851
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Merkenschlager M, Odom DT. CTCF and cohesin: linking gene regulatory elements with their targets. Cell 2013; 152:1285-97. [PMID: 23498937 DOI: 10.1016/j.cell.2013.02.029] [Citation(s) in RCA: 265] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 12/11/2022]
Abstract
Current epigenomics approaches have facilitated the genome-wide identification of regulatory elements based on chromatin features and transcriptional regulator binding and have begun to map long-range interactions between regulatory elements and their targets. Here, we focus on the emerging roles of CTCF and the cohesin in coordinating long-range interactions between regulatory elements. We discuss how species-specific transposable elements may influence such interactions by remodeling the CTCF binding repertoire and suggest that cohesin's association with enhancers, promoters, and sites defined by CTCF binding has the potential to form developmentally regulated networks of long-range interactions that reflect and promote cell-type-specific transcriptional programs.
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Affiliation(s)
- Matthias Merkenschlager
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK.
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852
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Abstract
The gene expression programs that establish and maintain specific cell states in humans are controlled by thousands of transcription factors, cofactors, and chromatin regulators. Misregulation of these gene expression programs can cause a broad range of diseases. Here, we review recent advances in our understanding of transcriptional regulation and discuss how these have provided new insights into transcriptional misregulation in disease.
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Affiliation(s)
- Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts
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853
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Aran D, Sabato S, Hellman A. DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol 2013; 14:R21. [PMID: 23497655 PMCID: PMC4053839 DOI: 10.1186/gb-2013-14-3-r21] [Citation(s) in RCA: 241] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 03/12/2013] [Indexed: 11/24/2022] Open
Abstract
Background Abnormal epigenetic marking is well documented in gene promoters of cancer cells, but the study of distal regulatory siteshas lagged behind.We performed a systematic analysis of DNA methylation sites connected with gene expression profilesacross normal and cancerous human genomes. Results Utilizing methylation and expression data in 58 cell types, we developed a model for methylation-expression relationships in gene promoters and extrapolated it to the genome. We mapped numerous sites at which DNA methylation was associated with expression of distal genes. These sites bind transcription factors in a methylation-dependent manner, and carry the chromatin marks of a particular class of transcriptional enhancers. In contrast to the traditional model of one enhancer site per cell type, we found that single enhancer sites may define gradients of expression levels across many different cell types. Strikingly, the identified sites were drastically altered in cancers: hypomethylated enhancer sites associated with upregulation of cancer-related genes and hypermethylated sites with downregulation. Moreover, the association between enhancer methylation and gene deregulation in cancerwas significantly stronger than the association of promoter methylationwith gene deregulation. Conclusions Methylation of distal regulatory sites is closely related to gene expression levels across the genome. Single enhancers may modulate ranges of cell-specific transcription levels, from constantlyopen promoters. In contrast to the remote relationships between promoter methylation and gene dysregulation in cancer, altered methylation of enhancer sites is closely related to gene expression profiles of transformed cells.
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854
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Cavalli G, Misteli T. Functional implications of genome topology. Nat Struct Mol Biol 2013; 20:290-9. [PMID: 23463314 PMCID: PMC6320674 DOI: 10.1038/nsmb.2474] [Citation(s) in RCA: 299] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/20/2012] [Indexed: 01/21/2023]
Abstract
Although genomes are defined by their sequence, the linear arrangement of nucleotides is only their most basic feature. A fundamental property of genomes is their topological organization in three-dimensional space in the intact cell nucleus. The application of imaging methods and genome-wide biochemical approaches, combined with functional data, is revealing the precise nature of genome topology and its regulatory functions in gene expression and genome maintenance. The emerging picture is one of extensive self-enforcing feedback between activity and spatial organization of the genome, suggestive of a self-organizing and self-perpetuating system that uses epigenetic dynamics to regulate genome function in response to regulatory cues and to propagate cell-fate memory.
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Affiliation(s)
- Giacomo Cavalli
- Institut de Génétique Humaine, UPR 1142, Centre National de la Recherche Scientifique, Montpellier, France.
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855
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Larkin JD, Papantonis A, Cook PR. Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites. J Cell Sci 2013; 126:2052-9. [PMID: 23444365 DOI: 10.1242/jcs.123653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Both the sequence of a promoter and the position of a gene in 3D nuclear space play crucial roles in gene regulation, but few studies address their inter-relationship. Using human and viral promoters on mini-chromosomes and RNA fluorescence in situ hybridization coupled to 'high-precision' localization, we show that promoters binding the same transcription factors and responding to the same signaling pathways tend to be co-transcribed in the same transcription factories. We go on to suggest how such spatial co-association might drive co-regulation of genes under the control of similar cis-elements.
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Affiliation(s)
- Joshua D Larkin
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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856
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Tanay A, Cavalli G. Chromosomal domains: epigenetic contexts and functional implications of genomic compartmentalization. Curr Opin Genet Dev 2013; 23:197-203. [PMID: 23414654 DOI: 10.1016/j.gde.2012.12.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 12/20/2012] [Indexed: 12/19/2022]
Abstract
We review recent developments in mapping chromosomal contacts and compare emerging insights on chromosomal contact domain organization in Drosophila and mammalian cells. Potential scenarios leading to the observation of Hi-C domains and their association with the epigenomic context of the chromosomal elements involved are discussed. We argue that even though the mechanisms and precise physical structure underlying chromosomal domain demarcation are yet to be fully resolved, the implications to genome regulation and genome evolution are profound. Specifically, we hypothesize that domains are facilitating genomic compartmentalization that support the implementation of complex, modular, and tissue specific transcriptional program in metazoa.
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Affiliation(s)
- Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel.
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857
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Davidson S, Macpherson N, Mitchell JA. Nuclear organization of RNA polymerase II transcription. Biochem Cell Biol 2013; 91:22-30. [PMID: 23442138 DOI: 10.1139/bcb-2012-0059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transcription occurs at distinct nuclear compartments termed transcription factories that are specialized for transcription by 1 of the 3 polymerase complexes (I, II, or III). Protein-coding genes appear to move in and out of RNA polymerase II (RNAPII) compartments as they are expressed and silenced. In addition, transcription factories are sites where several transcription units, either from the same chromosome or different chromosomes, are transcribed. Chromosomes occupy distinct territories in the interphase nucleus with active genes preferentially positioned on the periphery or even looped out of the territory. These chromosome territories have been observed to intermingle in the nucleus, and multiple interactions among different chromosomes have been identified in genome-wide studies. Deep sequencing of the transcriptome and RNAPII associated on DNA obtained by chromatin immunoprecipitation have revealed a plethora of noncoding transcription and intergenic accumulations of RNAPII that must also be considered in models of genome function. The organization of transcription into distinct regions of the nucleus has changed the way we view transcription with the evolving model for silencing or activation of gene expression involving physical relocation of the transcription unit to a silencing or activation compartment, thus, highlighting the need to consider the process of transcription in the 3-dimensional nuclear space.
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Affiliation(s)
- Scott Davidson
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
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858
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Remeseiro S, Losada A. Cohesin, a chromatin engagement ring. Curr Opin Cell Biol 2013; 25:63-71. [PMID: 23219370 DOI: 10.1016/j.ceb.2012.10.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/18/2012] [Indexed: 12/15/2022]
Abstract
Cohesin is a four subunit complex, conserved from yeast to man, with the ability to hold together two DNA segments within its ring-shaped structure. When the two segments belong to sister chromatids, cohesin is mediating cohesion, which is essential for chromosome segregation in mitosis and meiosis and for homologous DNA repair. When the two DNA segments are in the same chromatid, a loop is formed. These chromatin loops are emerging as a mechanism for controlling the communication between enhancers and promoters and thereby regulate gene expression. They also facilitate DNA replication and recombination. Given all its essential functions, it is not surprising that mutations in cohesin and its interacting factors have been associated to cancer and developmental syndromes known as cohesinopathies.
