | - Lina Cordeddu
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden
| | - Michelle Rönnerblad
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83 Sweden
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4015
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Path from schizophrenia genomics to biology: gene regulation and perturbation in neurons derived from induced pluripotent stem cells and genome editing. Neurosci Bull 2015; 31:113-27. [PMID: 25575480 DOI: 10.1007/s12264-014-1488-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 11/03/2014] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia (SZ) is a devastating mental disorder afflicting 1% of the population. Recent genome-wide association studies (GWASs) of SZ have identified >100 risk loci. However, the causal variants/genes and the causal mechanisms remain largely unknown, which hinders the translation of GWAS findings into disease biology and drug targets. Most risk variants are noncoding, thus likely regulate gene expression. A major mechanism of transcriptional regulation is chromatin remodeling, and open chromatin is a versatile predictor of regulatory sequences. MicroRNA-mediated post-transcriptional regulation plays an important role in SZ pathogenesis. Neurons differentiated from patient-specific induced pluripotent stem cells (iPSCs) provide an experimental model to characterize the genetic perturbation of regulatory variants that are often specific to cell type and/or developmental stage. The emerging genome-editing technology enables the creation of isogenic iPSCs and neurons to efficiently characterize the effects of SZ-associated regulatory variants on SZ-relevant molecular and cellular phenotypes involving dopaminergic, glutamatergic, and GABAergic neurotransmissions. SZ GWAS findings equipped with the emerging functional genomics approaches provide an unprecedented opportunity for understanding new disease biology and identifying novel drug targets.
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4016
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Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. ACTA ACUST UNITED AC 2015; 109:21.29.1-21.29.9. [PMID: 25559105 DOI: 10.1002/0471142727.mb2129s109] [Citation(s) in RCA: 1896] [Impact Index Per Article: 210.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This unit describes Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq), a method for mapping chromatin accessibility genome-wide. This method probes DNA accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin. Sequencing reads can then be used to infer regions of increased accessibility, as well as to map regions of transcription-factor binding and nucleosome position. The method is a fast and sensitive alternative to DNase-seq for assaying chromatin accessibility genome-wide, or to MNase-seq for assaying nucleosome positions in accessible regions of the genome.
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Affiliation(s)
- Jason D Buenrostro
- Department of Genetics, Stanford University School of Medicine, Stanford, California.,Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California
| | - Beijing Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Howard Y Chang
- Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, California
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4017
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Cumbie JS, Filichkin SA, Megraw M. Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana. PLANT METHODS 2015; 11:42. [PMID: 26339280 PMCID: PMC4558764 DOI: 10.1186/s13007-015-0087-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/21/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulatory DNA on a genome-wide scale. While this method was originally developed for human cell lines, later adaptations made the processing of plant tissues possible. Challenges still remain in processing recalcitrant tissues that have low DNA content. RESULTS By removing steps requiring the use of gel agarose plugs in DNase-seq, we were able to significantly reduce the time required to perform the protocol by at least 2 days, while also making possible the processing of difficult plant tissues. We refer to this simplified protocol as DNase I SIM (for simplified in-nucleus method). We were able to successfully create DNase-seq libraries for both leaf and root tissues in Arabidopsis using DNase I SIM. CONCLUSION This protocol simplifies and facilitates generation of DNase-seq libraries from plant tissues for high resolution mapping of DNase I hypersensitive sites.
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Affiliation(s)
- Jason S. Cumbie
- />Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 USA
| | - Sergei A. Filichkin
- />Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 USA
- />Center for Genome Research and Biocomputing, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331 USA
| | - Molly Megraw
- />Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 USA
- />Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331 USA
- />Center for Genome Research and Biocomputing, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331 USA
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4018
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Abstract
There is no obvious morphological counterpart of the autopod (wrist/ankle and digits) in living fishes. Comparative molecular data may provide insight into understanding both the homology of elements and the evolutionary developmental mechanisms behind the fin to limb transition. In mouse limbs the autopod is built by a "late" phase of Hoxd and Hoxa gene expression, orchestrated by a set of enhancers located at the 5' end of each cluster. Despite a detailed mechanistic understanding of mouse limb development, interpretation of Hox expression patterns and their regulation in fish has spawned multiple hypotheses as to the origin and function of "autopod" enhancers throughout evolution. Using phylogenetic footprinting, epigenetic profiling, and transgenic reporters, we have identified and functionally characterized hoxD and hoxA enhancers in the genomes of zebrafish and the spotted gar, Lepisosteus oculatus, a fish lacking the whole genome duplication of teleosts. Gar and zebrafish "autopod" enhancers drive expression in the distal portion of developing zebrafish pectoral fins, and respond to the same functional cues as their murine orthologs. Moreover, gar enhancers drive reporter gene expression in both the wrist and digits of mouse embryos in patterns that are nearly indistinguishable from their murine counterparts. These functional genomic data support the hypothesis that the distal radials of bony fish are homologous to the wrist and/or digits of tetrapods.
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4019
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MORC1 represses transposable elements in the mouse male germline. Nat Commun 2014; 5:5795. [PMID: 25503965 PMCID: PMC4268658 DOI: 10.1038/ncomms6795] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/07/2014] [Indexed: 12/30/2022] Open
Abstract
The Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA-methylated and silent genes. MORC1-deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homologue DNMT3L. Morc1 mutants show highly localized defects in the establishment of DNA methylation at specific classes of transposons, and this is associated with failed transposon silencing at these sites. Our results identify MORC1 as an important new regulator of the epigenetic landscape of male germ cells during the period of global de novo methylation. The Microrchidia (Morc) family of GHKL ATPases are important repressors of transposons and other DNA-methylated and silent genes in A. thaliana. Here, the authors show that MORC1 is responsible for repression and methylation of specific classes of transposons in the mouse male germline.
