151
|
Di Giammartino DC, Apostolou E. The Chromatin Signature of Pluripotency: Establishment and Maintenance. CURRENT STEM CELL REPORTS 2016; 2:255-262. [PMID: 27547710 PMCID: PMC4972866 DOI: 10.1007/s40778-016-0055-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The revolutionary discovery that somatic cells can be reprogrammed by a defined set transcription factors to induced pluripotent stem cells (iPSCs) changed dramatically the way we perceive cell fate determination. Importantly, iPSCs, similar to embryo-derived stem cells (ESCs), are characterized by a remarkable developmental plasticity and the capacity to self-renew "indefinitely" under appropriate culture conditions, opening new avenues for personalized therapy and disease modeling. Elucidating the molecular mechanisms that maintain, induce, or alter stem cell identity is crucial for a deeper understanding of cell fate determination and potential translational applications. Intense research over the last 10 years exploiting technological advances in epigenomics and genome editing has unraveled many of the mysteries of pluripotent identity enabling novel and efficient ways to manipulate it for biomedical purposes. In this review, we focus on the chromatin and epigenetic characteristics that distinguish stem cells from somatic cells and their dynamic changes during differentiation and reprogramming.
Collapse
Affiliation(s)
- Dafne Campigli Di Giammartino
- Weill Cornell Medicine, Division of Hematology and Medical Oncology, Sandra and Edward Meyer Cancer Center, 413E 69th Street, Belfer research Building, New York, NY 10021 USA
| | - Effie Apostolou
- Weill Cornell Medicine, Division of Hematology and Medical Oncology, Sandra and Edward Meyer Cancer Center, 413E 69th Street, Belfer research Building, New York, NY 10021 USA
| |
Collapse
|
152
|
QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. PLoS Comput Biol 2016; 12:e1004809. [PMID: 27336171 PMCID: PMC4919057 DOI: 10.1371/journal.pcbi.1004809] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/12/2016] [Indexed: 01/30/2023] Open
Abstract
Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.
Collapse
|
153
|
Wöhner M, Tagoh H, Bilic I, Jaritz M, Poliakova DK, Fischer M, Busslinger M. Molecular functions of the transcription factors E2A and E2-2 in controlling germinal center B cell and plasma cell development. J Exp Med 2016; 213:1201-21. [PMID: 27261530 PMCID: PMC4925024 DOI: 10.1084/jem.20152002] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/04/2016] [Indexed: 12/18/2022] Open
Abstract
Busslinger et al. showed that the transcription factors E2A and E2-2 control the expression of genes required for the development of GC B cells and plasma cells. E2A is an essential regulator of early B cell development. Here, we have demonstrated that E2A together with E2-2 controlled germinal center (GC) B cell and plasma cell development. As shown by the identification of regulated E2A,E2-2 target genes in activated B cells, these E-proteins directly activated genes with important functions in GC B cells and plasma cells by inducing and maintaining DNase I hypersensitive sites. Through binding to multiple enhancers in the Igh 3′ regulatory region and Aicda locus, E-proteins regulated class switch recombination by inducing both Igh germline transcription and AID expression. By regulating 3′ Igk and Igh enhancers and a distal element at the Prdm1 (Blimp1) locus, E-proteins contributed to Igk, Igh, and Prdm1 activation in plasmablasts. Together, these data identified E2A and E2-2 as central regulators of B cell immunity.
Collapse
Affiliation(s)
- Miriam Wöhner
- Research Institute of Molecular Pathology, Vienna Biocenter, A-1030 Vienna, Austria
| | - Hiromi Tagoh
- Research Institute of Molecular Pathology, Vienna Biocenter, A-1030 Vienna, Austria
| | - Ivan Bilic
- Research Institute of Molecular Pathology, Vienna Biocenter, A-1030 Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology, Vienna Biocenter, A-1030 Vienna, Austria
| | | | - Maria Fischer
- Research Institute of Molecular Pathology, Vienna Biocenter, A-1030 Vienna, Austria
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology, Vienna Biocenter, A-1030 Vienna, Austria
| |
Collapse
|
154
|
Kalchschmidt JS, Bashford-Rogers R, Paschos K, Gillman ACT, Styles CT, Kellam P, Allday MJ. Epstein-Barr virus nuclear protein EBNA3C directly induces expression of AID and somatic mutations in B cells. J Exp Med 2016; 213:921-8. [PMID: 27217538 PMCID: PMC4886369 DOI: 10.1084/jem.20160120] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/12/2016] [Indexed: 12/13/2022] Open
Abstract
Allday and collaborators demonstrate that the EBV transcription factor and oncoprotein EBNA3C directly induces the expression of AID and somatic mutations in B cells, providing a mechanism linking infection and lymphoma induction. Activation-induced cytidine deaminase (AID), the enzyme responsible for induction of sequence variation in immunoglobulins (Igs) during the process of somatic hypermutation (SHM) and also Ig class switching, can have a potent mutator phenotype in the development of lymphoma. Using various Epstein-Barr virus (EBV) recombinants, we provide definitive evidence that the viral nuclear protein EBNA3C is essential in EBV-infected primary B cells for the induction of AID mRNA and protein. Using lymphoblastoid cell lines (LCLs) established with EBV recombinants conditional for EBNA3C function, this was confirmed, and it was shown that transactivation of the AID gene (AICDA) is associated with EBNA3C binding to highly conserved regulatory elements located proximal to and upstream of the AICDA transcription start site. EBNA3C binding initiated epigenetic changes to chromatin at specific sites across the AICDA locus. Deep sequencing of cDNA corresponding to the IgH V-D-J region from the conditional LCL was used to formally show that SHM is activated by functional EBNA3C and induction of AID. These data, showing the direct targeting and induction of functional AID by EBNA3C, suggest a novel role for EBV in the etiology of B cell cancers, including endemic Burkitt lymphoma.
Collapse
Affiliation(s)
- Jens S Kalchschmidt
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, England, UK
| | | | - Kostas Paschos
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, England, UK
| | - Adam C T Gillman
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, England, UK
| | - Christine T Styles
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, England, UK
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, England, UK
| | - Martin J Allday
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, England, UK
| |
Collapse
|
155
|
Engel KL, Mackiewicz M, Hardigan AA, Myers RM, Savic D. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. Semin Cell Dev Biol 2016; 57:40-50. [PMID: 27224938 DOI: 10.1016/j.semcdb.2016.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/06/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022]
Abstract
Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research.
Collapse
Affiliation(s)
- Krysta L Engel
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States.
| |
Collapse
|
156
|
Liu T, Zhang J, Zhou T. Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression. PLoS Comput Biol 2016; 12:e1004917. [PMID: 27153118 PMCID: PMC4859557 DOI: 10.1371/journal.pcbi.1004917] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/14/2016] [Indexed: 01/09/2023] Open
Abstract
According to recent experimental evidence, the interaction between chromatin loops, which can be characterized by three factors-connection pattern, distance between regulatory elements, and communication form, play an important role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effect that addresses the question of how changes in these factors affect variability at the expression level in a systematic rather than case-by-case fashion. Here we make such an effort, based on a mechanic model that maps three fundamental patterns for two interacting DNA loops into a 4-state model of stochastic transcription. We first show that in contrast to side-by-side loops, nested loops enhance mRNA expression and reduce expression noise whereas alternating loops have just opposite effects. Then, we compare effects of facilitated tracking and direct looping on gene expression. We find that the former performs better than the latter in controlling mean expression and in tuning expression noise, but this control or tuning is distance-dependent, remarkable for moderate loop lengths, and there is a limit loop length such that the difference in effect between two communication forms almost disappears. Our analysis and results justify the facilitated chromatin-looping hypothesis.
Collapse
Affiliation(s)
- Tuoqi Liu
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jiajun Zhang
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Tianshou Zhou
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| |
Collapse
|
157
|
Becker PW, Sacilotto N, Nornes S, Neal A, Thomas MO, Liu K, Preece C, Ratnayaka I, Davies B, Bou-Gharios G, De Val S. An Intronic Flk1 Enhancer Directs Arterial-Specific Expression via RBPJ-Mediated Venous Repression. Arterioscler Thromb Vasc Biol 2016; 36:1209-19. [PMID: 27079877 PMCID: PMC4894770 DOI: 10.1161/atvbaha.116.307517] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 03/28/2016] [Indexed: 01/02/2023]
Abstract
Supplemental Digital Content is available in the text. Objective— The vascular endothelial growth factor (VEGF) receptor Flk1 is essential for vascular development, but the signaling and transcriptional pathways by which its expression is regulated in endothelial cells remain unclear. Although previous studies have identified 2 Flk1 regulatory enhancers, these are dispensable for Flk1 expression, indicating that additional enhancers contribute to Flk1 regulation in endothelial cells. In the present study, we sought to identify Flk1 enhancers contributing to expression in endothelial cells. Approach and Results— A region of the 10th intron of the Flk1 gene (Flk1in10) was identified as a putative enhancer and tested in mouse and zebrafish transgenic models. This region robustly directed reporter gene expression in arterial endothelial cells. Using a combination of targeted mutagenesis of transcription factor–binding sites and gene silencing of transcription factors, we found that Gata and Ets factors are required for Flk1in10 enhancer activity in all endothelial cells. Furthermore, we showed that activity of the Flk1in10 enhancer is restricted to arteries through repression of gene expression in venous endothelial cells by the Notch pathway transcriptional regulator Rbpj. Conclusions— This study demonstrates a novel mechanism of arterial–venous identity acquisition, indicates a direct link between the Notch and VEGF signaling pathways, and illustrates how cis-regulatory diversity permits differential expression outcomes from a limited repertoire of transcriptional regulators.
