1351
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Tanizawa H, Noma KI. Unravelling global genome organization by 3C-seq. Semin Cell Dev Biol 2011; 23:213-21. [PMID: 22120510 DOI: 10.1016/j.semcdb.2011.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 11/09/2011] [Accepted: 11/10/2011] [Indexed: 11/29/2022]
Abstract
Eukaryotic genomes exist in the cell nucleus as an elaborate three-dimensional structure which reflects various nuclear processes such as transcription, DNA replication and repair. Next-generation sequencing (NGS) combined with chromosome conformation capture (3C), referred to as 3C-seq in this article, has recently been applied to the yeast and human genomes, revealing genome-wide views of functional associations among genes and their regulatory elements. Here, we compare the latest genomic approaches such as 3C-seq and ChIA-PET, and provide a condensed overview of how eukaryotic genomes are functionally organized in the nucleus.
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1352
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Harnessing of the nucleosome-remodeling-deacetylase complex controls lymphocyte development and prevents leukemogenesis. Nat Immunol 2011; 13:86-94. [PMID: 22080921 PMCID: PMC3868219 DOI: 10.1038/ni.2150] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 09/24/2011] [Indexed: 12/11/2022]
Abstract
Cell fate decisions depend on the interplay between chromatin regulators and transcription factors. Here we show that activity of the Mi-2β nucleosome remodeling and deacetylase (NuRD) complex was controlled by the Ikaros family of lymphoid-lineage determining proteins. Ikaros, an integral component of the NuRD complex in lymphocytes, tethered this complex to active lymphoid differentiation genes. Loss in Ikaros DNA binding activity caused a local increase in Mi-2β chromatin remodeling and histone deacetylation and suppression of lymphoid gene expression. The NuRD complex also redistributed to transcriptionally poised non-Ikaros gene targets, involved in proliferation and metabolism, inducing their reactivation. Thus, release of NuRD from Ikaros regulation blocks lymphocyte maturation and mediates progression to a leukemic state by engaging functionally opposing epigenetic and genetic networks.
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1353
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Wang XQD, Crutchley JL, Dostie J. Shaping the Genome with Non-Coding RNAs. Curr Genomics 2011; 12:307-21. [PMID: 21874119 PMCID: PMC3145261 DOI: 10.2174/138920211796429772] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 05/16/2011] [Accepted: 05/17/2011] [Indexed: 01/19/2023] Open
Abstract
The human genome must be tightly packaged in order to fit inside the nucleus of a cell. Genome organization is functional rather than random, which allows for the proper execution of gene expression programs and other biological processes. Recently, three-dimensional chromatin organization has emerged as an important transcriptional control mechanism. For example, enhancers were shown to regulate target genes by physically interacting with them regardless of their linear distance and even if located on different chromosomes. These chromatin contacts can be measured with the "chromosome conformation capture" (3C) technology and other 3C-related techniques. Given the recent innovation of 3C-derived approaches, it is not surprising that we still know very little about the structure of our genome at high-resolution. Even less well understood is whether there exist distinct types of chromatin contacts and importantly, what regulates them. A new form of regulation involving the expression of long non-coding RNAs (lncRNAs) was recently identified. lncRNAs are a very abundant class of non-coding RNAs that are often expressed in a tissue-specific manner. Although their different subcellular localizations point to their involvement in numerous cellular processes, it is clear that lncRNAs play an important role in regulating gene expression. How they control transcription however is mostly unknown. In this review, we provide an overview of known lncRNA transcription regulation activities. We also discuss potential mechanisms by which ncRNAs might exert three-dimensional transcriptional control and what recent studies have revealed about their role in shaping our genome.