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4020
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Andersson R. Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model. Bioessays 2014; 37:314-23. [PMID: 25450156 DOI: 10.1002/bies.201400162] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Gene transcription is strictly controlled by the interplay of regulatory events at gene promoters and gene-distal regulatory elements called enhancers. Despite extensive studies of enhancers, we still have a very limited understanding of their mechanisms of action and their restricted spatio-temporal activities. A better understanding would ultimately lead to fundamental insights into the control of gene transcription and the action of regulatory genetic variants involved in disease. Here, I review and discuss pros and cons of state-of-the-art genomics methods to localize and infer the activity of enhancers. Among the different approaches, profiling of enhancer RNAs yields the highest specificity and may be superior in detecting in vivo activity. I discuss their apparent similarities to promoters, which challenge the established view of enhancers and promoters as distinct entities, and present a unifying model of regulatory elements in transcriptional regulation, in which activity, transcriptional output and regulatory function is context specific.
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Affiliation(s)
- Robin Andersson
- The Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Denmark
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4021
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Yu B, Doraiswamy H, Chen X, Miraldi E, Arrieta-Ortiz ML, Hafemeister C, Madar A, Bonneau R, Silva CT. Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2014; 20:1903-1912. [PMID: 26356904 DOI: 10.1109/tvcg.2014.2346753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Elucidation of transcriptional regulatory networks (TRNs) is a fundamental goal in biology, and one of the most important components of TRNs are transcription factors (TFs), proteins that specifically bind to gene promoter and enhancer regions to alter target gene expression patterns. Advances in genomic technologies as well as advances in computational biology have led to multiple large regulatory network models (directed networks) each with a large corpus of supporting data and gene-annotation. There are multiple possible biological motivations for exploring large regulatory network models, including: validating TF-target gene relationships, figuring out co-regulation patterns, and exploring the coordination of cell processes in response to changes in cell state or environment. Here we focus on queries aimed at validating regulatory network models, and on coordinating visualization of primary data and directed weighted gene regulatory networks. The large size of both the network models and the primary data can make such coordinated queries cumbersome with existing tools and, in particular, inhibits the sharing of results between collaborators. In this work, we develop and demonstrate a web-based framework for coordinating visualization and exploration of expression data (RNA-seq, microarray), network models and gene-binding data (ChIP-seq). Using specialized data structures and multiple coordinated views, we design an efficient querying model to support interactive analysis of the data. Finally, we show the effectiveness of our framework through case studies for the mouse immune system (a dataset focused on a subset of key cellular functions) and a model bacteria (a small genome with high data-completeness).
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4022
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Abstract
Large-scale genome-wide association studies (GWAS) have identified 46 loci that are associated with coronary heart disease (CHD). Additionally, 104 independent candidate variants (false discovery rate of 5 %) have been identified (Schunkert H, Konig IR, Kathiresan S, Reilly MP, Assimes TL, Holm H et al. Nat Genet 43:333-8, 2011; Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR et al. Nat Genet 45:25-33, 2012; C4D Genetics Consortium. Nat Genet 43:339-44, 2011). The majority of the causal genes in these loci function independently of conventional risk factors. It is postulated that a number of the CHD-associated genes regulate basic processes in the vascular cells involved in atherosclerosis, and that study of the signaling pathways that are modulated in this cell type by causal regulatory variation will provide critical new insights for targeting the initiation and progression of disease. In this review, we will discuss the types of experimental approaches and data that are critical to understanding the molecular processes that underlie the disease risk at 9p21.3, TCF21, SORT1, and other CHD-associated loci.
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4023
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Bornstein C, Winter D, Barnett-Itzhaki Z, David E, Kadri S, Garber M, Amit I. A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States. Mol Cell 2014; 56:749-62. [PMID: 25453760 DOI: 10.1016/j.molcel.2014.10.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/13/2014] [Accepted: 10/14/2014] [Indexed: 01/11/2023]
Abstract
During hematopoiesis, cells originating from the same stem cell reservoir differentiate into distinct cell types. The mechanisms enabling common progenitors to differentiate into alternative cell fates are not fully understood. Here, we identify cell-fate-determining transcription factors (TFs) governing dendritic cell (DC) development by annotating the enhancer landscapes of the DC lineage. Combining these analyses with detailed overexpression, knockdown, and ChIP-Seq studies, we show that Irf8 functions as a plasmacytoid DC epigenetic and fate-determining TF, regulating massive, cell-specific chromatin changes in thousands of pDC enhancers. Importantly, Irf8 forms a negative feedback loop with Cebpb, a monocyte-derived DC epigenetic fate-determining TF. We show that using this circuit logic, a pulse of TF expression can stably define epigenetic and transcriptional states, regardless of the microenvironment. More broadly, our study proposes a general paradigm that allows closely related cells with a similar set of signal-dependent factors to generate differential and persistent enhancer landscapes.
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Affiliation(s)
| | - Deborah Winter
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | | | - Eyal David
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | - Sabah Kadri
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology and Program in Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ido Amit
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel.