Collapse
Affiliation(s)
- Philipp W Becker
- From the Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine (P.W.B., N.S., S.N., A.N., M.O.T., I.R., S.D.V.) and The Wellcome Trust Centre for Human Genetics (C.P., B.D.), University of Oxford, Oxford, United Kingdom; and Institute of Ageing and Chronic Disease, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom (K.L., G.B.-G.)
| | - Natalia Sacilotto
- From the Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine (P.W.B., N.S., S.N., A.N., M.O.T., I.R., S.D.V.) and The Wellcome Trust Centre for Human Genetics (C.P., B.D.), University of Oxford, Oxford, United Kingdom; and Institute of Ageing and Chronic Disease, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom (K.L., G.B.-G.)
| | - Svanhild Nornes
- From the Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine (P.W.B., N.S., S.N., A.N., M.O.T., I.R., S.D.V.) and The Wellcome Trust Centre for Human Genetics (C.P., B.D.), University of Oxford, Oxford, United Kingdom; and Institute of Ageing and Chronic Disease, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom (K.L., G.B.-G.)
| | - Alice Neal
- From the Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine (P.W.B., N.S., S.N., A.N., M.O.T., I.R., S.D.V.) and The Wellcome Trust Centre for Human Genetics (C.P., B.D.), University of Oxford, Oxford, United Kingdom; and Institute of Ageing and Chronic Disease, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom (K.L., G.B.-G.)
| | - Max O Thomas
- From the Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine (P.W.B., N.S., S.N., A.N., M.O.T., I.R., S.D.V.) and The Wellcome Trust Centre for Human Genetics (C.P., B.D.), University of Oxford, Oxford, United Kingdom; and Institute of Ageing and Chronic Disease, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom (K.L., G.B.-G.)
| | - Ke Liu
- From the Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine (P.W.B., N.S., S.N., A.N., M.O.T., I.R., S.D.V.) and The Wellcome Trust Centre for Human Genetics (C.P., B.D.), University of Oxford, Oxford, United Kingdom; and Institute of Ageing and Chronic Disease, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom (K.L., G.B.-G.)
| | - Chris Preece
- From the Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine (P.W.B., N.S., S.N., A.N., M.O.T., I.R., S.D.V.) and The Wellcome Trust Centre for Human Genetics (C.P., B.D.), University of Oxford, Oxford, United Kingdom; and Institute of Ageing and Chronic Disease, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom (K.L., G.B.-G.)
| | - Indrika Ratnayaka
- From the Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine (P.W.B., N.S., S.N., A.N., M.O.T., I.R., S.D.V.) and The Wellcome Trust Centre for Human Genetics (C.P., B.D.), University of Oxford, Oxford, United Kingdom; and Institute of Ageing and Chronic Disease, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom (K.L., G.B.-G.)
| | - Benjamin Davies
- From the Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine (P.W.B., N.S., S.N., A.N., M.O.T., I.R., S.D.V.) and The Wellcome Trust Centre for Human Genetics (C.P., B.D.), University of Oxford, Oxford, United Kingdom; and Institute of Ageing and Chronic Disease, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom (K.L., G.B.-G.)
| | - George Bou-Gharios
- From the Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine (P.W.B., N.S., S.N., A.N., M.O.T., I.R., S.D.V.) and The Wellcome Trust Centre for Human Genetics (C.P., B.D.), University of Oxford, Oxford, United Kingdom; and Institute of Ageing and Chronic Disease, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom (K.L., G.B.-G.)
| | - Sarah De Val
- From the Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine (P.W.B., N.S., S.N., A.N., M.O.T., I.R., S.D.V.) and The Wellcome Trust Centre for Human Genetics (C.P., B.D.), University of Oxford, Oxford, United Kingdom; and Institute of Ageing and Chronic Disease, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom (K.L., G.B.-G.).
| |
Collapse
|
158
|
Chen Y, Wang Y, Xuan Z, Chen M, Zhang MQ. De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles. Nucleic Acids Res 2016; 44:e106. [PMID: 27060148 PMCID: PMC4914103 DOI: 10.1093/nar/gkw225] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/22/2016] [Indexed: 12/30/2022] Open
Abstract
Defining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been developed for exploring the global interactome, they are limited by high experimental complexity and costs. Here we describe a novel computational method, called CITD, for de novo prediction of the chromatin interaction map by integrating histone modification data. We used the public epigenomic data from human fibroblast IMR90 cell and embryonic stem cell (H1) to develop and test CITD, which can not only successfully reconstruct the chromatin interaction frequencies discovered by the Hi-C technology, but also provide additional novel details of chromosomal organizations. We predicted the chromatin interaction frequencies, topological domains and their states (e.g. active or repressive) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects. A total of 131 protein-coding genes located near 78 preserved boundaries among 100 cell types are found to be significantly enriched in functional categories of the nucleosome organization and chromatin assembly. CITD and its predicted results can be used for complementing the topological domains derived from limited Hi-C data and facilitating the understanding of spatial principles underlying the chromosomal organization.
Collapse
Affiliation(s)
- Yong Chen
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Yunfei Wang
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Min Chen
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Michael Q Zhang
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department Automation, Tsinghua University, Beijing 100084, China
| |
Collapse
|
159
|
Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, Dekker J, Young RA. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science 2016; 351:1454-1458. [PMID: 26940867 PMCID: PMC4884612 DOI: 10.1126/science.aad9024] [Citation(s) in RCA: 660] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/18/2016] [Indexed: 12/17/2022]
Abstract
Oncogenes are activated through well-known chromosomal alterations such as gene fusion, translocation, and focal amplification. In light of recent evidence that the control of key genes depends on chromosome structures called insulated neighborhoods, we investigated whether proto-oncogenes occur within these structures and whether oncogene activation can occur via disruption of insulated neighborhood boundaries in cancer cells. We mapped insulated neighborhoods in T cell acute lymphoblastic leukemia (T-ALL) and found that tumor cell genomes contain recurrent microdeletions that eliminate the boundary sites of insulated neighborhoods containing prominent T-ALL proto-oncogenes. Perturbation of such boundaries in nonmalignant cells was sufficient to activate proto-oncogenes. Mutations affecting chromosome neighborhood boundaries were found in many types of cancer. Thus, oncogene activation can occur via genetic alterations that disrupt insulated neighborhoods in malignant cells.
Collapse
Affiliation(s)
- Denes Hnisz
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Abraham S. Weintraub
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Daniel S. Day
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Anne-Laure Valton
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Rasmus O. Bak
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Charles H. Li
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Johanna Goldmann
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Bryan R. Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Zi Peng Fan
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alla A. Sigova
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Jessica Reddy
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Diego Borges-Rivera
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew H. Porteus
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
- Howard Hughes Medical Institute
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| |
Collapse
|
160
|
Solovei I, Thanisch K, Feodorova Y. How to rule the nucleus: divide et impera. Curr Opin Cell Biol 2016; 40:47-59. [PMID: 26938331 DOI: 10.1016/j.ceb.2016.02.014] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/04/2016] [Accepted: 02/14/2016] [Indexed: 01/14/2023]
Abstract
Genome-wide molecular studies have provided new insights into the organization of nuclear chromatin by revealing the presence of chromatin domains of differing transcriptional activity, frequency of cis-interactions, proximity to scaffolding structures and replication timing. These studies have not only brought our understanding of genome function to a new level, but also offered functional insight for many phenomena observed in microscopic studies. In this review, we discuss the major principles of nuclear organization based on the spatial segregation of euchromatin and heterochromatin, as well as the dynamic genome rearrangements occurring during cell differentiation and development. We hope to unite the existing molecular and microscopic data on genome organization to get a holistic view of the nucleus, and propose a model, in which repeat repertoire together with scaffolding structures blueprint the functional nuclear architecture.