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Affiliation(s)
- Silvia Remeseiro
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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859
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Verma M, Khoury MJ, Ioannidis JPA. Opportunities and challenges for selected emerging technologies in cancer epidemiology: mitochondrial, epigenomic, metabolomic, and telomerase profiling. Cancer Epidemiol Biomarkers Prev 2013; 22:189-200. [PMID: 23242141 PMCID: PMC3565041 DOI: 10.1158/1055-9965.epi-12-1263] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Remarkable progress has been made in the last decade in new methods for biologic measurements using sophisticated technologies that go beyond the established genome, proteome, and gene expression platforms. These methods and technologies create opportunities to enhance cancer epidemiologic studies. In this article, we describe several emerging technologies and evaluate their potential in epidemiologic studies. We review the background, assays, methods, and challenges and offer examples of the use of mitochondrial DNA and copy number assessments, epigenomic profiling (including methylation, histone modification, miRNAs, and chromatin condensation), metabolite profiling (metabolomics), and telomere measurements. We map the volume of literature referring to each one of these measurement tools and the extent to which efforts have been made at knowledge integration (e.g., systematic reviews and meta-analyses). We also clarify strengths and weaknesses of the existing platforms and the range of type of samples that can be tested with each of them. These measurement tools can be used in identifying at-risk populations and providing novel markers of survival and treatment response. Rigorous analytic and validation standards, transparent availability of massive data, and integration in large-scale evidence are essential in fulfilling the potential of these technologies.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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860
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Wang J, Lan X, Hsu PY, Hsu HK, Huang K, Parvin J, Huang THM, Jin VX. Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation. BMC Genomics 2013; 14:70. [PMID: 23368971 PMCID: PMC3599885 DOI: 10.1186/1471-2164-14-70] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 01/26/2013] [Indexed: 01/07/2023] Open
Abstract
Background An emerging Hi-C protocol has the ability to probe three-dimensional (3D) architecture and capture chromatin interactions in a genome-wide scale. It provides informative results to address how chromatin organization changes contribute to disease/tumor occurrence and progression in response to stimulation of environmental chemicals or hormones. Results In this study, using MCF7 cells as a model system, we found estrogen stimulation significantly impact chromatin interactions, leading to alteration of gene regulation and the associated histone modification states. Many chromosomal interaction regions at different levels of interaction frequency were identified. In particular, the top 10 hot regions with the highest interaction frequency are enriched with breast cancer specific genes. Furthermore, four types of E2-mediated strong differential (gain- or loss-) chromosomal (intra- or inter-) interactions were classified, in which the number of gain-chromosomal interactions is less than the number of loss-chromosomal interactions upon E2 stimulation. Finally, by integrating with eight histone modification marks, DNA methylation, regulatory elements regions, ERα and Pol-II binding activities, associations between epigenetic patterns and high chromosomal interaction frequency were revealed in E2-mediated gene regulation. Conclusions The work provides insight into the effect of chromatin interaction on E2/ERα regulated downstream genes in breast cancer cells.
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Affiliation(s)
- Junbai Wang
- Department of Pathology, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway.
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861
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Merkulova TI, Ananko EA, Ignatieva EV, Kolchanov NA. Transcription regulatory codes of eukaryotic genomes. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413010079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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862
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Abstract
In its first production phase, The ENCODE Project Consortium (ENCODE) has generated thousands of genome-scale data sets, resulting in a genomic “parts list” that encompasses transcripts, sites of transcription factor binding, and other functional features that now number in the millions of distinct elements. These data are reshaping many long-held beliefs concerning the information content of the human and other complex genomes, including the very definition of the gene. Here I discuss and place in context many of the leading findings of ENCODE, as well as trends that are shaping the generation and interpretation of ENCODE data. Finally, I consider prospects for the future, including maximizing the accuracy, completeness, and utility of ENCODE data for the community.
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Affiliation(s)
- John A Stamatoyannopoulos
- Departments of Genome Sciences and Medicine, University of Washington School of Medicine, Seattle, Washington 98195, USA.
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863
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Essential role of the IRF8-KLF4 transcription factor cascade in murine monocyte differentiation. Blood 2013; 121:1839-49. [PMID: 23319570 DOI: 10.1182/blood-2012-06-437863] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Monocytes regulate host defenses, inflammation, and tissue homeostasis. The transcription factor interferon regulatory factor-8 (IRF8) stimulates monocyte/macrophage differentiation, yet genome-wide understanding of the differentiation program initiated by IRF8 is lacking. By combining chromatin immunoprecipitation sequencing with gene expression profiling, we show that during IRF8-dependent monocyte differentiation, IRF8 binding occurs at both promoter-proximal and promotor-distal regions together with the transcription factor PU.1 and is associated with gene induction. Many of the promoter-distal IRF8 binding sites show an increase in histone H3 lysine 4 monomethylation, a signature for enhancers. However, about half the IRF8-induced genes were not bound by IRF8, suggesting the involvement of downstream transcription factors. Analysis of DNA motifs in cis-regulatory elements of these indirect IRF8 target genes predicted that Krüppel-like factor-4 (KLF4)-essential for Ly6C(+) monocyte development-is one such factor. Indeed, monocyte development in Irf8(-/-) mice is as defective as that in Klf4(-/-) chimeric mice. Moreover, Irf8(-/-) monocyte-dendritic cell progenitors do not express Klf4 messenger RNA. Introduction of KLF4 into an Irf8(-/-) myeloid progenitor cell line induced a subset of IRF8 target genes and caused partial monocyte differentiation. Taken together, our present results uncover genome-wide behavior of IRF8 and identify an IRF8-KLF4 axis that operates during monocyte differentiation.
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864
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Larkin JD, Papantonis A, Cook PR, Marenduzzo D. Space exploration by the promoter of a long human gene during one transcription cycle. Nucleic Acids Res 2013; 41:2216-27. [PMID: 23303786 PMCID: PMC3575846 DOI: 10.1093/nar/gks1441] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An RNA polymerase has been thought to transcribe by seeking out a promoter, initiating and then tracking down the template. We add tumor necrosis factor α to primary human cells, switch on transcription of a 221-kb gene and monitor promoter position during the ensuing transcription cycle (using RNA fluorescence in situ hybridization coupled to super-resolution localization, chromosome conformation capture and Monte Carlo simulations). Results are consistent with a polymerase immobilized in a ‘factory’ capturing a promoter and reeling in the template, as the transcript and promoter are extruded. Initially, the extruded promoter is tethered close to the factory and so likely to re-initiate; later, the tether becomes long enough to allow re-initiation in another factory. We suggest close tethering underlies enhancer function and transcriptional ‘bursting’.
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Affiliation(s)
- Joshua D Larkin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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865
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Soon WW, Hariharan M, Snyder MP. High-throughput sequencing for biology and medicine. Mol Syst Biol 2013; 9:640. [PMID: 23340846 PMCID: PMC3564260 DOI: 10.1038/msb.2012.61] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/29/2012] [Indexed: 02/06/2023] Open
Abstract
Advances in genome sequencing have progressed at a rapid pace, with increased throughput accompanied by plunging costs. But these advances go far beyond faster and cheaper. High-throughput sequencing technologies are now routinely being applied to a wide range of important topics in biology and medicine, often allowing researchers to address important biological questions that were not possible before. In this review, we discuss these innovative new approaches-including ever finer analyses of transcriptome dynamics, genome structure and genomic variation-and provide an overview of the new insights into complex biological systems catalyzed by these technologies. We also assess the impact of genotyping, genome sequencing and personal omics profiling on medical applications, including diagnosis and disease monitoring. Finally, we review recent developments in single-cell sequencing, and conclude with a discussion of possible future advances and obstacles for sequencing in biology and health.