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4024
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Tsompana M, Buck MJ. Chromatin accessibility: a window into the genome. Epigenetics Chromatin 2014; 7:33. [PMID: 25473421 PMCID: PMC4253006 DOI: 10.1186/1756-8935-7-33] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/05/2014] [Indexed: 01/09/2023] Open
Abstract
Transcriptional activation throughout the eukaryotic lineage has been tightly linked with disruption of nucleosome organization at promoters, enhancers, silencers, insulators and locus control regions due to transcription factor binding. Regulatory DNA thus coincides with open or accessible genomic sites of remodeled chromatin. Current chromatin accessibility assays are used to separate the genome by enzymatic or chemical means and isolate either the accessible or protected locations. The isolated DNA is then quantified using a next-generation sequencing platform. Wide application of these assays has recently focused on the identification of the instrumental epigenetic changes responsible for differential gene expression, cell proliferation, functional diversification and disease development. Here we discuss the limitations and advantages of current genome-wide chromatin accessibility assays with especial attention on experimental precautions and sequence data analysis. We conclude with our perspective on future improvements necessary for moving the field of chromatin profiling forward.
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Affiliation(s)
- Maria Tsompana
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 USA
| | - Michael J Buck
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 USA ; Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY USA
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4025
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Milon B, Sun Y, Chang W, Creasy T, Mahurkar A, Shetty A, Nurminsky D, Nurminskaya M. Map of open and closed chromatin domains in Drosophila genome. BMC Genomics 2014; 15:988. [PMID: 25407537 PMCID: PMC4289254 DOI: 10.1186/1471-2164-15-988] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 10/23/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Chromatin compactness has been considered a major determinant of gene activity and has been associated with specific chromatin modifications in studies on a few individual genetic loci. At the same time, genome-wide patterns of open and closed chromatin have been understudied, and are at present largely predicted from chromatin modification and gene expression data. However the universal applicability of such predictions is not self-evident, and requires experimental verification. RESULTS We developed and implemented a high-throughput analysis for general chromatin sensitivity to DNase I which provides a comprehensive epigenomic assessment in a single assay. Contiguous domains of open and closed chromatin were identified by computational analysis of the data, and correlated to other genome annotations including predicted chromatin "states", individual chromatin modifications, nuclear lamina interactions, and gene expression. While showing that the widely trusted predictions of chromatin structure are correct in the majority of cases, we detected diverse "exceptions" from the conventional rules. We found a profound paucity of chromatin modifications in a major fraction of closed chromatin, and identified a number of loci where chromatin configuration is opposite to that expected from modification and gene expression patterns. Further, we observed that chromatin of large introns tends to be closed even when the genes are expressed, and that a significant proportion of active genes including their promoters are located in closed chromatin. CONCLUSIONS These findings reveal limitations of the existing predictive models, indicate novel mechanisms of epigenetic regulation, and provide important insights into genome organization and function.
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Affiliation(s)
| | | | | | | | | | | | - Dmitry Nurminsky
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, 108 N, Greene St,, Baltimore, MD 21201, USA.
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4026
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Sammons MA, Zhu J, Drake AM, Berger SL. TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity. Genome Res 2014; 25:179-88. [PMID: 25391375 PMCID: PMC4315292 DOI: 10.1101/gr.181883.114] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Despite overwhelming evidence that transcriptional activation by TP53 is critical for its tumor suppressive activity, the mechanisms by which TP53 engages the genome in the context of chromatin to activate transcription are not well understood. Using a compendium of novel and existing genome-wide data sets, we examined the relationship between TP53 binding and the dynamics of the local chromatin environment. Our analysis revealed three distinct categories of TP53 binding events that differ based on the dynamics of the local chromatin environment. The first class of TP53 binding events occurs near transcriptional start sites (TSS) and is defined by previously characterized promoter-associated chromatin modifications. The second class comprises a large cohort of preestablished, promoter-distal enhancer elements that demonstrates dynamic histone acetylation and transcription upon TP53 binding. The third class of TP53 binding sites is devoid of classic chromatin modifications and, remarkably, fall within regions of inaccessible chromatin, suggesting that TP53 has intrinsic pioneer factor activity and binds within structurally inaccessible regions of chromatin. Intriguingly, these inaccessible TP53 binding sites feature several enhancer-like properties in cell types within the epithelial lineage, indicating that TP53 binding events include a group of “proto-enhancers” that become active enhancers given the appropriate cellular context. These data indicate that TP53, along with TP63, may act as pioneer factors to specify epithelial enhancers. Further, these findings suggest that rather than following a global cell-type invariant stress response program, TP53 may tune its response based on the lineage-specific epigenomic landscape.