Collapse
Affiliation(s)
- Irina Solovei
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany.
| | - Katharina Thanisch
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany
| | - Yana Feodorova
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany; Department of Medical Biology, Medical University-Plovdiv, Boulevard Vasil Aprilov 15A, Plovdiv 4000, Bulgaria
| |
Collapse
|
161
|
Mutations, kataegis and translocations in B cells: understanding AID promiscuous activity. Nat Rev Immunol 2016; 16:164-76. [PMID: 26898111 DOI: 10.1038/nri.2016.2] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
As B cells engage in the immune response, they express activation-induced cytidine deaminase (AID) to initiate the hypermutation and recombination of immunoglobulin genes, which are crucial processes for the efficient recognition and disposal of pathogens. However, AID must be tightly controlled in B cells to minimize off-target mutations, which can drive chromosomal translocations and the development of B cell malignancies, such as lymphomas. Recent genomic and biochemical analyses have begun to unravel the mechanisms of how AID-mediated deamination is targeted outside immunoglobulin genes. Here, we discuss the transcriptional and topological features that are emerging as key drivers of AID promiscuous activity.
Collapse
|
162
|
Aran D, Abu-Remaileh M, Levy R, Meron N, Toperoff G, Edrei Y, Bergman Y, Hellman A. Embryonic Stem Cell (ES)-Specific Enhancers Specify the Expression Potential of ES Genes in Cancer. PLoS Genet 2016; 12:e1005840. [PMID: 26886256 PMCID: PMC4757527 DOI: 10.1371/journal.pgen.1005840] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 01/12/2016] [Indexed: 11/18/2022] Open
Abstract
Cancers often display gene expression profiles resembling those of undifferentiated cells. The mechanisms controlling these expression programs have yet to be identified. Exploring transcriptional enhancers throughout hematopoietic cell development and derived cancers, we uncovered a novel class of regulatory epigenetic mutations. These epimutations are particularly enriched in a group of enhancers, designated ES-specific enhancers (ESSEs) of the hematopoietic cell lineage. We found that hematopoietic ESSEs are prone to DNA methylation changes, indicative of their chromatin activity states. Strikingly, ESSE methylation is associated with gene transcriptional activity in cancer. Methylated ESSEs are hypermethylated in cancer relative to normal somatic cells and co-localized with silenced genes, whereas unmethylated ESSEs tend to be hypomethylated in cancer and associated with reactivated genes. Constitutive or hematopoietic stem cell-specific enhancers do not show these trends, suggesting selective reactivation of ESSEs in cancer. Further analyses of a hypomethylated ESSE downstream to the VEGFA gene revealed a novel regulatory circuit affecting VEGFA transcript levels across cancers and patients. We suggest that the discovered enhancer sites provide a framework for reactivation of ES genes in cancer.
Collapse
Affiliation(s)
- Dvir Aran
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- Institute for Computational Health Sciences, University of California, San Francisco, California, United States of America
| | - Monther Abu-Remaileh
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Revital Levy
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Nurit Meron
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Gidon Toperoff
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yifat Edrei
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yehudit Bergman
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail: (YB); (AH)
| | - Asaf Hellman
- Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail: (YB); (AH)
| |
Collapse
|
163
|
Stavreva DA, Hager GL. Chromatin structure and gene regulation: a dynamic view of enhancer function. Nucleus 2016; 6:442-8. [PMID: 26765055 DOI: 10.1080/19491034.2015.1107689] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Localized chromatin organization is now recognized as an important determinant of cell identity and developmental pathways. Recent studies have demonstrated that these epigenetic states are unexpectedly dynamic and malleable. In this Extra view we will highlight the transient nature of stimulus-induced enhancer accessibility and its importance for transcription regulation. Using glucocorticoid receptor (GR) as a model system we will discuss spatiotemporal relationships between receptor/chromatin interactions, lifetimes of the DNase I hypersensitivity sites (DHSs), long-range interactions, and gene regulation. We propose that differential temporal activation and utilization of distal regulatory elements plays a role in directing divergent stimulus-induced transcriptional programs.
Collapse
Affiliation(s)
- Diana A Stavreva
- a Laboratory of Receptor Biology and Gene Expression; National Cancer Institute; National Institutes of Health ; Bethesda , MD USA
| | - Gordon L Hager
- a Laboratory of Receptor Biology and Gene Expression; National Cancer Institute; National Institutes of Health ; Bethesda , MD USA
| |
Collapse
|
164
|
Abstract
Mammals have at least 210 histologically diverse cell types (Alberts, Molecular biology of the cell. Garland Science, New York, 2008) and the number would be even higher if functional differences are taken into account. The genome in each of these cell types is differentially programmed to express the specific set of genes needed to fulfill the phenotypical requirements of the cell. Furthermore, in each of these cell types, the gene program can be differentially modulated by exposure to external signals such as hormones or nutrients. The basis for the distinct gene programs relies on cell type-selective activation of transcriptional enhancers, which in turn are particularly sensitive to modulation. Until recently we had only fragmented insight into the regulation of a few of these enhancers; however, the recent advances in high-throughput sequencing technologies have enabled the development of a large number of technologies that can be used to obtain genome-wide insight into how genomes are reprogrammed during development and in response to specific external signals. By applying such technologies, we have begun to reveal the cross-talk between metabolism and the genome, i.e., how genomes are reprogrammed in response to metabolites, and how the regulation of metabolic networks is coordinated at the genomic level.
Collapse
Affiliation(s)
- Alexander Rauch
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark.
| |
Collapse
|
165
|
Sander S, Chu VT, Yasuda T, Franklin A, Graf R, Calado DP, Li S, Imami K, Selbach M, Di Virgilio M, Bullinger L, Rajewsky K. PI3 Kinase and FOXO1 Transcription Factor Activity Differentially Control B Cells in the Germinal Center Light and Dark Zones. Immunity 2015; 43:1075-86. [PMID: 26620760 DOI: 10.1016/j.immuni.2015.10.021] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/28/2015] [Accepted: 10/28/2015] [Indexed: 12/17/2022]
Abstract
Phosphatidylinositol 3' OH kinase (PI3K) signaling and FOXO transcription factors play opposing roles at several B cell developmental stages. We show here abundant nuclear FOXO1 expression in the proliferative compartment of the germinal center (GC), its dark zone (DZ), and PI3K activity, downregulating FOXO1, in the light zone (LZ), where cells are selected for further differentiation. In the LZ, however, FOXO1 was expressed in a fraction of cells destined for DZ reentry. Upon FOXO1 ablation or induction of PI3K activity, GCs lost their DZ, owing at least partly to downregulation of the chemokine receptor CXCR4. Although this prevented proper cyclic selection of cells in GCs, somatic hypermutation and proliferation were maintained. Class switch recombination was partly lost due to a failure of switch region targeting by activation-induced deaminase (AID).
Collapse
Affiliation(s)
- Sandrine Sander
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany.
| | - Van Trung Chu
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Tomoharu Yasuda
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Andrew Franklin
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Robin Graf
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Dinis Pedro Calado
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany; Cancer Research UK, London Research Institute, London WC2A 3LY, UK; Peter Gorer Department of Immunobiology, Kings College London, London SE1 9RT, UK
| | - Shuang Li
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Koshi Imami
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Michela Di Virgilio
- DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany
| | - Lars Bullinger
- Department of Internal Medicine III, University Hospital Ulm, Ulm 89081, Germany
| | - Klaus Rajewsky
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Alliance, Berlin-Buch 13125, Germany.
| |
Collapse
|
166
|
Matharu N, Ahituv N. Minor Loops in Major Folds: Enhancer-Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease. PLoS Genet 2015; 11:e1005640. [PMID: 26632825 PMCID: PMC4669122 DOI: 10.1371/journal.pgen.1005640] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The organization and folding of chromatin within the nucleus can determine the outcome of gene expression. Recent technological advancements have enabled us to study chromatin interactions in a genome-wide manner at high resolution. These studies have increased our understanding of the hierarchy and dynamics of chromatin domains that facilitate cognate enhancer–promoter looping, defining the transcriptional program of different cell types. In this review, we focus on vertebrate chromatin long-range interactions as they relate to transcriptional regulation. In addition, we describe how the alteration of boundaries that mark discrete regions in the genome with high interaction frequencies within them, called topological associated domains (TADs), could lead to various phenotypes, including human diseases, which we term as “TADopathies.”
Collapse
Affiliation(s)
- Navneet Matharu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
167
|
The FOXO1 Transcription Factor Instructs the Germinal Center Dark Zone Program. Immunity 2015; 43:1064-74. [PMID: 26620759 DOI: 10.1016/j.immuni.2015.10.015] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/30/2015] [Accepted: 10/22/2015] [Indexed: 12/18/2022]
Abstract
The pathways regulating formation of the germinal center (GC) dark zone (DZ) and light zone (LZ) are unknown. In this study we show that FOXO1 transcription factor expression was restricted to the GC DZ and was required for DZ formation, since its absence in mice led to the loss of DZ gene programs and the formation of LZ-only GCs. FOXO1-negative GC B cells displayed normal somatic hypermutation but defective affinity maturation and class switch recombination. The function of FOXO1 in sustaining the DZ program involved the trans-activation of the chemokine receptor CXCR4, and cooperation with the BCL6 transcription factor in the trans-repression of genes involved in immune activation, DNA repair, and plasma cell differentiation. These results also have implications for the role of FOXO1 in lymphomagenesis because they suggest that constitutive FOXO1 activity might be required for the oncogenic activity of deregulated BCL6 expression.