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Affiliation(s)
- Xue Q D Wang
- Department of Biochemistry, and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir-William- Osler, Room 815A, Montréal, Québec, H3G1Y6, Canada
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1354
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Tena JJ, Alonso ME, de la Calle-Mustienes E, Splinter E, de Laat W, Manzanares M, Gómez-Skarmeta JL. An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation. Nat Commun 2011; 2:310. [PMID: 21556064 DOI: 10.1038/ncomms1301] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 04/04/2011] [Indexed: 01/22/2023] Open
Abstract
Developmental gene clusters are paradigms for the study of gene regulation; however, the mechanisms that mediate phenomena such as coregulation and enhancer sharing remain largely elusive. Here we address this issue by analysing the vertebrate Irx clusters. We first present a deep enhancer screen of a 2-Mbp span covering the IrxA cluster. Using chromosome conformation capture, we show that enhancer sharing is widespread within the cluster, explaining its evolutionarily conserved organization. We also identify a three-dimensional architecture, probably formed through interactions with CCCTC-binding factor, which is present within both Irx clusters of mouse, Xenopus and zebrafish. This architecture brings the promoters of the first two genes together in the same chromatin landscape. We propose that this unique and evolutionarily conserved genomic architecture of the vertebrate Irx clusters is essential for the coregulation of the first two genes and simultaneously maintains the third gene in a partially independent regulatory landscape.
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Affiliation(s)
- Juan J Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Carretera de Utrera Km1, 41013 Sevilla, Spain
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1355
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Panigrahi AK, Zhang N, Mao Q, Pati D. Calpain-1 cleaves Rad21 to promote sister chromatid separation. Mol Cell Biol 2011; 31:4335-47. [PMID: 21876002 PMCID: PMC3209327 DOI: 10.1128/mcb.06075-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 08/18/2011] [Indexed: 01/24/2023] Open
Abstract
Defining the mechanisms of chromosomal cohesion and dissolution of the cohesin complex from chromatids is important for understanding the chromosomal missegregation seen in many tumor cells. Here we report the identification of a novel cohesin-resolving protease and describe its role in chromosomal segregation. Sister chromatids are held together by cohesin, a multiprotein ring-like complex comprised of Rad21, Smc1, Smc3, and SA2 (or SA1). Cohesin is known to be removed from vertebrate chromosomes by two distinct mechanisms, namely, the prophase and anaphase pathways. First, PLK1-mediated phosphorylation of SA2 in prophase leads to release of cohesin from chromosome arms, leaving behind centromeric cohesins that continue to hold the sisters together. Then, at the onset of anaphase, activated separase cleaves the centromeric cohesin Rad21, thereby opening the cohesin ring and allowing the sister chromatids to separate. We report here that the calcium-dependent cysteine endopeptidase calpain-1 is a Rad21 peptidase and normally localizes to the interphase nuclei and chromatin. Calpain-1 cleaves Rad21 at L192, in a calcium-dependent manner. We further show that Rad21 cleavage by calpain-1 promotes separation of chromosome arms, which coincides with a calcium-induced partial loss of cohesin at several chromosomal loci. Engineered cleavage of Rad21 at the calpain-cleavable site without activation of calpain-1 can lead to a loss of sister chromatid cohesion. Collectively, our work reveals a novel function of calpain-1 and describes an additional pathway for sister chromatid separation in humans.
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Affiliation(s)
- Anil K Panigrahi
- Department of Pediatric Hematology/Oncology, Baylor College of Medicine, 1102 Bates Avenue, Suite 1220, Houston, TX 77030.
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1356
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Newkirk D, Biesinger J, Chon A, Yokomori K, Xie X. AREM: aligning short reads from ChIP-sequencing by expectation maximization. J Comput Biol 2011; 18:1495-505. [PMID: 22035330 PMCID: PMC3216101 DOI: 10.1089/cmb.2011.0185] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
High-throughput sequencing coupled to chromatin immunoprecipitation (ChIP-Seq) is widely used in characterizing genome-wide binding patterns of transcription factors, cofactors, chromatin modifiers, and other DNA binding proteins. A key step in ChIP-Seq data analysis is to map short reads from high-throughput sequencing to a reference genome and identify peak regions enriched with short reads. Although several methods have been proposed for ChIP-Seq analysis, most existing methods only consider reads that can be uniquely placed in the reference genome, and therefore have low power for detecting peaks located within repeat sequences. Here, we introduce a probabilistic approach for ChIP-Seq data analysis that utilizes all reads, providing a truly genome-wide view of binding patterns. Reads are modeled using a mixture model corresponding to K enriched regions and a null genomic background. We use maximum likelihood to estimate the locations of the enriched regions, and implement an expectation-maximization (E-M) algorithm, called AREM (aligning reads by expectation maximization), to update the alignment probabilities of each read to different genomic locations. We apply the algorithm to identify genome-wide binding events of two proteins: Rad21, a component of cohesin and a key factor involved in chromatid cohesion, and Srebp-1, a transcription factor important for lipid/cholesterol homeostasis. Using AREM, we were able to identify 19,935 Rad21 peaks and 1,748 Srebp-1 peaks in the mouse genome with high confidence, including 1,517 (7.6%) Rad21 peaks and 227 (13%) Srebp-1 peaks that were missed using only uniquely mapped reads. The open source implementation of our algorithm is available at http://sourceforge.net/projects/arem.