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Affiliation(s)
- Morgan A Sammons
- Departments of Cell and Developmental Biology, Genetics, and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Penn Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jiajun Zhu
- Departments of Cell and Developmental Biology, Genetics, and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Penn Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Adam M Drake
- Departments of Cell and Developmental Biology, Genetics, and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Penn Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Shelley L Berger
- Departments of Cell and Developmental Biology, Genetics, and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Penn Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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4027
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Kratochwil CF, Meyer A. Closing the genotype-phenotype gap: emerging technologies for evolutionary genetics in ecological model vertebrate systems. Bioessays 2014; 37:213-26. [PMID: 25380076 DOI: 10.1002/bies.201400142] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The analysis of genetic and epigenetic mechanisms of the genotype-phenotypic connection has, so far, only been possible in a handful of genetic model systems. Recent technological advances, including next-generation sequencing methods such as RNA-seq, ChIP-seq and RAD-seq, and genome-editing approaches including CRISPR-Cas, now permit to address these fundamental questions of biology also in organisms that have been studied in their natural habitats. We provide an overview of the benefits and drawbacks of these novel techniques and experimental approaches that can now be applied to ecological and evolutionary vertebrate models such as sticklebacks and cichlid fish. We can anticipate that these new methods will increase the understanding of the genetic and epigenetic factors influencing adaptations and phenotypic variation in ecological settings. These new arrows in the methodological quiver of ecologist will drastically increase the understanding of the genetic basis of adaptive traits - leading to a further closing of the genotype-phenotype gap.
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Affiliation(s)
- Claudius F Kratochwil
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany; Zukunftskolleg, University of Konstanz, Konstanz, Germany
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4028
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Greenleaf WJ. Assaying the epigenome in limited numbers of cells. Methods 2014; 72:51-6. [PMID: 25461774 DOI: 10.1016/j.ymeth.2014.10.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/03/2014] [Accepted: 10/09/2014] [Indexed: 12/13/2022] Open
Abstract
Spectacular advances in the throughput of DNA sequencing have allowed genome-wide analysis of epigenetic features such as methylation, nucleosome position and post-translational modification, chromatin accessibility and connectivity, and transcription factor binding. However, for rare or precious biological samples, input requirements of many of these methods limit their application. In this review we discuss recent advances for low-input genome-wide analysis of chromatin immunoprecipitation, methylation, DNA accessibility, and chromatin conformation.
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Affiliation(s)
- William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, United States.
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4029
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Saadeh H, Schulz R. Protection of CpG islands against de novo DNA methylation during oogenesis is associated with the recognition site of E2f1 and E2f2. Epigenetics Chromatin 2014; 7:26. [PMID: 25478011 PMCID: PMC4255709 DOI: 10.1186/1756-8935-7-26] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/19/2014] [Indexed: 01/01/2023] Open
Abstract
Background Epigenetic reprogramming during early mammalian embryonic and germ cell development is a genome-wide process. CpG islands (CGIs), central to the regulation of mammalian gene expression, are exceptional in terms of whether, when and how they are affected by epigenetic reprogramming. Results We investigated the DNA sequences of CGIs in the context of genome-wide data on DNA methylation and transcription during oogenesis and early embryogenesis to identify signals associated with methylation establishment and protection from de novo methylation in oocytes and associated with post-fertilisation methylation maintenance. We find no evidence for a characteristic DNA sequence motif in oocyte-methylated CGIs. Neither do we find evidence for a general role of regular CpG spacing in methylation establishment at CGIs in oocytes. In contrast, the resistance of most CGIs to de novo methylation during oogenesis is associated with the motif CGCGC, the recognition site of E2f1 and E2f2, transcription factors highly expressed specifically in oocytes. This association is independent of prominent known hypomethylation-associated factors: CGI promoter activity, H3K4me3, Cfp1 binding or R-loop formation potential. Conclusions Our results support a DNA sequence-independent and transcription-driven model of de novo CGI methylation during oogenesis. In contrast, our results for CGIs that remain unmethylated are consistent with a model of protection from methylation involving sequence recognition by DNA-binding proteins, E2f1 and E2f2 being probable candidates.
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Affiliation(s)
- Heba Saadeh
- Department of Medical & Molecular Genetics, King's College London, 8th Floor Tower Wing, Guy's Hospital, London SE1 9RT, UK ; Current address: Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Reiner Schulz
- Department of Medical & Molecular Genetics, King's College London, 8th Floor Tower Wing, Guy's Hospital, London SE1 9RT, UK
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4030
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Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res 2014; 24:2041-9. [PMID: 25327137 PMCID: PMC4248320 DOI: 10.1101/gr.178319.114] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We describe a method that exploits contiguity preserving transposase sequencing (CPT-seq) to facilitate the scaffolding of de novo genome assemblies. CPT-seq is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to >1 megabase. These pools are “subhaploid,” in that the lengths of fragments contained in each pool sums to ∼5% to 10% of the full genome. The scaffolding approach described here, termed fragScaff, leverages coincidences between the content of different pools as a source of contiguity information. Specifically, CPT-seq data is mapped to a de novo genome assembly, followed by the identification of pairs of contigs or scaffolds whose ends disproportionately co-occur in the same indexed pools, consistent with true adjacency in the genome. Such candidate “joins” are used to construct a graph, which is then resolved by a minimum spanning tree. As a proof-of-concept, we apply CPT-seq and fragScaff to substantially boost the contiguity of de novo assemblies of the human, mouse, and fly genomes, increasing the scaffold N50 of de novo assemblies by eight- to 57-fold with high accuracy. We also demonstrate that fragScaff is complementary to Hi-C-based contact probability maps, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps. Finally, we demonstrate CPT-seq as a means of anchoring unplaced novel human contigs to the reference genome as well as for detecting misassembled sequences.