Collapse
|
168
|
Remeseiro S, Hörnblad A, Spitz F. Gene regulation during development in the light of topologically associating domains. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:169-85. [PMID: 26558551 DOI: 10.1002/wdev.218] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 08/31/2015] [Accepted: 09/15/2015] [Indexed: 01/20/2023]
Abstract
During embryonic development, complex transcriptional programs govern the precision of gene expression. Many key developmental genes are regulated via cis-regulatory elements that are located far away in the linear genome. How sequences located hundreds of kilobases away from a promoter can influence its activity has been the subject of numerous speculations, which all underline the importance of the 3D-organization of the genome. The recent advent of chromosome conformation capture techniques has put into focus the subdivision of the genome into topologically associating domains (TADs). TADs may influence regulatory activities on multiple levels. The relative invariance of TAD limits across cell types suggests that they may form fixed structural domains that could facilitate and/or confine long-range regulatory interactions. However, most recent studies suggest that interactions within TADs are more variable and dynamic than initially described. Hence, different models are emerging regarding how TADs shape the complex 3D conformations, and thereafter influence the networks of cis-interactions that govern gene expression during development. For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Silvia Remeseiro
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Hörnblad
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| |
Collapse
|
169
|
Witte S, Bradley A, Enright AJ, Muljo SA. High-density P300 enhancers control cell state transitions. BMC Genomics 2015; 16:903. [PMID: 26546038 PMCID: PMC4636788 DOI: 10.1186/s12864-015-1905-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/08/2015] [Indexed: 12/11/2022] Open
Abstract
Background Transcriptional enhancers are frequently bound by a set of transcription factors that collaborate to activate lineage-specific gene expression. Recently, it was appreciated that a subset of enhancers comprise extended clusters dubbed stretch- or super-enhancers (SEs). These SEs are located near key cell identity genes, and enriched for non-coding genetic variations associated with disease. Previously, SEs have been defined as having the highest density of Med1, Brd4 or H3K27ac by ChIP-seq. The histone acetyltransferase P300 has been used as a marker of enhancers, but little is known about its binding to SEs. Results We establish that P300 marks a similar SE repertoire in embryonic stem cells as previously reported using Med1 and H3K27ac. We also exemplify a role for SEs in mouse T helper cell fate decision. Similarly, upon activation of macrophages by bacterial endotoxin, we found that many SE-associated genes encode inflammatory proteins that are strongly up-regulated. These SEs arise from small, low-density enhancers in unstimulated macrophages. We also identified expression quantitative trait loci (eQTL) in human monocytes that lie within such SEs. In macrophages and Th17 cells, inflammatory SEs can be perturbed either genetically or pharmacologically thus revealing new avenues to target inflammation. Conclusions Our findings support the notion that P300-marked SEs can help identify key nodes of transcriptional control during cell fate decisions. The SE landscape changes drastically during cell differentiation and cell activation. As these processes are crucial in immune responses, SEs may be useful in revealing novel targets for treating inflammatory diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1905-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Steven Witte
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. .,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Allan Bradley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Anton J Enright
- EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Stefan A Muljo
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
170
|
Bortnick A, Murre C. Cellular and chromatin dynamics of antibody-secreting plasma cells. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:136-49. [PMID: 26488117 DOI: 10.1002/wdev.213] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/10/2015] [Accepted: 08/15/2015] [Indexed: 12/12/2022]
Abstract
Plasma cells are terminally differentiated B cells responsible for maintaining protective serum antibody titers. Despite their clinical importance, our understanding of the linear genomic features and chromatin structure of plasma cells is incomplete. The plasma cell differentiation program can be triggered by different signals and in multiple, diverse peripheral B cell subsets. This heterogeneity raises questions about the gene regulatory circuits required for plasma cell specification. Recently, new regulators of plasma cell differentiation have been identified and the enhancer landscapes of naïve B cells have been described. Other studies have revealed that the bone marrow niche harbors heterogeneous plasma cell subsets. Still undefined are the minimal requirements to become a plasma cell and what molecular features make peripheral B cell subsets competent to become antibody-secreting plasma cells. New technologies promise to reveal underlying chromatin configurations that promote efficient antibody secretion. For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Alexandra Bortnick
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Cornelis Murre
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| |
Collapse
|
171
|
Douglas AT, Hill RD. Variation in vertebrate cis-regulatory elements in evolution and disease. Transcription 2015; 5:e28848. [PMID: 25764334 DOI: 10.4161/trns.28848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Much of the genetic information that drives animal diversity lies within the vast non-coding regions of the genome. Multi-species sequence conservation in non-coding regions of the genome flags important regulatory elements and more recently, techniques that look for functional signatures predicted for regulatory sequences have added to the identification of thousands more. For some time, biologists have argued that changes in cis-regulatory sequences creates the basic genetic framework for evolutionary change. Recent advances support this notion and show that there is extensive genomic variability in non-coding regulatory elements associated with trait variation, speciation and disease.
Collapse
Affiliation(s)
- Adam Thomas Douglas
- a MRC Human Genetics Unit; MRC Institute of Genetics and Molecular Medicine; University of Edinburgh; Edinburgh, UK
| | | |
Collapse
|
172
|
Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol 2015; 50:550-73. [PMID: 26446758 PMCID: PMC4666684 DOI: 10.3109/10409238.2015.1087961] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Enhancers are short regulatory sequences bound by sequence-specific transcription factors and play a major role in the spatiotemporal specificity of gene expression patterns in development and disease. While it is now possible to identify enhancer regions genomewide in both cultured cells and primary tissues using epigenomic approaches, it has been more challenging to develop methods to understand the function of individual enhancers because enhancers are located far from the gene(s) that they regulate. However, it is essential to identify target genes of enhancers not only so that we can understand the role of enhancers in disease but also because this information will assist in the development of future therapeutic options. After reviewing models of enhancer function, we discuss recent methods for identifying target genes of enhancers. First, we describe chromatin structure-based approaches for directly mapping interactions between enhancers and promoters. Second, we describe the use of correlation-based approaches to link enhancer state with the activity of nearby promoters and/or gene expression. Third, we describe how to test the function of specific enhancers experimentally by perturbing enhancer–target relationships using high-throughput reporter assays and genome editing. Finally, we conclude by discussing as yet unanswered questions concerning how enhancers function, how target genes can be identified, and how to distinguish direct from indirect changes in gene expression mediated by individual enhancers.
Collapse
Affiliation(s)
- Lijing Yao
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
| | - Benjamin P Berman
- b Department of Biomedical Sciences , Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Peggy J Farnham
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
| |
Collapse
|
173
|
Lee BK, Shen W, Lee J, Rhee C, Chung H, Kim KY, Park IH, Kim J. Tgif1 Counterbalances the Activity of Core Pluripotency Factors in Mouse Embryonic Stem Cells. Cell Rep 2015; 13:52-60. [PMID: 26411691 DOI: 10.1016/j.celrep.2015.08.067] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/24/2015] [Accepted: 08/24/2015] [Indexed: 11/16/2022] Open
Abstract
Core pluripotency factors, such as Oct4, Sox2, and Nanog, play important roles in maintaining embryonic stem cell (ESC) identity by autoregulatory feedforward loops. Nevertheless, the mechanism that provides precise control of the levels of the ESC core factors without indefinite amplification has remained elusive. Here, we report the direct repression of core pluripotency factors by Tgif1, a previously known terminal repressor of TGFβ/activin/nodal signaling. Overexpression of Tgif1 reduces the levels of ESC core factors, whereas its depletion leads to the induction of the pluripotency factors. We confirm the existence of physical associations between Tgif1 and Oct4, Nanog, and HDAC1/2 and further show the level of Tgif1 is not significantly altered by treatment with an activator/inhibitor of the TGFβ/activin/nodal signaling. Collectively, our findings establish Tgif1 as an integral member of the core regulatory circuitry of mouse ESCs that counterbalances the levels of the core pluripotency factors in a TGFβ/activin/nodal-independent manner.