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Affiliation(s)
- Wendy Weijia Soon
- Department of Genetics, Stanford University School of Medicine, Alway Building, 300 Pasteur Drive, Stanford, CA, USA
| | - Manoj Hariharan
- Department of Genetics, Stanford University School of Medicine, Alway Building, 300 Pasteur Drive, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Alway Building, 300 Pasteur Drive, Stanford, CA, USA
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866
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Ntziachristos P, Mullenders J, Trimarchi T, Aifantis I. Mechanisms of epigenetic regulation of leukemia onset and progression. Adv Immunol 2013; 117:1-38. [PMID: 23611284 DOI: 10.1016/b978-0-12-410524-9.00001-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the past decade, it has become clear that both genetics and epigenetics play pivotal roles in cancer onset and progression. The importance of epigenetic regulation in proper maintenance of cellular state is highlighted by the frequent mutation of chromatin modulating factors across cancer subtypes. Identification of these mutations has created an interest in designing drugs that target enzymes involved in DNA methylation and posttranslational modification of histones. In this review, we discuss recurrent genetic alterations to epigenetic modulators in both myeloid and lymphoid leukemias. Furthermore, we review how these perturbations contribute to leukemogenesis and impact disease outcome and treatment efficacy. Finally, we discuss how the recent advances in our understanding of chromatin biology may impact treatment of leukemia.
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867
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Göttgens B. Genome-scale technology driven advances to research into normal and malignant haematopoiesis. SCIENTIFICA 2012; 2012:437956. [PMID: 24278696 PMCID: PMC3820533 DOI: 10.6064/2012/437956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Accepted: 12/16/2012] [Indexed: 06/02/2023]
Abstract
Haematopoiesis or blood development has long served as a model system for adult stem cell biology. Moreover, when combined, the various cancers of the blood represent one of the commonest human malignancies. Large numbers of researchers have therefore dedicated their scientific careers to studying haematopoiesis for more than a century. Throughout this period, many new technologies have first been applied towards the study of blood cells, and the research fields of normal and malignant haematopoiesis have also been some of the earliest adopters of genome-scale technologies. This has resulted in significant new insights with implications ranging from basic biological mechanisms to patient diagnosis and prognosis and also produced lessons likely to be relevant for many other areas of biomedical research. This paper discusses the current state of play for a range of genome-scale applications within haemopoiesis research, including gene expression profiling, ChIP-sequencing, genomewide association analysis, and cancer genome sequencing. A concluding outlook section explores likely future areas of progress as well as potential technological and educational bottlenecks.
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Affiliation(s)
- Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University and Wellcome Trust and MRC Stem Cell Institute, Hills Road, Cambridge CB2 0XY, UK
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868
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Lin C, Garruss AS, Luo Z, Guo F, Shilatifard A. The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation. Cell 2012; 152:144-56. [PMID: 23273992 DOI: 10.1016/j.cell.2012.12.015] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 09/10/2012] [Accepted: 12/04/2012] [Indexed: 01/27/2023]
Abstract
Enhancers play a central role in precisely regulating the expression of developmentally regulated genes. However, the machineries required for enhancer-promoter communication have remained largely unknown. We have found that Ell3, a member of the Ell (eleven-nineteen lysine-rich leukemia gene) family of RNA Pol II elongation factors, occupies enhancers in embryonic stem cells. Ell3's association with enhancers is required for setting up proper Pol II occupancy at the promoter-proximal regions of developmentally regulated genes and for the recruitment of the super elongation complex (SEC) to these loci following differentiation signals. Furthermore, Ell3 binding to inactive or poised enhancers is essential for stem cell specification. We have also detected the presence of Pol II and Ell3 in germ cell nuclei. These findings raise the possibility that transcription factors could prime gene expression by marking enhancers in ES cells or even as early as in the germ cell state.
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Affiliation(s)
- Chengqi Lin
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
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869
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Lin YC, Murre C. Nuclear location and the control of developmental progression. Curr Opin Genet Dev 2012; 23:104-8. [PMID: 23266214 DOI: 10.1016/j.gde.2012.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/09/2012] [Accepted: 11/19/2012] [Indexed: 11/30/2022]
Abstract
It is now well established that the mammalian genome is highly organized. Chromosomes are structured as territories that only sporadically intermingle. Chromosome territories themselves are segregated into distinct environments, that is, the transcriptionally inert/repressive (heterochromatic) and permissive (euchromatic) compartments. The transcriptionally permissive compartment is organized into domains (∼0.5-3 Mb) that consist of bundles of loops, are gene-rich and closely associated by activating epigenetic marks. During ontogeny and developmental progression chromatin states are highly dynamic. Recent studies have shown that loci and domains readily switch compartments. Switching nuclear neighborhoods is closely associated with changes in transcriptional activity and extensive chromatin reorganization. Here we discuss the implications of a dynamic genome and how it relates to the control of developmental progression.
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Affiliation(s)
- Yin C Lin
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, United States
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870
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Wilczynski B, Liu YH, Yeo ZX, Furlong EEM. Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state. PLoS Comput Biol 2012; 8:e1002798. [PMID: 23236268 PMCID: PMC3516547 DOI: 10.1371/journal.pcbi.1002798] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 10/08/2012] [Indexed: 12/31/2022] Open
Abstract
Precise patterns of spatial and temporal gene expression are central to metazoan complexity and act as a driving force for embryonic development. While there has been substantial progress in dissecting and predicting cis-regulatory activity, our understanding of how information from multiple enhancer elements converge to regulate a gene's expression remains elusive. This is in large part due to the number of different biological processes involved in mediating regulation as well as limited availability of experimental measurements for many of them. Here, we used a Bayesian approach to model diverse experimental regulatory data, leading to accurate predictions of both spatial and temporal aspects of gene expression. We integrated whole-embryo information on transcription factor recruitment to multiple cis-regulatory modules, insulator binding and histone modification status in the vicinity of individual gene loci, at a genome-wide scale during Drosophila development. The model uses Bayesian networks to represent the relation between transcription factor occupancy and enhancer activity in specific tissues and stages. All parameters are optimized in an Expectation Maximization procedure providing a model capable of predicting tissue- and stage-specific activity of new, previously unassayed genes. Performing the optimization with subsets of input data demonstrated that neither enhancer occupancy nor chromatin state alone can explain all gene expression patterns, but taken together allow for accurate predictions of spatio-temporal activity. Model predictions were validated using the expression patterns of more than 600 genes recently made available by the BDGP consortium, demonstrating an average 15-fold enrichment of genes expressed in the predicted tissue over a naïve model. We further validated the model by experimentally testing the expression of 20 predicted target genes of unknown expression, resulting in an accuracy of 95% for temporal predictions and 50% for spatial. While this is, to our knowledge, the first genome-wide approach to predict tissue-specific gene expression in metazoan development, our results suggest that integrative models of this type will become more prevalent in the future. Development is a complex process in which a single cell gives rise to a multi-cellular organism comprised of diverse cell types and well-organized tissues. This transformation requires tightly coordinated expression, both spatially and temporally, of hundreds to thousands of genes specific to any given tissue. To orchestrate these patterns, gene expression is regulated at multiple steps, from TF binding to cis-regulatory modules, general transcription factor and RNA polymerase II recruitment to promoters, chromatin remodeling, and three-dimensional looping interactions. Despite this level of complexity, the regulation of gene expression is typically modeled in the context of transcription factor binding and a single enhancer's activity as this is where the majority of experimental data is available. Recent advances in the measurement of chromatin modifications and insulator binding during embryogenesis provide new datasets that can be used for modeling gene expression. Here we use a Bayesian approach to integrate all three levels of information to combine the activity of multiple regulatory elements into a single model of a gene's expression, implementing an expectation maximization strategy to overcome the problem of missing data. Importantly, while the data for histone modifications and insulator binding represents merged signals from all cells in the embryo, the model can extract cell type specific and stage-specific predictions on gene expression for hundreds of genes of unknown expression.