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Affiliation(s)
- Andrew Adey
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
| | - Jacob O Kitzman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
| | - Joshua N Burton
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
| | - Riza Daza
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
| | - Akash Kumar
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
| | - Lena Christiansen
- Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA
| | - Mostafa Ronaghi
- Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA
| | - Sasan Amini
- Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA
| | - Kevin L Gunderson
- Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA
| | - Frank J Steemers
- Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA;
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4031
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An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development. PLoS Genet 2014; 10:e1004645. [PMID: 25330008 PMCID: PMC4199491 DOI: 10.1371/journal.pgen.1004645] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/02/2014] [Indexed: 12/15/2022] Open
Abstract
The regulatory logic underlying global transcriptional programs controlling development of visceral organs like the pancreas remains undiscovered. Here, we profiled gene expression in 12 purified populations of fetal and adult pancreatic epithelial cells representing crucial progenitor cell subsets, and their endocrine or exocrine progeny. Using probabilistic models to decode the general programs organizing gene expression, we identified co-expressed gene sets in cell subsets that revealed patterns and processes governing progenitor cell development, lineage specification, and endocrine cell maturation. Purification of Neurog3 mutant cells and module network analysis linked established regulators such as Neurog3 to unrecognized gene targets and roles in pancreas development. Iterative module network analysis nominated and prioritized transcriptional regulators, including diabetes risk genes. Functional validation of a subset of candidate regulators with corresponding mutant mice revealed that the transcription factors Etv1, Prdm16, Runx1t1 and Bcl11a are essential for pancreas development. Our integrated approach provides a unique framework for identifying regulatory genes and functional gene sets underlying pancreas development and associated diseases such as diabetes mellitus. Discovery of specific pancreas developmental regulators has accelerated in recent years. In contrast, the global regulatory programs controlling pancreas development are poorly understood compared to other organs or tissues like heart or blood. Decoding this regulatory logic may accelerate development of replacement organs from renewable sources like stem cells, but this goal requires identification of regulators and assessment of their functions on a global scale. To address this important challenge for pancreas biology, we combined purification of normal and mutant cells with genome-scale methods to generate and analyze expression profiles from developing pancreas cells. Our work revealed regulatory gene sets governing development of pancreas progenitor cells and their progeny. Our integrative approach nominated multiple pancreas developmental regulators, including suspected risk genes for human diabetes, which we validated by phenotyping mutant mice on a scale not previously reported. Selection of these candidate regulators was unbiased; thus it is remarkable that all were essential for pancreatic islet development. Thus, our studies provide a new heuristic resource for identifying genetic functions underlying pancreas development and diseases like diabetes mellitus.
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4032
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Abstract
The widespread adoption of short-read DNA sequencing as a digital epigenomic readout platform has motivated the development of genome-wide tools that achieve base-pair resolution. New methods for footprinting and affinity purification of nucleosomes, RNA polymerases, chromatin remodellers and transcription factors have increased the resolution of epigenomic profiling by two orders of magnitude, leading to new insights into how the chromatin landscape affects gene regulation. These digital epigenomic tools have also been applied to directly profile both turnover kinetics and transcription in situ. In this Review, we describe how these new genome-wide tools allow interrogation of diverse aspects of the epigenome.
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4033
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4034
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Abstract
Enhancers are selectively utilized to orchestrate gene expression programs that first govern pluripotency and then proceed to highly specialized programs required for the process of cellular differentiation. Whereas gene-proximal promoters are typically active across numerous cell types, distal enhancer activation is cell-type-specific and central to cell fate determination, thereby accounting for cell identity. Recent studies have highlighted the diversity of enhancer usage, cataloguing millions of such elements in the human genome. The disruption of enhancer activity, through genetic or epigenetic alterations, can impact cell-type-specific functions, resulting in a wide range of pathologies. In cancer, these alterations can promote a 'cell identity crisis', in which enhancers associated with oncogenes and multipotentiality are activated, while those promoting cell fate commitment are inactivated. Overall, these alterations favor an undifferentiated cellular phenotype. Here, we review the current knowledge regarding the role of enhancers in normal cell function, and discuss how genetic and epigenetic changes in enhancer elements potentiate oncogenesis. In addition, we discuss how understanding the mechanisms regulating enhancer activity can inform therapeutic opportunities in cancer cells and highlight key challenges that remain in understanding enhancer biology as it relates to oncology.
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Affiliation(s)
- Ken J Kron
- The Princess Margaret Cancer Centre - University Health Network, Toronto, ON M5G 1 L7 Canada ; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Swneke D Bailey
- The Princess Margaret Cancer Centre - University Health Network, Toronto, ON M5G 1 L7 Canada ; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Mathieu Lupien
- The Princess Margaret Cancer Centre - University Health Network, Toronto, ON M5G 1 L7 Canada ; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1 L7 Canada ; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3 Canada
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4035
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Meyer CA, Liu XS. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat Rev Genet 2014; 15:709-21. [PMID: 25223782 DOI: 10.1038/nrg3788] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) technologies have been used in diverse ways to investigate various aspects of chromatin biology by identifying genomic loci that are bound by transcription factors, occupied by nucleosomes or accessible to nuclease cleavage, or loci that physically interact with remote genomic loci. However, reaching sound biological conclusions from such NGS enrichment profiles requires many potential biases to be taken into account. In this Review, we discuss common ways in which biases may be introduced into NGS chromatin profiling data, approaches to diagnose these biases and analytical techniques to mitigate their effect.