Collapse
Affiliation(s)
- Bum-Kyu Lee
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Wenwen Shen
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA
| | - Jiwoon Lee
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Catherine Rhee
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Haewon Chung
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
174
|
González AJ, Setty M, Leslie CS. Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation. Nat Genet 2015; 47:1249-59. [PMID: 26390058 PMCID: PMC4626279 DOI: 10.1038/ng.3402] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 08/19/2015] [Indexed: 12/23/2022]
Abstract
We carried out an integrative analysis of enhancer landscape and gene expression dynamics during hematopoietic differentiation using DNase-seq, histone mark ChIP-seq and RNA sequencing to model how the early establishment of enhancers and regulatory locus complexity govern gene expression changes at cell state transitions. We found that high-complexity genes-those with a large total number of DNase-mapped enhancers across the lineage-differ architecturally and functionally from low-complexity genes, achieve larger expression changes and are enriched for both cell type-specific and transition enhancers, which are established in hematopoietic stem and progenitor cells and maintained in one differentiated cell fate but lost in others. We then developed a quantitative model to accurately predict gene expression changes from the DNA sequence content and lineage history of active enhancers. Our method suggests a new mechanistic role for PU.1 at transition peaks during B cell specification and can be used to correct assignments of enhancers to genes.
Collapse
Affiliation(s)
- Alvaro J González
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Manu Setty
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
175
|
Bartman CR, Blobel GA. Perturbing Chromatin Structure to Understand Mechanisms of Gene Expression. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:207-12. [PMID: 26370411 DOI: 10.1101/sqb.2015.80.027359] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The study of nuclear structure falls between the fields of cell biology and molecular biology and draws on techniques from both fields. In recent years, many exciting advances have been made in these areas, including single-molecule and superresolution imaging and the development of chromosome conformation capture (3C)-based technologies, which have brought the advent of genome-wide analysis of chromatin structure and contacts. However, many questions remain as to the function of nuclear structures, in particular their influence on transcription. Here we describe studies that have directly manipulated nuclear architecture at various levels and thus have clarified the causal influence of structure on transcription. We will also highlight open questions in the field, most notably regarding our understanding of the dynamics and variability in nuclear structure and its influence on gene expression.
Collapse
Affiliation(s)
- Caroline R Bartman
- Division of Hematology, Children's Hospital of Pennsylvania, Philadelphia, Pennsylvania 19104 Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Pennsylvania, Philadelphia, Pennsylvania 19104 Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| |
Collapse
|
176
|
Romanoski CE, Link VM, Heinz S, Glass CK. Exploiting genomics and natural genetic variation to decode macrophage enhancers. Trends Immunol 2015; 36:507-18. [PMID: 26298065 PMCID: PMC4548828 DOI: 10.1016/j.it.2015.07.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/15/2015] [Accepted: 07/17/2015] [Indexed: 12/18/2022]
Abstract
The mammalian genome contains on the order of a million enhancer-like regions that are required to establish the identities and functions of specific cell types. Here, we review recent studies in immune cells that have provided insight into the mechanisms that selectively activate certain enhancers in response to cell lineage and environmental signals. We describe a working model wherein distinct classes of transcription factors define the repertoire of active enhancers in macrophages through collaborative and hierarchical interactions, and discuss important challenges to this model, specifically providing examples from T cells. We conclude by discussing the use of natural genetic variation as a powerful approach for decoding transcription factor combinations that play dominant roles in establishing the enhancer landscapes, and the potential that these insights have for advancing our understanding of the molecular causes of human disease.
Collapse
Affiliation(s)
- Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA; Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Planegg-Martinsried 85152, Germany
| | - Sven Heinz
- Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.
| |
Collapse
|
177
|
|
178
|
Matharu NK, Ahanger SH. Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture. Genes (Basel) 2015; 6:790-811. [PMID: 26340639 PMCID: PMC4584330 DOI: 10.3390/genes6030790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/10/2015] [Accepted: 08/20/2015] [Indexed: 01/21/2023] Open
Abstract
The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. It is imperative to understand the mechanisms that shape the 3D organization of the eukaryotic genomes. Chromatin insulators have emerged as one of the central components of the genome organization tool-kit across species. Recent advancements in chromatin conformation capture technologies have provided important insights into the architectural role of insulators in genomic structuring. Insulators are involved in 3D genome organization at multiple spatial scales and are important for dynamic reorganization of chromatin structure during reprogramming and differentiation. In this review, we will discuss the classical view and our renewed understanding of insulators as global genome organizers. We will also discuss the plasticity of chromatin structure and its re-organization during pluripotency and differentiation and in situations of cellular stress.
Collapse
Affiliation(s)
- Navneet K Matharu
- Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Sajad H Ahanger
- Department of Ophthalmology, Lab for Retinal Cell Biology, University of Zurich, Wagistrasse 14, Zurich 8952, Switzerland.
| |
Collapse
|
179
|
Abstract
Islets of Langerhans contain multiple hormone-producing endocrine cells controlling glucose homeostasis. Transcription establishes and maintains islet cellular fates and identities. Genetic and environmental disruption of islet transcription triggers cellular dysfunction and disease. Early transcriptional regulation studies of specific islet genes, including insulin (INS) and the transcription factor PDX1, identified the first cis-regulatory DNA sequences and trans-acting factors governing islet function. Here, we review how human islet "omics" studies are reshaping our understanding of transcriptional regulation in islet (dys)function and diabetes. First, we highlight the expansion of islet transcript number, form, and function and of DNA transcriptional regulatory elements controlling their production. Next, we cover islet transcriptional effects of genetic and environmental perturbation. Finally, we discuss how these studies' emerging insights should empower our diabetes research community to build mechanistic understanding of diabetes pathophysiology and to equip clinicians with tailored, precision medicine options to prevent and treat islet dysfunction and diabetes.
Collapse
Affiliation(s)
- Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine (JAX-GM), Farmington, CT, USA,
| | | | | | | |
Collapse
|
180
|
Chandra S, Terragni J, Zhang G, Pradhan S, Haushka S, Johnston D, Baribault C, Lacey M, Ehrlich M. Tissue-specific epigenetics in gene neighborhoods: myogenic transcription factor genes. Hum Mol Genet 2015; 24:4660-73. [PMID: 26041816 PMCID: PMC4512632 DOI: 10.1093/hmg/ddv198] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/18/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022] Open
Abstract
Myogenic regulatory factor (MRF) genes, MYOD1, MYOG, MYF6 and MYF5, are critical for the skeletal muscle lineage. Here, we used various epigenome profiles from human myoblasts (Mb), myotubes (Mt), muscle and diverse non-muscle samples to elucidate the involvement of multigene neighborhoods in the regulation of MRF genes. We found more far-distal enhancer chromatin associated with MRF genes in Mb and Mt than previously reported from studies in mice. For the MYF5/MYF6 gene-pair, regions of Mb-associated enhancer chromatin were located throughout the adjacent 236-kb PTPRQ gene even though Mb expressed negligible amounts of PTPRQ mRNA. Some enhancer chromatin regions inside PTPRQ in Mb were also seen in PTPRQ mRNA-expressing non-myogenic cells. This suggests dual-purpose PTPRQ enhancers that upregulate expression of PTPRQ in non-myogenic cells and MYF5/MYF6 in myogenic cells. In contrast, the myogenic enhancer chromatin regions distal to MYOD1 were intergenic and up to 19 kb long. Two of them contain small, known MYOD1 enhancers, and one displayed an unusually high level of 5-hydroxymethylcytosine in a quantitative DNA hydroxymethylation assay. Unexpectedly, three regions of MYOD1-distal enhancer chromatin in Mb and Mt overlapped enhancer chromatin in umbilical vein endothelial cells, which might upregulate a distant gene (PIK3C2A). Lastly, genes surrounding MYOG were preferentially transcribed in Mt, like MYOG itself, and exhibited nearby myogenic enhancer chromatin. These neighboring chromatin regions may be enhancers acting in concert to regulate myogenic expression of multiple adjacent genes. Our findings reveal the very different and complex organization of gene neighborhoods containing closely related transcription factor genes.