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Affiliation(s)
- Bartek Wilczynski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Institute of Informatics, University of Warsaw, Warsaw, Poland
- * E-mail: (BW); (EEMF)
| | - Ya-Hsin Liu
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Zhen Xuan Yeo
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eileen E. M. Furlong
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- * E-mail: (BW); (EEMF)
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871
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Eun B, Sampley ML, Good AL, Gebert CM, Pfeifer K. Promoter cross-talk via a shared enhancer explains paternally biased expression of Nctc1 at the Igf2/H19/Nctc1 imprinted locus. Nucleic Acids Res 2012; 41:817-26. [PMID: 23221643 PMCID: PMC3553941 DOI: 10.1093/nar/gks1182] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Developmentally regulated transcription often depends on physical interactions between distal enhancers and their cognate promoters. Recent genomic analyses suggest that promoter–promoter interactions might play a similarly critical role in organizing the genome and establishing cell-type-specific gene expression. The Igf2/H19 locus has been a valuable model for clarifying the role of long-range interactions between cis-regulatory elements. Imprinted expression of the linked, reciprocally imprinted genes is explained by parent-of-origin-specific chromosomal loop structures between the paternal Igf2 or maternal H19 promoters and their shared tissue-specific enhancer elements. Here, we further analyze these loop structures for their composition and their impact on expression of the linked long non-coding RNA, Nctc1. We show that Nctc1 is co-regulated with Igf2 and H19 and physically interacts with the shared muscle enhancer. In fact, all three co-regulated genes have the potential to interact not only with the shared enhancer but also with each other via their enhancer interactions. Furthermore, developmental and genetic analyses indicate functional significance for these promoter–promoter interactions. Altogether, we present a novel mechanism to explain developmental specific imprinting of Nctc1 and provide new information about enhancer mechanisms and about the role of chromatin domains in establishing gene expression patterns.
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Affiliation(s)
- Bokkee Eun
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, National Institutes of Health, Bethesda, MD 20892, USA
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872
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Sandhu KS, Li G, Poh HM, Quek YLK, Sia YY, Peh SQ, Mulawadi FH, Lim J, Sikic M, Menghi F, Thalamuthu A, Sung WK, Ruan X, Fullwood MJ, Liu E, Csermely P, Ruan Y. Large-scale functional organization of long-range chromatin interaction networks. Cell Rep 2012; 2:1207-19. [PMID: 23103170 PMCID: PMC4181841 DOI: 10.1016/j.celrep.2012.09.022] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 07/31/2012] [Accepted: 09/24/2012] [Indexed: 11/27/2022] Open
Abstract
Chromatin interactions play important roles in transcription regulation. To better understand the underlying evolutionary and functional constraints of these interactions, we implemented a systems approach to examine RNA polymerase-II-associated chromatin interactions in human cells. We found that 40% of the total genomic elements involved in chromatin interactions converged to a giant, scale-free-like, hierarchical network organized into chromatin communities. The communities were enriched in specific functions and were syntenic through evolution. Disease-associated SNPs from genome-wide association studies were enriched among the nodes with fewer interactions, implying their selection against deleterious interactions by limiting the total number of interactions, a model that we further reconciled using somatic and germline cancer mutation data. The hubs lacked disease-associated SNPs, constituted a nonrandomly interconnected core of key cellular functions, and exhibited lethality in mouse mutants, supporting an evolutionary selection that favored the nonrandom spatial clustering of the least-evolving key genomic domains against random genetic or transcriptional errors in the genome. Altogether, our analyses reveal a systems-level evolutionary framework that shapes functionally compartmentalized and error-tolerant transcriptional regulation of human genome in three dimensions.
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Affiliation(s)
- Kuljeet Singh Sandhu
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Knowledge City, Sector 81, Mohali 140306, India
| | - Guoliang Li
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Huay Mei Poh
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Yu Ling Kelly Quek
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Australia
| | - Yee Yen Sia
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Su Qin Peh
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | | | - Joanne Lim
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Mile Sikic
- Bioinformatics Institute, 30 Biopolis Street, Singapore 138671
- Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR 10000 Zagreb, Croatia
| | - Francesca Menghi
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | | | - Wing Kin Sung
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- School of Computing, National University of Singapore, Singapore 117417
| | - Xiaoan Ruan
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Melissa Jane Fullwood
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- A*STAR-Duke-NUS Neuroscience Research Partnership, 8 College Road, Singapore 169857
| | - Edison Liu
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Peter Csermely
- Department of Medical Chemistry, School of Medicine, Semmelweis University, Tuzolto Street 37-47, Budapest 1094, Hungary
| | - Yijun Ruan
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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873
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Abstract
Cells face the challenge of storing two meters of DNA in the three-dimensional (3D) space of the nucleus that spans only a few microns. The nuclear organization that is required to overcome this challenge must allow for the accessibility of the gene regulatory machinery to the DNA and, in the case of embryonic stem cells (ESCs), for the transcriptional and epigenetic changes that accompany differentiation. Recent technological advances have allowed for the mapping of genome organization at an unprecedented resolution and scale. These breakthroughs have led to a deluge of new data, and a sophisticated understanding of the relationship between gene regulation and 3D genome organization is beginning to form. In this review we summarize some of the recent findings illuminating the 3D structure of the eukaryotic genome, as well as the relationship between genome topology and function from the level of whole chromosomes to enhancer-promoter loops with a focus on features affecting genome organization in ESCs and changes in nuclear organization during differentiation.
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Affiliation(s)
- Matthew Denholtz
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Molecular Biology Institute, Department of Biological Chemistry, David Geffen School of Medicine of the University of California, Los Angeles, CA, United States
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874
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Theodorou V, Stark R, Menon S, Carroll JS. GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility. Genome Res 2012; 23:12-22. [PMID: 23172872 PMCID: PMC3530671 DOI: 10.1101/gr.139469.112] [Citation(s) in RCA: 260] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Estrogen receptor (ESR1) drives growth in the majority of human breast cancers by binding to regulatory elements and inducing transcription events that promote tumor growth. Differences in enhancer occupancy by ESR1 contribute to the diverse expression profiles and clinical outcome observed in breast cancer patients. GATA3 is an ESR1-cooperating transcription factor mutated in breast tumors; however, its genomic properties are not fully defined. In order to investigate the composition of enhancers involved in estrogen-induced transcription and the potential role of GATA3, we performed extensive ChIP-sequencing in unstimulated breast cancer cells and following estrogen treatment. We find that GATA3 is pivotal in mediating enhancer accessibility at regulatory regions involved in ESR1-mediated transcription. GATA3 silencing resulted in a global redistribution of cofactors and active histone marks prior to estrogen stimulation. These global genomic changes altered the ESR1-binding profile that subsequently occurred following estrogen, with events exhibiting both loss and gain in binding affinity, implying a GATA3-mediated redistribution of ESR1 binding. The GATA3-mediated redistributed ESR1 profile correlated with changes in gene expression, suggestive of its functionality. Chromatin loops at the TFF locus involving ESR1-bound enhancers occurred independently of ESR1 when GATA3 was silenced, indicating that GATA3, when present on the chromatin, may serve as a licensing factor for estrogen–ESR1-mediated interactions between cis-regulatory elements. Together, these experiments suggest that GATA3 directly impacts ESR1 enhancer accessibility, and may potentially explain the contribution of mutant-GATA3 in the heterogeneity of ESR1+ breast cancer.
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Affiliation(s)
- Vasiliki Theodorou
- Nuclear Receptor Transcription Lab, Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
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875
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Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC, Yao WD, Myers RH, Chen JF, Preuss TM, Rogaev EI, Jensen JD, Weng Z, Akbarian S. Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS Biol 2012; 10:e1001427. [PMID: 23185133 PMCID: PMC3502543 DOI: 10.1371/journal.pbio.1001427] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 10/12/2012] [Indexed: 11/18/2022] Open
Abstract
Cognitive abilities and disorders unique to humans are thought to result from adaptively driven changes in brain transcriptomes, but little is known about the role of cis-regulatory changes affecting transcription start sites (TSS). Here, we mapped in human, chimpanzee, and macaque prefrontal cortex the genome-wide distribution of histone H3 trimethylated at lysine 4 (H3K4me3), an epigenetic mark sharply regulated at TSS, and identified 471 sequences with human-specific enrichment or depletion. Among these were 33 loci selectively methylated in neuronal but not non-neuronal chromatin from children and adults, including TSS at DPP10 (2q14.1), CNTN4 and CHL1 (3p26.3), and other neuropsychiatric susceptibility genes. Regulatory sequences at DPP10 and additional loci carried a strong footprint of hominid adaptation, including elevated nucleotide substitution rates and regulatory motifs absent in other primates (including archaic hominins), with evidence for selective pressures during more recent evolution and adaptive fixations in modern populations. Chromosome conformation capture at two neurodevelopmental disease loci, 2q14.1 and 16p11.2, revealed higher order chromatin structures resulting in physical contact of multiple human-specific H3K4me3 peaks spaced 0.5-1 Mb apart, in conjunction with a novel cis-bound antisense RNA linked to Polycomb repressor proteins and downregulated DPP10 expression. Therefore, coordinated epigenetic regulation via newly derived TSS chromatin could play an important role in the emergence of human-specific gene expression networks in brain that contribute to cognitive functions and neurological disease susceptibility in modern day humans.