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Affiliation(s)
- Clifford A Meyer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA; and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA; and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
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4036
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Hyun BR, McElwee JL, Soloway PD. Single molecule and single cell epigenomics. Methods 2014; 72:41-50. [PMID: 25204781 DOI: 10.1016/j.ymeth.2014.08.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 08/19/2014] [Accepted: 08/27/2014] [Indexed: 01/24/2023] Open
Abstract
Dynamically regulated changes in chromatin states are vital for normal development and can produce disease when they go awry. Accordingly, much effort has been devoted to characterizing these states under normal and pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most widely used method to characterize where in the genome transcription factors, modified histones, modified nucleotides and chromatin binding proteins are found; bisulfite sequencing (BS-seq) and its variants are commonly used to characterize the locations of DNA modifications. Though very powerful, these methods are not without limitations. Notably, they are best at characterizing one chromatin feature at a time, yet chromatin features arise and function in combination. Investigators commonly superimpose separate ChIP-seq or BS-seq datasets, and then infer where chromatin features are found together. While these inferences might be correct, they can be misleading when the chromatin source has distinct cell types, or when a given cell type exhibits any cell to cell variation in chromatin state. These ambiguities can be eliminated by robust methods that directly characterize the existence and genomic locations of combinations of chromatin features in very small inputs of cells or ideally, single cells. Here we review single molecule epigenomic methods under development to overcome these limitations, the technical challenges associated with single molecule methods and their potential application to single cells.
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Affiliation(s)
- Byung-Ryool Hyun
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - John L McElwee
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Paul D Soloway
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
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4037
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Cohen RL, Settleman J. From cancer genomics to precision oncology--tissue's still an issue. Cell 2014; 157:1509-14. [PMID: 24949964 DOI: 10.1016/j.cell.2014.05.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/21/2014] [Indexed: 10/25/2022]
Abstract
Rapidly evolving genome technology has enabled extensive molecular analysis of limited tumor biopsy material, thereby facilitating the broader implementation of personalized cancer medicine. However, genomics-based patient stratification across diverse tumor types is unlikely to supplant tissue-of-origin considerations in addressing clinical needs, including the development and application of novel "rationally targeted" cancer therapies.
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Affiliation(s)
- Robert L Cohen
- Calico Life Sciences, Suite 1200, 601 Gateway Boulevard, South San Francisco, CA 94080, USA
| | - Jeff Settleman
- Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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4038
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Shih HY, Sciumè G, Poholek AC, Vahedi G, Hirahara K, Villarino AV, Bonelli M, Bosselut R, Kanno Y, Muljo SA, O'Shea JJ. Transcriptional and epigenetic networks of helper T and innate lymphoid cells. Immunol Rev 2014; 261:23-49. [PMID: 25123275 PMCID: PMC4321863 DOI: 10.1111/imr.12208] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The discovery of the specification of CD4(+) helper T cells to discrete effector 'lineages' represented a watershed event in conceptualizing mechanisms of host defense and immunoregulation. However, our appreciation for the actual complexity of helper T-cell subsets continues unabated. Just as the Sami language of Scandinavia has 1000 different words for reindeer, immunologists recognize the range of fates available for a CD4(+) T cell is numerous and may be underestimated. Added to the crowded scene for helper T-cell subsets is the continuously growing family of innate lymphoid cells (ILCs), endowed with common effector responses and the previously defined 'master regulators' for CD4(+) helper T-cell subsets are also shared by ILC subsets. Within the context of this extraordinary complexity are concomitant advances in the understanding of transcriptomes and epigenomes. So what do terms like 'lineage commitment' and helper T-cell 'specification' mean in the early 21st century? How do we put all of this together in a coherent conceptual framework? It would be arrogant to assume that we have a sophisticated enough understanding to seriously answer these questions. Instead, we review the current status of the flexibility of helper T-cell responses in relation to their genetic regulatory networks and epigenetic landscapes. Recent data have provided major surprises as to what master regulators can or cannot do, how they interact with other transcription factors and impact global genome-wide changes, and how all these factors come together to influence helper cell function.
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Affiliation(s)
- Han-Yu Shih
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
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4039
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Perspective for special Gurdon issue for differentiation: can cell fusion inform nuclear reprogramming? Differentiation 2014; 88:27-28. [PMID: 25150886 DOI: 10.1016/j.diff.2014.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/17/2014] [Accepted: 07/24/2014] [Indexed: 11/24/2022]
Abstract
Nuclear reprogramming was first shown to be possible by Sir John Gurdon over a half century ago. The process has been revolutionized by the production of induced pluripotent cells by overexpression of the four transcription factors discovered by Shinya Yamanaka, which now enables mammalian applications. Yet, reprogramming by a few transcription factors remains incomplete and inefficient, whether to pluripotent or differentiated cells. We propose that a better understanding of mechanistic insights based on developmental principles gained from heterokaryon studies may inform the process of directing cell fate, fundamentally and clinically.
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4040
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Abstract
ENCODE projects exist for many eukaryotes, including humans, but as of yet no defined project exists for plants. A plant ENCODE would be invaluable to the research community and could be more readily produced than its metazoan equivalents by capitalizing on the preexisting infrastructure provided from similar projects. Collecting and normalizing plant epigenomic data for a range of species will facilitate hypothesis generation, cross-species comparisons, annotation of genomes, and an understanding of epigenomic functions throughout plant evolution. Here, we discuss the need for such a project, outline the challenges it faces, and suggest ways forward to build a plant ENCODE.