Collapse
Affiliation(s)
- Sruti Chandra
- Program in Human Genetics, Tulane Cancer Center, and Center for Bioinformatics and Genomics, Tulane Health Sciences Center, New Orleans, LA 70122, USA
| | | | | | | | - Stephen Haushka
- Department of Biochemistry, University of Washington, Seattle, WA 98109, USA, and
| | - Douglas Johnston
- Department of Microbiology, Immunology and Parasitology, LSU Health Sciences Center, New Orleans, LA 70112, USA
| | - Carl Baribault
- Tulane Cancer Center and Department of Mathematics, Tulane Health Sciences Center and Tulane University, New Orleans, LA 70122, USA
| | - Michelle Lacey
- Tulane Cancer Center and Department of Mathematics, Tulane Health Sciences Center and Tulane University, New Orleans, LA 70122, USA
| | - Melanie Ehrlich
- Program in Human Genetics, Tulane Cancer Center, and Center for Bioinformatics and Genomics, Tulane Health Sciences Center, New Orleans, LA 70122, USA,
| |
Collapse
|
181
|
Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape. Nat Rev Immunol 2015; 15:585-94. [DOI: 10.1038/nri3884] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
182
|
Teng G, Maman Y, Resch W, Kim M, Yamane A, Qian J, Kieffer-Kwon KR, Mandal M, Ji Y, Meffre E, Clark MR, Cowell LG, Casellas R, Schatz DG. RAG Represents a Widespread Threat to the Lymphocyte Genome. Cell 2015; 162:751-65. [PMID: 26234156 PMCID: PMC4537821 DOI: 10.1016/j.cell.2015.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 04/14/2015] [Accepted: 06/02/2015] [Indexed: 11/26/2022]
Abstract
The RAG1 endonuclease, together with its cofactor RAG2, is essential for V(D)J recombination but is a potent threat to genome stability. The sources of RAG1 mis-targeting and the mechanisms that have evolved to suppress it are poorly understood. Here, we report that RAG1 associates with chromatin at thousands of active promoters and enhancers in the genome of developing lymphocytes. The mouse and human genomes appear to have responded by reducing the abundance of "cryptic" recombination signals near RAG1 binding sites. This depletion operates specifically on the RSS heptamer, whereas nonamers are enriched at RAG1 binding sites. Reversing this RAG-driven depletion of cleavage sites by insertion of strong recombination signals creates an ectopic hub of RAG-mediated V(D)J recombination and chromosomal translocations. Our findings delineate rules governing RAG binding in the genome, identify areas at risk of RAG-mediated damage, and highlight the evolutionary struggle to accommodate programmed DNA damage in developing lymphocytes.
Collapse
Affiliation(s)
- Grace Teng
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Yaakov Maman
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Wolfgang Resch
- Genomics and Immunity, NIAMS, Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Min Kim
- Division of Biomedical Informatics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Box 9066, Dallas, TX 75390-9066, USA
| | - Arito Yamane
- Genomics and Immunity, NIAMS, Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Qian
- Genomics and Immunity, NIAMS, Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyong-Rim Kieffer-Kwon
- Genomics and Immunity, NIAMS, Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Malay Mandal
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Yanhong Ji
- Department of Immunology and Microbiology, College of Medicine, Xi'an Jiao Tong University, 76 Yan Ta West Road, Box 37, Xian, Shaanxi 710061, PRC
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Marcus R Clark
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Lindsay G Cowell
- Division of Biomedical Informatics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Box 9066, Dallas, TX 75390-9066, USA
| | - Rafael Casellas
- Genomics and Immunity, NIAMS, Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA.
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA; Howard Hughes Medical Institute, 295 Congress Avenue, New Haven, CT 06511, USA.
| |
Collapse
|
183
|
Witte S, O'Shea JJ, Vahedi G. Super-enhancers: Asset management in immune cell genomes. Trends Immunol 2015; 36:519-26. [PMID: 26277449 DOI: 10.1016/j.it.2015.07.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/17/2015] [Accepted: 07/17/2015] [Indexed: 12/29/2022]
Abstract
Super-enhancers (SEs) are regions of the genome consisting of clusters of regulatory elements bound with very high amounts of transcription factors, and this architecture appears to be the hallmark of genes and noncoding RNAs linked with cell identity. Recent studies have identified SEs in CD4(+) T cells and have further linked these regions to single nucleotide polymorphisms (SNPs) associated with immune-mediated disorders, pointing to an important role for these structures in the T cell differentiation and function. Here we review the features that define SEs, and discuss their function within the broader understanding of the mechanisms that define immune cell identity and function. We propose that SEs present crucial regulatory hubs, coordinating intrinsic and extrinsic differentiation signals, and argue that delineating these regions will provide important insight into the factors and mechanisms that define immune cell identity.
Collapse
Affiliation(s)
- Steven Witte
- Lymphocyte Cell Biology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John J O'Shea
- Lymphocyte Cell Biology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Golnaz Vahedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
184
|
Chandra V, Bortnick A, Murre C. AID targeting: old mysteries and new challenges. Trends Immunol 2015; 36:527-35. [PMID: 26254147 DOI: 10.1016/j.it.2015.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/14/2015] [Accepted: 07/14/2015] [Indexed: 01/09/2023]
Abstract
Activation-induced cytidine deaminase (AID) mediates cytosine deamination and underlies two central processes in antibody diversification: somatic hypermutation and class-switch recombination. AID deamination is not exclusive to immunoglobulin loci; it can instigate DNA lesions in non-immunoglobulin genes and thus stringent checks are in place to constrain and restrict its activity. Recent findings have provided new insights into the mechanisms that target AID activity to specific genomic regions, revealing an involvement for noncoding RNAs associated with polymerase pausing and with enhancer transcription as well as genomic architecture. We review these findings and integrate them into a model for multilevel regulation of AID expression and targeting in immunoglobulin and non-immunoglobulin loci. Within this framework we discuss gaps in understanding, and outline important areas of further research.
Collapse
Affiliation(s)
- Vivek Chandra
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0377, USA
| | - Alexandra Bortnick
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0377, USA
| | - Cornelis Murre
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0377, USA.
| |
Collapse
|
185
|
Raz S, Stark M, Assaraf YG. Binding of a Smad4/Ets-1 complex to a novel intragenic regulatory element in exon12 of FPGS underlies decreased gene expression and antifolate resistance in leukemia. Oncotarget 2015; 5:9183-98. [PMID: 25229333 PMCID: PMC4253427 DOI: 10.18632/oncotarget.2399] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Polyglutamylation of antifolates catalyzed by folylpoly-γ-glutamate synthetase (FPGS) is essential for their intracellular retention and cytotoxic activity. Hence, loss of FPGS expression and/or function results in lack of antifolate polyglutamylation and drug resistance. Members of the TGF-β/Smad signaling pathway are negative regulators of hematopoiesis and deregulation of this pathway is considered a major contributor to leukemogenesis. Here we show that FPGS gene expression is inversely correlated with the binding of a Smad4/Ets-1 complex to exon12 of FPGS in both acute lymphoblastic leukemia cells and acute myeloid leukemia blast specimens. We demonstrate that antifolate resistant leukemia cells harbor a heterozygous point mutation in exon12 of FPGS which disrupts FPGS activity by abolishing ATP binding, and alters the binding pattern of transcription factors to the genomic region of exon12. This in turn results in the near complete silencing of the wild type allele leading to a 97% loss of FPGS activity. We show that exon12 is a novel intragenic transcriptional regulator, endowed with the ability to drive transcription in vitro, and is occupied by transcription factors and chromatin remodeling agents (e.g. Smad4/Ets-1, HP-1 and Brg1) in vivo. These findings bear important implications for the rational overcoming of antifolate resistance in leukemia.
Collapse
Affiliation(s)
- Shachar Raz
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Michal Stark
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| |
Collapse
|
186
|
Ryan RJH, Drier Y, Whitton H, Cotton MJ, Kaur J, Issner R, Gillespie S, Epstein CB, Nardi V, Sohani AR, Hochberg EP, Bernstein BE. Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma. Cancer Discov 2015; 5:1058-71. [PMID: 26229090 DOI: 10.1158/2159-8290.cd-15-0370] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/27/2015] [Indexed: 02/07/2023]
Abstract
UNLABELLED B-cell lymphomas frequently contain genomic rearrangements that lead to oncogene activation by heterologous distal regulatory elements. We used a novel approach called "pinpointing enhancer-associated rearrangements by chromatin immunoprecipitation," or PEAR-ChIP, to simultaneously map enhancer activity and proximal rearrangements in lymphoma cell lines and patient biopsies. This method detects rearrangements involving known cancer genes, including CCND1, BCL2, MYC, PDCD1LG2, NOTCH1, CIITA, and SGK1, as well as novel enhancer duplication events of likely oncogenic significance. We identify lymphoma subtype-specific enhancers in the MYC locus that are silenced in lymphomas with MYC-activating rearrangements and are associated with germline polymorphisms that alter lymphoma risk. We show that BCL6-locus enhancers are acetylated by the BCL6-activating transcription factor MEF2B, and can undergo genomic duplication, or target the MYC promoter for activation in the context of a "pseudo-double-hit" t(3;8)(q27;q24) rearrangement linking the BCL6 and MYC loci. Our work provides novel insights regarding enhancer-driven oncogene activation in lymphoma. SIGNIFICANCE We demonstrate a novel approach for simultaneous detection of genomic rearrangements and enhancer activity in tumor biopsies. We identify novel mechanisms of enhancer-driven regulation of the oncogenes MYC and BCL6, and show that the BCL6 locus can serve as an enhancer donor in an "enhancer hijacking" translocation.