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Affiliation(s)
- Hennady P. Shulha
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jessica L. Crisci
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Denis Reshetov
- Department of Human Genetics and Genomics, Vavilov Institute of General Genetics, Moscow, Russian Federation
| | - Jogender S. Tushir
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Iris Cheung
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Rahul Bharadwaj
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Hsin-Jung Chou
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Isaac B. Houston
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Cyril J. Peter
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Amanda C. Mitchell
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Wei-Dong Yao
- New England Primate Center, Southboro, Massachusetts, United States of America
| | - Richard H. Myers
- Department of Neurology, Boston University, Boston, Massachusetts, United States of America
| | - Jiang-fan Chen
- Department of Neurology, Boston University, Boston, Massachusetts, United States of America
| | - Todd M. Preuss
- Yerkes National Primate Research Center/Emory University, Atlanta, Georgia, United States of America
| | - Evgeny I. Rogaev
- Department of Human Genetics and Genomics, Vavilov Institute of General Genetics, Moscow, Russian Federation
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
| | - Jeffrey D. Jensen
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Schahram Akbarian
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Departments of Psychiatry and Neuroscience, Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York, United States of America
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876
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Alcina A, Fedetz M, Fernández O, Saiz A, Izquierdo G, Lucas M, Leyva L, García-León JA, Abad-Grau MDM, Alloza I, Antigüedad A, Garcia-Barcina MJ, Vandenbroeck K, Varadé J, de la Hera B, Arroyo R, Comabella M, Montalban X, Petit-Marty N, Navarro A, Otaegui D, Olascoaga J, Blanco Y, Urcelay E, Matesanz F. Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis. J Med Genet 2012; 50:25-33. [PMID: 23160276 PMCID: PMC3538279 DOI: 10.1136/jmedgenet-2012-101085] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background and aim Several studies have highlighted the association of the 12q13.3–12q14.1 region with coeliac disease, type 1 diabetes, rheumatoid arthritis and multiple sclerosis (MS); however, the causal variants underlying diseases are still unclear. The authors sought to identify the functional variant of this region associated with MS. Methods Tag-single nucleotide polymorphism (SNP) analysis of the associated region encoding 15 genes was performed in 2876 MS patients and 2910 healthy Caucasian controls together with expression regulation analyses. Results rs6581155, which tagged 18 variants within a region where 9 genes map, was sufficient to model the association. This SNP was in total linkage disequilibrium (LD) with other polymorphisms that associated with the expression levels of FAM119B, AVIL, TSFM, TSPAN31 and CYP27B1 genes in different expression quantitative trait loci studies. Functional annotations from Encyclopedia of DNA Elements (ENCODE) showed that six out of these rs6581155-tagged-SNPs were located in regions with regulatory potential and only one of them, rs10877013, exhibited allele-dependent (ratio A/G=9.5-fold) and orientation-dependent (forward/reverse=2.7-fold) enhancer activity as determined by luciferase reporter assays. This enhancer is located in a region where a long-range chromatin interaction among the promoters and promoter-enhancer of several genes has been described, possibly affecting their expression simultaneously. Conclusions This study determines a functional variant which alters the enhancer activity of a regulatory element in the locus affecting the expression of several genes and explains the association of the 12q13.3–12q14.1 region with MS.
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Affiliation(s)
- Antonio Alcina
- Department of Cell Biology and Immunology Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas (IPBLNCSIC), Granada, Spain
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877
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McEwan MV, Eccles MR, Horsfield JA. Cohesin is required for activation of MYC by estradiol. PLoS One 2012; 7:e49160. [PMID: 23145106 PMCID: PMC3493498 DOI: 10.1371/journal.pone.0049160] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 10/09/2012] [Indexed: 12/13/2022] Open
Abstract
Cohesin is best known as a multi-subunit protein complex that holds together replicated sister chromatids from S phase until G2. Cohesin also has an important role in the regulation of gene expression. We previously demonstrated that the cohesin complex positively regulates expression of the oncogene MYC. Cell proliferation driven by MYC contributes to many cancers, including breast cancer. The MYC oncogene is estrogen-responsive and a transcriptional target of estrogen receptor alpha (ERα). Estrogen-induced cohesin binding sites coincide with ERα binding at the MYC locus, raising the possibility that cohesin and ERα combine actions to regulate MYC transcription. The objective of this study was to investigate a putative role for cohesin in estrogen induction of MYC expression. We found that siRNA-targeted depletion of a cohesin subunit, RAD21, decreased MYC expression in ER-positive (MCF7 and T47D) and ER-negative (MDA-MB-231) breast cancer cell lines. In addition, RAD21 depletion blocked estradiol-mediated activation of MYC in ER-positive cell lines, and decreased ERα binding to estrogen response elements (EREs) upstream of MYC, without affecting total ERα levels. Treatment of MCF7 cells with estradiol caused enrichment of RAD21 binding at upstream enhancers and at the P2 promoter of MYC. Enriched binding at all sites, except the P2 promoter, was dependent on ERα. Since RAD21 depletion did not affect transcription driven by an exogenous reporter construct containing a naked ERE, chromatin-based mechanisms are likely to be involved in cohesin-dependent MYC transcription. This study demonstrates that ERα activation of MYC can be modulated by cohesin. Together, these results demonstrate a novel role for cohesin in estrogen-mediated regulation of MYC and the first evidence that cohesin plays a role in ERα binding.
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Affiliation(s)
- Miranda V. McEwan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Michael R. Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Julia A. Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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878
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Anamika K, Gyenis À, Tora L. How to stop: the mysterious links among RNA polymerase II occupancy 3' of genes, mRNA 3' processing and termination. Transcription 2012; 4:7-12. [PMID: 23131668 DOI: 10.4161/trns.22300] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic genes are transcribed by RNA polymerase II (RNAP II) through cycles of initiation, elongation and termination. Termination remains the least understood stage of transcription. Here we discuss the role of RNAP II occupancy downstream of the 3'ends of genes and its links with termination and mRNA 3' processing.
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Affiliation(s)
- Krishanpal Anamika
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch Cedex, France
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879
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880
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Marsman J, Horsfield JA. Long distance relationships: enhancer-promoter communication and dynamic gene transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:1217-27. [PMID: 23124110 DOI: 10.1016/j.bbagrm.2012.10.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/18/2012] [Accepted: 10/22/2012] [Indexed: 11/27/2022]
Abstract
The three-dimensional regulation of gene transcription involves loop formation between enhancer and promoter elements, controlling spatiotemporal gene expression in multicellular organisms. Enhancers are usually located in non-coding DNA and can activate gene transcription by recruiting transcription factors, chromatin remodeling factors and RNA Polymerase II. Research over the last few years has revealed that enhancers have tell-tale characteristics that facilitate their detection by several approaches, although the hallmarks of enhancers are not always uniform. Enhancers likely play an important role in the activation of genes by functioning as a primary point of contact for transcriptional activators, and by making physical contact with gene promoters often by means of a chromatin loop. Although numerous transcriptional regulators participate in the formation of chromatin loops that bring enhancers into proximity with promoters, the mechanism(s) of enhancer-promoter connectivity remain enigmatic. Here we discuss enhancer function, review some of the many proteins shown to be involved in establishing enhancer-promoter loops, and describe the dynamics of enhancer-promoter contacts during development, differentiation and in specific cell types.