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Affiliation(s)
- Amanda K Lane
- Department of Genetics, University of Georgia, Athens, Georgia 30602;
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4041
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Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R. Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci 2014; 39:381-99. [PMID: 25129887 DOI: 10.1016/j.tibs.2014.07.002] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/21/2022]
Abstract
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a genome. TFs recognize DNA in a specific manner; the mechanisms underlying this specificity have been identified for many TFs based on 3D structures of protein-DNA complexes. More recently, structural views have been complemented with data from high-throughput in vitro and in vivo explorations of the DNA-binding preferences of many TFs. Together, these approaches have greatly expanded our understanding of TF-DNA interactions. However, the mechanisms by which TFs select in vivo binding sites and alter gene expression remain unclear. Recent work has highlighted the many variables that influence TF-DNA binding, while demonstrating that a biophysical understanding of these many factors will be central to understanding TF function.
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Affiliation(s)
- Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Tianyin Zhou
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Lin Yang
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Ana Carolina Dantas Machado
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Departments of Biostatistics and Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA.
| | - Remo Rohs
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
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4042
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Abstract
Leukemia is a disease that develops as a result of changes in the genomes of hematopoietic cells, a fact first appreciated by microscopic examination of the bone marrow cell chromosomes of affected patients. These studies revealed that specific subtypes of leukemia diagnoses correlated with specific chromosomal abnormalities, such as the t(15;17) of acute promyelocytic leukemia and the t(9;22) of chronic myeloid leukemia. Over time, our genomic characterization of hematologic malignancies has moved beyond the resolution of the microscope to that of individual nucleotides in the analysis of whole-genome sequencing (WGS) data using state-of-the-art massively parallel sequencing (MPS) instruments and algorithmic analyses of the resulting data. In addition to studying the genomic sequence alterations that occur in patients' genomes, these same instruments can decode the methylation landscape of the leukemia genome and the resulting RNA expression landscape of the leukemia transcriptome. Broad correlative analyses can then integrate these 3 data types to better inform researchers and clinicians about the biology of individual acute myeloid leukemia (AML) cases, facilitating improvements in care and prognosis.
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Affiliation(s)
- Elaine R Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, MO.
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4043
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Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I, Jaitin DA, David E, Keren-Shaul H, Mildner A, Winter D, Jung S, Friedman N, Amit I. Immunogenetics. Chromatin state dynamics during blood formation. Science 2014; 345:943-9. [PMID: 25103404 DOI: 10.1126/science.1256271] [Citation(s) in RCA: 574] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chromatin modifications are crucial for development, yet little is known about their dynamics during differentiation. Hematopoiesis provides a well-defined model to study chromatin state dynamics; however, technical limitations impede profiling of homogeneous differentiation intermediates. We developed a high-sensitivity indexing-first chromatin immunoprecipitation approach to profile the dynamics of four chromatin modifications across 16 stages of hematopoietic differentiation. We identify 48,415 enhancer regions and characterize their dynamics. We find that lineage commitment involves de novo establishment of 17,035 lineage-specific enhancers. These enhancer repertoire expansions foreshadow transcriptional programs in differentiated cells. Combining our enhancer catalog with gene expression profiles, we elucidate the transcription factor network controlling chromatin dynamics and lineage specification in hematopoiesis. Together, our results provide a comprehensive model of chromatin dynamics during development.
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Affiliation(s)
- David Lara-Astiaso
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Weiner
- Institute of Life Sciences, The Hebrew University, Jerusalem, Israel. School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
| | | | - Irina Zaretsky
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Mildner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Winter
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Jung
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Friedman
- Institute of Life Sciences, The Hebrew University, Jerusalem, Israel. School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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4044
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Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, Cherry JM, Brunet A. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell 2014; 158:673-88. [PMID: 25083876 PMCID: PMC4137894 DOI: 10.1016/j.cell.2014.06.027] [Citation(s) in RCA: 348] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 04/03/2014] [Accepted: 06/10/2014] [Indexed: 12/15/2022]
Abstract
Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to mark the transcription start sites of active genes. Here, we show that H3K4me3 domains that spread more broadly over genes in a given cell type preferentially mark genes that are essential for the identity and function of that cell type. Using the broadest H3K4me3 domains as a discovery tool in neural progenitor cells, we identify novel regulators of these cells. Machine learning models reveal that the broadest H3K4me3 domains represent a distinct entity, characterized by increased marks of elongation. The broadest H3K4me3 domains also have more paused polymerase at their promoters, suggesting a unique transcriptional output. Indeed, genes marked by the broadest H3K4me3 domains exhibit enhanced transcriptional consistency and [corrected] increased transcriptional levels, and perturbation of H3K4me3 breadth leads to changes in transcriptional consistency. Thus, H3K4me3 breadth contains information that could ensure transcriptional precision at key cell identity/function genes.
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Affiliation(s)
- Bérénice A Benayoun
- Department of Genetics, Stanford University, Stanford CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA
| | - Elizabeth A Pollina
- Department of Genetics, Stanford University, Stanford CA 94305, USA; Cancer Biology Program, Stanford University, Stanford CA 94305, USA
| | - Duygu Ucar
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Salah Mahmoudi
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Edith D Wong
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | | | | | - Anshul B Kundaje
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Elena Mancini
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Benjamin C Hitz
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Rakhi Gupta
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Thomas A Rando
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford CA 94305, USA; RR&D REAP, VA Palo Alto Health Care Systems, Palo Alto, CA 94304,USA
| | - Julie C Baker
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA; Cancer Biology Program, Stanford University, Stanford CA 94305, USA.