Collapse
Affiliation(s)
- Russell J H Ryan
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Yotam Drier
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Holly Whitton
- Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - M Joel Cotton
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Jasleen Kaur
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Robbyn Issner
- Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Shawn Gillespie
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Charles B Epstein
- Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Aliyah R Sohani
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ephraim P Hochberg
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts.
| |
Collapse
|
187
|
Grimmer MR, Farnham PJ. Can genome engineering be used to target cancer-associated enhancers? Epigenomics 2015; 6:493-501. [PMID: 25431942 DOI: 10.2217/epi.14.30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Transcriptional misregulation is involved in the development of many diseases, especially neoplastic transformation. Distal regulatory elements, such as enhancers, play a major role in specifying cell-specific transcription patterns in both normal and diseased tissues, suggesting that enhancers may be prime targets for therapeutic intervention. By focusing on modulating gene regulation mediated by cell type-specific enhancers, there is hope that normal epigenetic patterning in an affected tissue could be restored with fewer side effects than observed with treatments employing relatively nonspecific inhibitors such as epigenetic drugs. New methods employing genomic nucleases and site-specific epigenetic regulators targeted to specific genomic regions, using either artificial DNA-binding proteins or RNA-DNA interactions, may allow precise genome engineering at enhancers. However, this field is still in its infancy and further refinements that increase specificity and efficiency are clearly required.
Collapse
Affiliation(s)
- Matthew R Grimmer
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9601, USA
| | | |
Collapse
|
188
|
Lopes Novo C, Rugg-Gunn PJ. Chromatin organization in pluripotent cells: emerging approaches to study and disrupt function. Brief Funct Genomics 2015. [PMID: 26206085 PMCID: PMC4958138 DOI: 10.1093/bfgp/elv029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Translating the vast amounts of genomic and epigenomic information accumulated on the linear genome into three-dimensional models of nuclear organization is a current major challenge. In response to this challenge, recent technological innovations based on chromosome conformation capture methods in combination with increasingly powerful functional approaches have revealed exciting insights into key aspects of genome regulation. These findings have led to an emerging model where the genome is folded and compartmentalized into highly conserved topological domains that are further divided into functional subdomains containing physical loops that bring cis-regulatory elements to close proximity. Targeted functional experiments, largely based on designable DNA-binding proteins, have begun to define the major architectural proteins required to establish and maintain appropriate genome regulation. Here, we focus on the accessible and well-characterized system of pluripotent cells to review the functional role of chromatin organization in regulating pluripotency, differentiation and reprogramming.
Collapse
|
189
|
Erokhin M, Vassetzky Y, Georgiev P, Chetverina D. Eukaryotic enhancers: common features, regulation, and participation in diseases. Cell Mol Life Sci 2015; 72:2361-75. [PMID: 25715743 PMCID: PMC11114076 DOI: 10.1007/s00018-015-1871-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/07/2015] [Accepted: 02/20/2015] [Indexed: 01/01/2023]
Abstract
Enhancers are positive DNA regulatory sequences controlling temporal and tissue-specific gene expression. These elements act independently of their orientation and distance relative to the promoters of target genes. Enhancers act through a variety of transcription factors that ensure their correct match with target promoters and consequent gene activation. There is a growing body of evidence on association of enhancers with transcription factors, co-activators, histone chromatin marks, and lncRNAs. Alterations in enhancers lead to misregulation of gene expression, causing a number of human diseases. In this review, we focus on the common characteristics of enhancers required for transcription stimulation.
Collapse
Affiliation(s)
- Maksim Erokhin
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334 Russia
- LIA 1066, Laboratoire Franco-Russe de recherche en oncologie, 119334 Moscow, Russia
| | - Yegor Vassetzky
- LIA 1066, Laboratoire Franco-Russe de recherche en oncologie, 119334 Moscow, Russia
- UMR8126, Université Paris-Sud, CNRS, Institut de cancérologie Gustave Roussy, 94805 Villejuif, France
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334 Russia
- LIA 1066, Laboratoire Franco-Russe de recherche en oncologie, 119334 Moscow, Russia
| | - Darya Chetverina
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334 Russia
| |
Collapse
|
190
|
Moore BL, Aitken S, Semple CA. Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization. Genome Biol 2015; 16:110. [PMID: 26013771 PMCID: PMC4443654 DOI: 10.1186/s13059-015-0661-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 04/24/2015] [Indexed: 12/31/2022] Open
Abstract
Background Interphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic regions associated with DNA-binding proteins at the order of tens or hundreds of bases, through larger regions with active or repressed chromatin states, up to multi-megabase-scale domains associated with nuclear positioning, replication timing and other qualities. However, we have lacked detailed, quantitative models to understand the interactions between these different strata. Results Here we collate large collections of matched locus-level chromatin features and Hi-C interaction data, representing higher-order organization, across three human cell types. We use quantitative modeling approaches to assess whether locus-level features are sufficient to explain higher-order structure, and identify the most influential underlying features. We identify structurally variable domains between cell types and examine the underlying features to discover a general association with cell-type-specific enhancer activity. We also identify the most prominent features marking the boundaries of two types of higher-order domains at different scales: topologically associating domains and nuclear compartments. We find parallel enrichments of particular chromatin features for both types, including features associated with active promoters and the architectural proteins CTCF and YY1. Conclusions We show that integrative modeling of large chromatin dataset collections using random forests can generate useful insights into chromosome structure. The models produced recapitulate known biological features of the cell types involved, allow exploration of the antecedents of higher-order structures and generate testable hypotheses for further experimental studies. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0661-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Benjamin L Moore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Stuart Aitken
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Colin A Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
| |
Collapse
|
191
|
High resolution mapping of enhancer-promoter interactions. PLoS One 2015; 10:e0122420. [PMID: 25970635 PMCID: PMC4430501 DOI: 10.1371/journal.pone.0122420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/20/2015] [Indexed: 01/19/2023] Open
Abstract
RNA Polymerase II ChIA-PET data has revealed enhancers that are active in a profiled cell type and the genes that the enhancers regulate through chromatin interactions. The most commonly used computational method for analyzing ChIA-PET data, the ChIA-PET Tool, discovers interaction anchors at a spatial resolution that is insufficient to accurately identify individual enhancers. We introduce Germ, a computational method that estimates the likelihood that any two narrowly defined genomic locations are jointly occupied by RNA Polymerase II. Germ takes a blind deconvolution approach to simultaneously estimate the likelihood of RNA Polymerase II occupation as well as a model of the arrangement of read alignments relative to locations occupied by RNA Polymerase II. Both types of information are utilized to estimate the likelihood that RNA Polymerase II jointly occupies any two genomic locations. We apply Germ to RNA Polymerase II ChIA-PET data from embryonic stem cells to identify the genomic locations that are jointly occupied along with transcription start sites. We show that these genomic locations align more closely with features of active enhancers measured by ChIP-Seq than the locations identified using the ChIA-PET Tool. We also apply Germ to RNA Polymerase II ChIA-PET data from motor neuron progenitors. Based on the Germ results, we observe that a combination of cell type specific and cell type independent regulatory interactions are utilized by cells to regulate gene expression.
Collapse
|
192
|
Sexton T, Cavalli G. The role of chromosome domains in shaping the functional genome. Cell 2015; 160:1049-59. [PMID: 25768903 DOI: 10.1016/j.cell.2015.02.040] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Indexed: 10/23/2022]
Abstract
The genome must be highly compacted to fit within eukaryotic nuclei but must be accessible to the transcriptional machinery to allow appropriate expression of genes in different cell types and throughout developmental pathways. A growing body of work has shown that the genome, analogously to proteins, forms an ordered, hierarchical structure that closely correlates and may even be causally linked with regulation of functions such as transcription. This review describes our current understanding of how these functional genomic "secondary and tertiary structures" form a blueprint for global nuclear architecture and the potential they hold for understanding and manipulating genomic regulation.
Collapse
Affiliation(s)
- Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67404 Illkirch, France.
| | - Giacomo Cavalli
- Institute of Human Genetics (IGH), 141 rue de la Cardonille, 34396 Montpellier, France.
| |
Collapse
|
193
|
Abstract
In immune cells, as in all mammalian cells, nuclear DNA is wrapped around histones to form nucleosomes. The positioning and modifications of nucleosomes throughout the genome defines the chromatin state of the cell and has a large impact on gene regulation. Chromatin state is dynamic throughout immune cell development and activation. High-throughput open chromatin assays, such as DNase-seq, can be used to find regulatory element across the genome and, when combined with histone modifications, can specify their function. During hematopoiesis, distal regulatory elements, known as enhancers, are established by pioneer factors that alter chromatin state. Some of these enhancers are lost, some are gained, and some are maintained as a memory of the cell's developmental origin. The enhancer landscape is unique to the cell lineage-with different enhancers regulating the same promoter-and determines the mechanism of cell type-specific activation after exposure to stimuli. Histone modification and promoter architecture govern the diverse responses to stimulation. Furthermore, chromatin dynamics may explain the high plasticity of certain tissue-resident immune cell types. Future epigenomic research will depend on the development of more efficient experiments and better methods to associate enhancers with genes. The ultimate goal of mapping genome-wide chromatin state throughout the hematopoietic tree will help illuminate the mechanisms behind immune cell development and function.