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Affiliation(s)
- Judith Marsman
- Department of Pathology, The University of Otago, Dunedin, New Zealand
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881
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Papantonis A, Kohro T, Baboo S, Larkin JD, Deng B, Short P, Tsutsumi S, Taylor S, Kanki Y, Kobayashi M, Li G, Poh HM, Ruan X, Aburatani H, Ruan Y, Kodama T, Wada Y, Cook PR. TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J 2012; 31:4404-14. [PMID: 23103767 PMCID: PMC3512387 DOI: 10.1038/emboj.2012.288] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 09/24/2012] [Indexed: 11/09/2022] Open
Abstract
Tumour necrosis factor alpha (TNFα) is a potent cytokine that signals through nuclear factor kappa B (NFκB) to activate a subset of human genes. It is usually assumed that this involves RNA polymerases transcribing responsive genes wherever they might be in the nucleus. Using primary human endothelial cells, variants of chromosome conformation capture (including 4C and chromatin interaction analysis with paired-end tag sequencing), and fluorescence in situ hybridization to detect single nascent transcripts, we show that TNFα induces responsive genes to congregate in discrete 'NFκB factories'. Some factories further specialize in transcribing responsive genes encoding micro-RNAs that target downregulated mRNAs. We expect all signalling pathways to contain this extra leg, where responding genes are transcribed in analogous specialized factories.
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Affiliation(s)
- Argyris Papantonis
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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882
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ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 2012; 13:840-52. [PMID: 23090257 DOI: 10.1038/nrg3306] [Citation(s) in RCA: 485] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chromatin immunoprecipitation experiments followed by sequencing (ChIP-seq) detect protein-DNA binding events and chemical modifications of histone proteins. Challenges in the standard ChIP-seq protocol have motivated recent enhancements in this approach, such as reducing the number of cells that are required and increasing the resolution. Complementary experimental approaches - for example, DNaseI hypersensitive site mapping and analysis of chromatin interactions that are mediated by particular proteins - provide additional information about DNA-binding proteins and their function. These data are now being used to identify variability in the functions of DNA-binding proteins across genomes and individuals. In this Review, I describe the latest advances in methods to detect and functionally characterize DNA-bound proteins.
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883
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Holwerda S, de Laat W. Chromatin loops, gene positioning, and gene expression. Front Genet 2012; 3:217. [PMID: 23087710 PMCID: PMC3473233 DOI: 10.3389/fgene.2012.00217] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/01/2012] [Indexed: 01/09/2023] Open
Abstract
Technological developments and intense research over the last years have led to a better understanding of the 3D structure of the genome and its influence on genome function inside the cell nucleus. We will summarize topological studies performed on four model gene loci: the α- and β-globin gene loci, the antigen receptor loci, the imprinted H19-Igf2 locus and the Hox gene clusters. Collectively, these studies show that regulatory DNA sequences physically contact genes to control their transcription. Proteins set up the 3D configuration of the genome and we will discuss the roles of the key structural organizers CTCF and cohesin, the nuclear lamina and the transcription machinery. Finally, genes adopt non-random positions in the nuclear interior. We will review studies on gene positioning and propose that cell-specific genome conformations can juxtapose a regulatory sequence on one chromosome to a responsive gene on another chromosome to cause altered gene expression in subpopulations of cells.
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Affiliation(s)
- Sjoerd Holwerda
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht Utrecht, Netherlands
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884
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Neutralizing the function of a β-globin-associated cis-regulatory DNA element using an artificial zinc finger DNA-binding domain. Proc Natl Acad Sci U S A 2012; 109:17948-53. [PMID: 23074246 DOI: 10.1073/pnas.1207677109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene expression is primarily regulated by cis-regulatory DNA elements and trans-interacting proteins. Transcription factors bind in a DNA sequence-specific manner and recruit activities that modulate the association and activity of transcription complexes at specific genes. Often, transcription factors belong to families of related proteins that interact with similar DNA sequences. Furthermore, genes are regulated by multiple, sometimes redundant, cis-regulatory elements. Thus, the analysis of the role of a specific DNA regulatory sequence and the interacting proteins in the context of intact cells is challenging. In this study, we designed and functionally characterized an artificial DNA-binding domain that neutralizes the function of a cis-regulatory DNA element associated with adult β-globin gene expression. The zinc finger DNA-binding domain (ZF-DBD), comprising six ZFs, interacted specifically with a CACCC site located 90 bp upstream of the transcription start site (-90 β-ZF-DBD), which is normally occupied by KLF1, a major regulator of adult β-globin gene expression. Stable expression of the -90 β-ZF-DBD in mouse erythroleukemia cells reduced the binding of KLF1 with the β-globin gene, but not with locus control region element HS2, and led to reduced transcription. Transient transgenic embryos expressing the -90 β-ZF-DBD developed normally but revealed reduced expression of the adult β-globin gene. These results demonstrate that artificial DNA-binding proteins lacking effector domains are useful tools for studying and modulating the function of cis-regulatory DNA elements.
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885
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Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nat Immunol 2012; 13:1196-204. [PMID: 23064439 PMCID: PMC3501570 DOI: 10.1038/ni.2432] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 08/27/2012] [Indexed: 12/14/2022]
Abstract
The genome is folded into domains located in either transcriptionally inert or permissive compartments. Here we used genome-wide strategies to characterize domains during B cell development. Structured Interaction Matrix Analysis revealed that CTCF occupancy was primarily associated with intra-domain interactions, whereas p300, E2A and PU.1 bound sites were associated with intra- and inter-domain interactions that are developmentally regulated. We identified a spectrum of genes that switched nuclear location during early B cell development. In progenitors the transcriptionally inactive Ebf1 locus was sequestered at the nuclear lamina, thereby preserving multipotency. Upon development into the pro-B cell stage Ebf1 and other genes switched compartments to establish de novo intra- and inter-domain interactions that are associated with a B lineage specific transcription signature.
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886
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Abstract
Enhancers are regulatory DNA sequences that activate transcription over long distances. Recent studies revealed a widespread role of distant activation in eukaryotic gene regulation and in development of various human diseases, including cancer. Genomic and gene-targeted studies of enhancer action revealed novel mechanisms of transcriptional activation over a distance. They include formation of stable, inactive DNA-protein complexes at the enhancer and target promoter before activation, facilitated distant communication by looping of the spacer chromatin-covered DNA, and promoter activation by mechanisms that are different from classic recruiting. These studies suggest the similarity between the looping mechanisms involved in enhancer action on DNA in bacteria and in chromatin of higher organisms.
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887
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Xu Z, Lefevre GM, Felsenfeld G. Chromatin structure, epigenetic mechanisms and long-range interactions in the human insulin locus. Diabetes Obes Metab 2012; 14 Suppl 3:1-11. [PMID: 22928559 PMCID: PMC6398329 DOI: 10.1111/j.1463-1326.2012.01645.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Regulation of gene expression in eukaryotes is largely dependent on variations in chromatin structure. More recently, it has become clear that this may involve not only local chromatin organization but also distant regulatory elements that participate in large-scale chromatin architecture within the nucleus. We describe recent methods that make possible the detection of such structures and apply them to analysis of the human insulin (INS) locus in pancreatic islets. We show that the INS gene is part of an extended 'open' chromatin domain that includes adjacent genes as well. We also find that in islets, the INS promoter is in physical contact with distant sites on the same human chromosome and notably, with the SYT8 gene, located nearly 300 kb away. The strength of the contact between INS and SYT8 is increased by glucose, and this results in stimulation of SYT8 expression. Inhibition of INS transcription decreases SYT8 expression. Furthermore, downregulation of SYT8 results in decreased secretion of insulin. Our results thus establish the existence of a regulatory network between the INS gene and other distant genes through long-range physical interactions, and suggest that such networks may have general importance for insulin biology and diabetes.