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4045
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When genetics meets epigenetics: deciphering the mechanisms controlling inter-individual variation in immune responses to infection. Curr Opin Immunol 2014; 29:119-26. [PMID: 24981784 DOI: 10.1016/j.coi.2014.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/31/2014] [Accepted: 06/04/2014] [Indexed: 11/23/2022]
Abstract
The response of host immune cells to microbial stimuli is dependent on robust and coordinated gene expression programs involving the transcription of thousands of genes. The dysregulation of such regulatory programs is likely to significantly contribute to the marked differences in susceptibility to infectious diseases observed among individuals and between human populations. Although the specific factors leading to a dysfunctional immune response to infection remain largely unknown, we are increasingly appreciating the importance of genetic variants in altering the expression levels of immune-related genes, possibly via epigenetic changes. This review describes how recent technological advances have profoundly contributed to our current understanding of the genetic architecture and the epigenetic rules controlling immune responses to infectious agents and how genetic and epigenetic data can be combined to unravel the mechanisms associated with host variation in transcriptional responses to infection.
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4046
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Abstract
Instructions for when, where and to what level each gene should be expressed are encoded within regulatory sequences. The importance of motifs recognized by DNA-binding regulators has long been known, but their extensive characterization afforded by recent technologies only partly accounts for how regulatory instructions are encoded in the genome. Here, we review recent advances in our understanding of regulatory sequences that influence transcription and go beyond the description of motifs. We discuss how understanding different aspects of the sequence-encoded regulation can help to unravel the genotype-phenotype relationship, which would lead to a more accurate and mechanistic interpretation of personal genome sequences.
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Affiliation(s)
- Michal Levo
- Department of Molecular Cell Biology, and Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Segal
- Department of Molecular Cell Biology, and Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
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4047
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Zhang W, Zhang T, Wu Y, Jiang J. Open Chromatin in Plant Genomes. Cytogenet Genome Res 2014; 143:18-27. [DOI: 10.1159/000362827] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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4048
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Buenrostro JD, Chircus LM, Araya CL, Layton CJ, Chang HY, Snyder MP, Greenleaf WJ. Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nat Biotechnol 2014; 32:562-8. [PMID: 24727714 PMCID: PMC4414031 DOI: 10.1038/nbt.2880] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 03/19/2014] [Indexed: 01/13/2023]
Abstract
RNA-protein interactions drive fundamental biological processes and are targets for molecular engineering, yet quantitative and comprehensive understanding of the sequence determinants of affinity remains limited. Here we repurpose a high-throughput sequencing instrument to quantitatively measure binding and dissociation of a fluorescently labeled protein to >10(7) RNA targets generated on a flow cell surface by in situ transcription and intermolecular tethering of RNA to DNA. Studying the MS2 coat protein, we decompose the binding energy contributions from primary and secondary RNA structure, and observe that differences in affinity are often driven by sequence-specific changes in both association and dissociation rates. By analyzing the biophysical constraints and modeling mutational paths describing the molecular evolution of MS2 from low- to high-affinity hairpins, we quantify widespread molecular epistasis and a long-hypothesized, structure-dependent preference for G:U base pairs over C:A intermediates in evolutionary trajectories. Our results suggest that quantitative analysis of RNA on a massively parallel array (RNA-MaP) provides generalizable insight into the biophysical basis and evolutionary consequences of sequence-function relationships.
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Affiliation(s)
- Jason D. Buenrostro
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren M. Chircus
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carlos L. Araya
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Curtis J. Layton
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y. Chang
- Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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4049
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Paul F, Amit I. Plasticity in the transcriptional and epigenetic circuits regulating dendritic cell lineage specification and function. Curr Opin Immunol 2014; 30:1-8. [PMID: 24820527 DOI: 10.1016/j.coi.2014.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 04/09/2014] [Indexed: 12/23/2022]
Abstract
Dendritic cells (DC) are critical and functionally versatile innate immune sentinels. Here, we coarsely partition the adult DC lineage into three developmental subtypes and argue that pioneer transcription factors and chromatin remodeling are responsible for specification and plasticity between the DC subsets. Subsequently, intricate signaling-dependent transcription factor networks generate different functional states in response to pathogen stimuli within a specified DC subtype. To expand our understanding of lineage heterogeneity and functional activation states, we discuss the use of single cell genomics approaches in the context of a newly emerging systems immunology era, complementing the dichotomous definition of immune cells based solely on their surface marker expression. Rapid developments in single cell genomics are beginning to provide us with robust tools to potentially revise the working models of DC specification and the common hematopoietic tree.
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Affiliation(s)
- Franziska Paul
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
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4050
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Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet 2014; 15:272-86. [PMID: 24614317 DOI: 10.1038/nrg3682] [Citation(s) in RCA: 919] [Impact Index Per Article: 91.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cellular development, morphology and function are governed by precise patterns of gene expression. These are established by the coordinated action of genomic regulatory elements known as enhancers or cis-regulatory modules. More than 30 years after the initial discovery of enhancers, many of their properties have been elucidated; however, despite major efforts, we only have an incomplete picture of enhancers in animal genomes. In this Review, we discuss how properties of enhancer sequences and chromatin are used to predict enhancers in genome-wide studies. We also cover recently developed high-throughput methods that allow the direct testing and identification of enhancers on the basis of their activity. Finally, we discuss recent technological advances and current challenges in the field of regulatory genomics.
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