Collapse
Affiliation(s)
- Deborah R Winter
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | |
Collapse
|
194
|
Architectural hallmarks of the pluripotent genome. FEBS Lett 2015; 589:2905-13. [PMID: 25957773 DOI: 10.1016/j.febslet.2015.04.055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 01/03/2023]
Abstract
Pluripotent stem cells (PSCs) have the ability to self-renew and are capable of generating all embryonic germ layers (Evans and Kaufman, 1981; Thomson et al., 1998). PSCs can be isolated from early embryos or may be induced via overexpression of pluripotency transcription factors in differentiated cells (Takahashi and Yamanaka, 2006). As PSCs hold great promise for regenerative medicine, the mechanisms underlying pluripotency and induction thereof are studied intensively. Pluripotency is characterized by a unique transcriptional program that is in part controlled by an exceptionally plastic regulatory chromatin landscape. In recent years, 3D genome configuration has emerged as an important regulator of transcriptional control and cellular identity (Taddei et al., 2004 [4]; Lanctot et al., 2007 [5]; Gibcus and Dekker, 2013; Misteli, 2009 [7]). Here we provide an overview of recent findings on the 3D genome organization in PSCs and discuss its putative functional role in regulation of the pluripotent state.
Collapse
|
195
|
Factor DC, Corradin O, Zentner GE, Saiakhova A, Song L, Chenoweth JG, McKay RD, Crawford GE, Scacheri PC, Tesar PJ. Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency. Cell Stem Cell 2015; 14:854-63. [PMID: 24905169 DOI: 10.1016/j.stem.2014.05.005] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/01/2014] [Accepted: 05/13/2014] [Indexed: 12/21/2022]
Abstract
Naive mouse embryonic stem cells (mESCs) and primed epiblast stem cells (mEpiSCs) represent successive snapshots of pluripotency during embryogenesis. Using transcriptomic and epigenomic mapping we show that a small fraction of transcripts are differentially expressed between mESCs and mEpiSCs and that these genes show expected changes in chromatin at their promoters and enhancers. Unexpectedly, the cis-regulatory circuitry of genes that are expressed at identical levels between these cell states also differs dramatically. In mESCs, these genes are associated with dominant proximal enhancers and dormant distal enhancers, which we term seed enhancers. In mEpiSCs, the naive-dominant enhancers are lost, and the seed enhancers take up primary transcriptional control. Seed enhancers have increased sequence conservation and show preferential usage in downstream somatic tissues, often expanding into super enhancers. We propose that seed enhancers ensure proper enhancer utilization and transcriptional fidelity as mammalian cells transition from naive pluripotency to a somatic regulatory program.
Collapse
Affiliation(s)
- Daniel C Factor
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Olivia Corradin
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Gabriel E Zentner
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Lingyun Song
- Institute for Genome Sciences & Policy, Duke University, Durham, NC 27709, USA
| | - Josh G Chenoweth
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
| | - Ronald D McKay
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
| | - Gregory E Crawford
- Institute for Genome Sciences & Policy, Duke University, Durham, NC 27709, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Paul J Tesar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; National Center for Regenerative Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| |
Collapse
|
196
|
Gorkin DU, Leung D, Ren B. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell 2015; 14:762-75. [PMID: 24905166 DOI: 10.1016/j.stem.2014.05.017] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
It can be convenient to think of the genome as simply a string of nucleotides, the linear order of which encodes an organism's genetic blueprint. However, the genome does not exist as a linear entity within cells where this blueprint is actually utilized. Inside the nucleus, the genome is organized in three-dimensional (3D) space, and lineage-specific transcriptional programs that direct stem cell fate are implemented in this native 3D context. Here, we review principles of 3D genome organization in mammalian cells. We focus on the emerging relationship between genome organization and lineage-specific transcriptional regulation, which we argue are inextricably linked.
Collapse
Affiliation(s)
- David U Gorkin
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Danny Leung
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| |
Collapse
|
197
|
Comparative analysis of T4 DNA ligases and DNA polymerases used in chromosome conformation capture assays. Biotechniques 2015; 58:195-9. [DOI: 10.2144/000114276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/27/2015] [Indexed: 11/23/2022] Open
Abstract
Three-dimensional (3-D) genome organization in the nuclear space affects various genomic functions. Circular chromosome conformation capture (4C-seq) is a powerful technique that allows researchers to measure long-range chromosomal interactions with a locus of interest across the entire genome. This method relies on enzymatic cleavage of cross-linked chromatin and consecutive ligation to create ligation junctions between physically adjacent loci, followed by PCR amplification of locus-specific associating loci. The enzymes used must meet 4C standards because variations in their efficiency and performance may affect the quality of the obtained data. Here we systematically compare the efficiency and reliability of different T4 DNA ligases and PCR DNA polymerases, assessing the most critical and technically challenging steps in 4C. The results of this analysis enable the use of cost-effective enzymes with superior specificity and efficiency for 4C and save time in screening for appropriate primers. This information provides users with flexibility in their experimental design and guidelines for adapting and testing any enzyme of choice for obtaining standardized results.
Collapse
|
198
|
Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res 2015; 25:582-97. [PMID: 25752748 PMCID: PMC4381529 DOI: 10.1101/gr.185272.114] [Citation(s) in RCA: 313] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/11/2015] [Indexed: 12/17/2022]
Abstract
The mammalian genome harbors up to one million regulatory elements often located at great distances from their target genes. Long-range elements control genes through physical contact with promoters and can be recognized by the presence of specific histone modifications and transcription factor binding. Linking regulatory elements to specific promoters genome-wide is currently impeded by the limited resolution of high-throughput chromatin interaction assays. Here we apply a sequence capture approach to enrich Hi-C libraries for >22,000 annotated mouse promoters to identify statistically significant, long-range interactions at restriction fragment resolution, assigning long-range interacting elements to their target genes genome-wide in embryonic stem cells and fetal liver cells. The distal sites contacting active genes are enriched in active histone modifications and transcription factor occupancy, whereas inactive genes contact distal sites with repressive histone marks, demonstrating the regulatory potential of the distal elements identified. Furthermore, we find that coregulated genes cluster nonrandomly in spatial interaction networks correlated with their biological function and expression level. Interestingly, we find the strongest gene clustering in ES cells between transcription factor genes that control key developmental processes in embryogenesis. The results provide the first genome-wide catalog linking gene promoters to their long-range interacting elements and highlight the complex spatial regulatory circuitry controlling mammalian gene expression.
Collapse
Affiliation(s)
- Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Mayra Furlan-Magaril
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Borbala Mifsud
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Filipe Tavares-Cadete
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Robert Sugar
- Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom; EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Biola-Maria Javierre
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Takashi Nagano
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Yulia Katsman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Moorthy Sakthidevi
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Steven W Wingett
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom; Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Emilia Dimitrova
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Andrew Dimond
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Lucas B Edelman
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Sarah Elderkin
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Kristina Tabbada
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Elodie Darbo
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Bram Herman
- Agilent Technologies, Inc., Santa Clara, California 95051, USA
| | - Andy Higgs
- Agilent Technologies, Inc., Santa Clara, California 95051, USA
| | - Emily LeProust
- Agilent Technologies, Inc., Santa Clara, California 95051, USA
| | - Cameron S Osborne
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Nicholas M Luscombe
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom; Okinawa Institute for Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom;
| |
Collapse
|
199
|
Ignatieva EV, Podkolodnaya OA, Orlov YL, Vasiliev GV, Kolchanov NA. Regulatory genomics: Combined experimental and computational approaches. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415040067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
200
|
Makova KD, Hardison RC. The effects of chromatin organization on variation in mutation rates in the genome. Nat Rev Genet 2015; 16:213-23. [PMID: 25732611 PMCID: PMC4500049 DOI: 10.1038/nrg3890] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The variation in local rates of mutations can affect both the evolution of genes and their function in normal and cancer cells. Deciphering the molecular determinants of this variation will be aided by the elucidation of distinct types of mutations, as they differ in regional preferences and in associations with genomic features. Chromatin organization contributes to regional variation in mutation rates, but its contribution differs among mutation types. In both germline and somatic mutations, base substitutions are more abundant in regions of closed chromatin, perhaps reflecting error accumulation late in replication. By contrast, a distinctive mutational state with very high levels of insertions and deletions (indels) and substitutions is enriched in regions of open chromatin. These associations indicate an intricate interplay between the nucleotide sequence of DNA and its dynamic packaging into chromatin, and have important implications for current biomedical research. This Review focuses on recent studies showing associations between chromatin state and mutation rates, including pairwise and multivariate investigations of germline and somatic (particularly cancer) mutations.
Collapse
Affiliation(s)
- Kateryna D Makova
- Department of Biology, Huck Institute for Genome Sciences, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institute for Genome Sciences, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, USA
| |
Collapse
|