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Affiliation(s)
- Z Xu
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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888
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Palstra RJ, Grosveld F. Transcription factor binding at enhancers: shaping a genomic regulatory landscape in flux. Front Genet 2012; 3:195. [PMID: 23060900 PMCID: PMC3460357 DOI: 10.3389/fgene.2012.00195] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 09/12/2012] [Indexed: 12/26/2022] Open
Abstract
The mammalian genome is packed tightly in the nucleus of the cell. This packing is primarily facilitated by histone proteins and results in an ordered organization of the genome in chromosome territories that can be roughly divided in heterochromatic and euchromatic domains. On top of this organization several distinct gene regulatory elements on the same chromosome or other chromosomes are thought to dynamically communicate via chromatin looping. Advances in genome-wide technologies have revealed the existence of a plethora of these regulatory elements in various eukaryotic genomes. These regulatory elements are defined by particular in vitro assays as promoters, enhancers, insulators, and boundary elements. However, recent studies indicate that the in vivo distinction between these elements is often less strict. Regulatory elements are bound by a mixture of common and lineage-specific transcription factors which mediate the long-range interactions between these elements. Inappropriate modulation of the binding of these transcription factors can alter the interactions between regulatory elements, which in turn leads to aberrant gene expression with disease as an ultimate consequence. Here we discuss the bi-modal behavior of regulatory elements that act in cis (with a focus on enhancers), how their activity is modulated by transcription factor binding and the effect this has on gene regulation.
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Affiliation(s)
- Robert-Jan Palstra
- Department of Cell Biology, Erasmus MC University Medical Center Rotterdam, Netherlands
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889
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Decker KF, Zheng D, He Y, Bowman T, Edwards JR, Jia L. Persistent androgen receptor-mediated transcription in castration-resistant prostate cancer under androgen-deprived conditions. Nucleic Acids Res 2012; 40:10765-79. [PMID: 23019221 PMCID: PMC3510497 DOI: 10.1093/nar/gks888] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The androgen receptor (AR) is a ligand-inducible transcription factor that mediates androgen action in target tissues. Upon ligand binding, the AR binds to thousands of genomic loci and activates a cell-type specific gene program. Prostate cancer growth and progression depend on androgen-induced AR signaling. Treatment of advanced prostate cancer through medical or surgical castration leads to initial response and durable remission, but resistance inevitably develops. In castration-resistant prostate cancer (CRPC), AR activity remains critical for tumor growth despite androgen deprivation. Although previous studies have focused on ligand-dependent AR signaling, in this study we explore AR function under the androgen-deprived conditions characteristic of CRPC. Our data demonstrate that AR persistently occupies a distinct set of genomic loci after androgen deprivation in CRPC. These androgen-independent AR occupied regions have constitutively open chromatin structures that lack the canonical androgen response element and are independent of FoxA1, a transcription factor involved in ligand-dependent AR targeting. Many AR binding events occur at proximal promoters, which can act as enhancers to augment transcriptional activities of other promoters through DNA looping. We further show that androgen-independent AR binding directs a gene expression program in CRPC, which is necessary for the growth of CRPC after androgen withdrawal.
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Affiliation(s)
- Keith F Decker
- Department of Medicine, Center for Pharmacogenomics, Washington University School of Medicine, St. Louis, MO 63110, USA
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890
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El-Kasti MM, Wells T, Carter DA. A novel long-range enhancer regulates postnatal expression of Zeb2: implications for Mowat-Wilson syndrome phenotypes. Hum Mol Genet 2012; 21:5429-42. [PMID: 23001561 DOI: 10.1093/hmg/dds389] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The zinc-finger, E-box-binding homeobox-2 (Zeb2) gene encodes a SMAD-interacting transcription factor that has diverse roles in development and disease. Mutations at the hZeb2 locus cause Mowat-Wilson syndrome (MWS), a genetic disorder that is associated with mental retardation and other, case- and sex-dependent clinical features. Recent studies have detailed microRNA-mediated control of Zeb2, but little is known about the genomic context of this gene or of enhancer sequences that may direct its diverse functions. Here, we describe a novel transgenic rodent model in which Zeb2 regulatory sequence has been disrupted, resulting in a postnatal developmental phenotype that is autosomal dominant. The phenotype exhibits a genotype-by-sex interaction and manifests primarily as an acute attenuation of postnatal kidney development in males. Other aspects of embryonic and neonatal development, including neuronal, are unaffected. The transgene insertion site is associated with a 12 kb deletion, 1.2 Mb upstream of Zeb2, within a 4.1 Mb gene desert. A conserved sequence, derived from the deleted region, enhanced Zeb2 promoter activity in transcription assays. Tissue and temporal restriction of this enhancer activity may involve postnatal changes in proteins that bind this sequence. A control human/mouse VISTA enhancer (62 kb upstream of Zeb2) also up-regulated the Zeb2 promoter, providing evidence of a string of conserved distal enhancers. The phenotype arising from deletion of one copy of the extreme long-range enhancer indicates a critical role for this enhancer at one developmental stage. Haploinsufficiency of Zeb2 in this developmental context reflects inheritance of MWS and may underlie some sex-dependent, non-neural characteristics of this human inherited disorder.
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Affiliation(s)
- Muna M El-Kasti
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford, UK
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891
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Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods 2012; 9:969-72. [PMID: 22961246 DOI: 10.1038/nmeth.2173] [Citation(s) in RCA: 293] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/17/2012] [Indexed: 01/22/2023]
Abstract
Regulatory DNA elements can control the expression of distant genes via physical interactions. Here we present a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using chromosome conformation capture combined with high-throughput sequencing (4C-seq). Our approach can be multiplexed and routinely integrated with other functional genomics assays to facilitate physical characterization of gene regulation.
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892
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Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, Sandstrom R, Bates D, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Harding L, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature 2012; 489:75-82. [PMID: 22955617 PMCID: PMC3721348 DOI: 10.1038/nature11232] [Citation(s) in RCA: 1920] [Impact Index Per Article: 160.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/15/2012] [Indexed: 02/07/2023]
Abstract
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation.
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Affiliation(s)
- Robert E. Thurman
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Eric Rynes
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Richard Humbert
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | | | - Hao Wang
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Kavita Garg
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Abigail K. Ebersol
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Tristan Frum
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Lisa Harding
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Audra K. Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Ericka M. Johnson
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Tanya Kutyavin
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Bryan Lajoie
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | - Bum-Kyu Lee
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Darin London
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Dimitra Lotakis
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Fidencio Neri
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Eric D. Nguyen
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Alex P. Reynolds
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Vaughn Roach
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexias Safi
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Minerva E. Sanchez
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Amartya Sanyal
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | - Anthony Shafer
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Jeremy M. Simon
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Lingyun Song
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Molly Weaver
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Zhancheng Zhang
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Zhuzhu Zhang
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Boris Lenhard
- Bergen Center for Computational Science, University of Bergen, Bergen, Norway
| | - Muneesh Tewari
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Michael O. Dorschner
- Dept. of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA
| | - R. Scott Hansen
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Patrick A. Navas
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | | | - Vishwanath R. Iyer
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
| | - Jason D. Lieb
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Shamil R. Sunyaev
- Dept. of Medicine, Division of Genetics, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Peter J. Sabo
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Rajinder Kaul
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Terrence S. Furey
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Job Dekker
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | | | - John A. Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Medicine, Division of Oncology, University of Washington, Seattle, WA
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893
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Abstract
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.
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894
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Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA. Systematic localization of common disease-associated variation in regulatory DNA. Science 2012; 337:1190-5. [PMID: 22955828 DOI: 10.1126/science.1222794] [Citation(s) in RCA: 2506] [Impact Index Per Article: 208.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies have identified many noncoding variants associated with common diseases and traits. We show that these variants are concentrated in regulatory DNA marked by deoxyribonuclease I (DNase I) hypersensitive sites (DHSs). Eighty-eight percent of such DHSs are active during fetal development and are enriched in variants associated with gestational exposure-related phenotypes. We identified distant gene targets for hundreds of variant-containing DHSs that may explain phenotype associations. Disease-associated variants systematically perturb transcription factor recognition sequences, frequently alter allelic chromatin states, and form regulatory networks. We also demonstrated tissue-selective enrichment of more weakly disease-associated variants within DHSs and the de novo identification of pathogenic cell types for Crohn's disease, multiple sclerosis, and an electrocardiogram trait, without prior knowledge of physiological mechanisms. Our results suggest pervasive involvement of regulatory DNA variation in common human disease and provide pathogenic insights into diverse disorders.
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Affiliation(s)
- Matthew T Maurano
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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895
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Euskirchen G, Auerbach RK, Snyder M. SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions. J Biol Chem 2012; 287:30897-905. [PMID: 22952240 PMCID: PMC3438922 DOI: 10.1074/jbc.r111.309302] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromatin-remodeling enzymes play essential roles in many biological processes, including gene expression, DNA replication and repair, and cell division. Although one such complex, SWI/SNF, has been extensively studied, new discoveries are still being made. Here, we review SWI/SNF biochemistry; highlight recent genomic and proteomic advances; and address the role of SWI/SNF in human diseases, including cancer and viral infections. These studies have greatly increased our understanding of complex nuclear processes.
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Affiliation(s)
- Ghia Euskirchen
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA
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896
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A map of the cis-regulatory sequences in the mouse genome. Nature 2012; 488:116-20. [PMID: 22763441 DOI: 10.1038/nature11243] [Citation(s) in RCA: 1061] [Impact Index Per Article: 88.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 05/18/2012] [Indexed: 01/19/2023]
Abstract
The laboratory mouse is the most widely used mammalian model organism in biomedical research. The 2.6 × 10(9) bases of the mouse genome possess a high degree of conservation with the human genome, so a thorough annotation of the mouse genome will be of significant value to understanding the function of the human genome. So far, most of the functional sequences in the mouse genome have yet to be found, and the cis-regulatory sequences in particular are still poorly annotated. Comparative genomics has been a powerful tool for the discovery of these sequences, but on its own it cannot resolve their temporal and spatial functions. Recently, ChIP-Seq has been developed to identify cis-regulatory elements in the genomes of several organisms including humans, Drosophila melanogaster and Caenorhabditis elegans. Here we apply the same experimental approach to a diverse set of 19 tissues and cell types in the mouse to produce a map of nearly 300,000 murine cis-regulatory sequences. The annotated sequences add up to 11% of the mouse genome, and include more than 70% of conserved non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we show that much of the mouse genome is organized into domains of coordinately regulated enhancers and promoters. Our results provide a resource for the annotation of functional elements in the mammalian genome and for the study of mechanisms regulating tissue-specific gene expression.
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897
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Chen H, Monte E, Parvatiyar MS, Rosa-Garrido M, Franklin S, Vondriska TM. Structural considerations for chromatin state models with transcription as a functional readout. FEBS Lett 2012; 586:3548-54. [PMID: 22940112 DOI: 10.1016/j.febslet.2012.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 08/16/2012] [Accepted: 08/16/2012] [Indexed: 02/07/2023]
Abstract
Lacking from the rapidly evolving field of chromatin regulation is a discrete model of chromatin states. We propose that each state in such a model should meet two conditions: a structural component and a quantifiable effect on transcription. The practical benefits to the field of a model with greater than two states (including one with six states, as described herein) would be to improve interpretation of data from disparate organ systems, to reflect temporal and developmental dynamics and to integrate the, at present, conceptually and experimentally disparate analyses of individual genetic loci (in vitro or using single gene approaches) and genome-wide features (including ChlP-seq, chromosomal capture and mRNA expression via microarrays/sequencing).
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Affiliation(s)
- Haodong Chen
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, United States
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898
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Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J. Normalization of a chromosomal contact map. BMC Genomics 2012; 13:436. [PMID: 22935139 PMCID: PMC3534615 DOI: 10.1186/1471-2164-13-436] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 08/21/2012] [Indexed: 12/23/2022] Open
Abstract
Background Chromatin organization has been increasingly studied in relation with its important influence on DNA-related metabolic processes such as replication or regulation of gene expression. Since its original design ten years ago, capture of chromosome conformation (3C) has become an essential tool to investigate the overall conformation of chromosomes. It relies on the capture of long-range trans and cis interactions of chromosomal segments whose relative proportions in the final bank reflect their frequencies of interactions, hence their spatial proximity in a population of cells. The recent coupling of 3C with deep sequencing approaches now allows the generation of high resolution genome-wide chromosomal contact maps. Different protocols have been used to generate such maps in various organisms. This includes mammals, drosophila and yeast. The massive amount of raw data generated by the genomic 3C has to be carefully processed to alleviate the various biases and byproducts generated by the experiments. Our study aims at proposing a simple normalization procedure to minimize the influence of these unwanted but inevitable events on the final results. Results Careful analysis of the raw data generated previously for budding yeast S. cerevisiae led to the identification of three main biases affecting the final datasets, including a previously unknown bias resulting from the circularization of DNA molecules. We then developed a simple normalization procedure to process the data and allow the generation of a normalized, highly contrasted, chromosomal contact map for S. cerevisiae. The same method was then extended to the first human genome contact map. Using the normalized data, we revisited the preferential interactions originally described between subsets of discrete chromosomal features. Notably, the detection of preferential interactions between tRNA in yeast and CTCF, PolII binding sites in human can vary with the normalization procedure used. Conclusions We quantitatively reanalyzed the genomic 3C data obtained for S. cerevisiae, identified some of the biases inherent to the technique and proposed a simple normalization procedure to analyse them. Such an approach can be easily generalized for genomic 3C experiments in other organisms. More experiments and analysis will be necessary to reach optimal resolution and accuracies of the maps generated through these approaches. Working with cell population presenting highest levels of homogeneity will prove useful in this regards.
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Affiliation(s)
- Axel Cournac
- LPTMC, UMR 7600, Tour 12-13/13-23, Boîte 121, 4, Place Jussieu, 75252 Paris Cedex 05, France
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899
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Lelli KM, Slattery M, Mann RS. Disentangling the many layers of eukaryotic transcriptional regulation. Annu Rev Genet 2012; 46:43-68. [PMID: 22934649 DOI: 10.1146/annurev-genet-110711-155437] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Regulation of gene expression in eukaryotes is an extremely complex process. In this review, we break down several critical steps, emphasizing new data and techniques that have expanded current gene regulatory models. We begin at the level of DNA sequence where cis-regulatory modules (CRMs) provide important regulatory information in the form of transcription factor (TF) binding sites. In this respect, CRMs function as instructional platforms for the assembly of gene regulatory complexes. We discuss multiple mechanisms controlling complex assembly, including cooperative DNA binding, combinatorial codes, and CRM architecture. The second section of this review places CRM assembly in the context of nucleosomes and condensed chromatin. We discuss how DNA accessibility and histone modifications contribute to TF function. Lastly, new advances in chromosomal mapping techniques have provided increased understanding of intra- and interchromosomal interactions. We discuss how these topological maps influence gene regulatory models.
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Affiliation(s)
- Katherine M Lelli
- Department of Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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900
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Zhang J, Poh HM, Peh SQ, Sia YY, Li G, Mulawadi FH, Goh Y, Fullwood MJ, Sung WK, Ruan X, Ruan Y. ChIA-PET analysis of transcriptional chromatin interactions. Methods 2012; 58:289-99. [PMID: 22926262 DOI: 10.1016/j.ymeth.2012.08.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 08/16/2012] [Accepted: 08/16/2012] [Indexed: 11/19/2022] Open
Abstract
Long-range chromatin contacts between specific DNA regulatory elements play a pivotal role in gene expression regulation, and a global characterization of these interactions in the 3-dimensional (3D) chromatin structure is imperative in understanding signaling networks and cell states. Chromatin Interaction Analysis using Paired-End Tag sequencing (ChIA-PET) is a method which converts functional chromatin structure into millions of short tag sequences. Combining Chromatin Immunoprecipitation (ChIP), proximity ligation and high-throughput sequencing, ChIA-PET provides a global and unbiased interrogation of higher-order chromatin structures associated with specific protein factors. Here, we describe the detailed procedures of the ChIA-PET methodology, unraveling transcription-associated chromatin contacts in a model human cell line.
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Affiliation(s)
- Jingyao Zhang
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
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