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Affiliation(s)
- Daniel Newkirk
- Department of Biological Chemistry, University of California, Irvine, California
- The Institute for Genomics and Bioinformatics, University of California, Irvine, California
| | - Jacob Biesinger
- Department of Computer Science, University of California, Irvine, California
- The Institute for Genomics and Bioinformatics, University of California, Irvine, California
| | - Alvin Chon
- Department of Computer Science, University of California, Irvine, California
- The Institute for Genomics and Bioinformatics, University of California, Irvine, California
| | - Kyoko Yokomori
- Department of Biological Chemistry, University of California, Irvine, California
| | - Xiaohui Xie
- Department of Computer Science, University of California, Irvine, California
- The Institute for Genomics and Bioinformatics, University of California, Irvine, California
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Abstract
Genome instability is a hallmark of cancer cells and how it arises is still not completely understood. Correct chromosome segregation is a pre-requisite for preserving genome integrity. Cohesin helps to ensure faithful chromosome segregation during cell cycle, however, much evidence regarding its functions have come to light over the last few years and suggest that cohesin plays multiple roles in the maintenance of genome stability. Here we review our rapidly increasing knowledge on the involvement of cohesin pathway in genome stability and cancer.
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Affiliation(s)
- Linda Mannini
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Richerche, Pisa, Italy
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1358
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Kang H, Lieberman PM. Mechanism of glycyrrhizic acid inhibition of Kaposi's sarcoma-associated herpesvirus: disruption of CTCF-cohesin-mediated RNA polymerase II pausing and sister chromatid cohesion. J Virol 2011; 85:11159-69. [PMID: 21880767 PMCID: PMC3194953 DOI: 10.1128/jvi.00720-11] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 08/22/2011] [Indexed: 12/24/2022] Open
Abstract
Glycyrrhizic acid (GA), a derivative of licorice, selectively inhibits the growth of lymphocytes latently infected with Kaposi's sarcoma-associated herpesvirus. The mechanism involves the deregulation of the multicistronic latency transcript, including the failure to generate the mature forms of viral mRNA encoding LANA. We show here that GA disrupts an RNA polymerase II (RNAPII) complex that accumulates at the CTCF-cohesin binding site within the first intron of the latency transcript. GA altered the enrichment of the RNAPII pausing complex, along with pausing factors SPT5 and NELF-A, at the intragenic CTCF-cohesin binding sites. GA blocked the interaction of cohesin subunit SMC3 with another cohesin subunit, RAD21, and reduced SPT5 interaction with RNAPII. Covalent coupling of GA to a solid support revealed that GA interacts with several cellular proteins, including SMC3 and SPT5, but not their respective interaction partners RAD21 and RNAPII. GA treatment also inhibited the transcription of some cellular genes, like c-myc, which contain a similar CTCF-cohesin binding site within the first intron. We also found that GA leads to a more general loss of sister chromatid cohesion for cellular chromosomes. These findings suggest that RNAPII pauses at intragenic CTCF-cohesin binding sites and that abrogation of this pausing by GA leads to loss of proper mRNA production and defects in sister chromatid cohesion, a process important for both viral and cellular chromosome stability.
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Affiliation(s)
- Hyojeung Kang
- The Wistar Institute, Philadelphia, Pennsylvania 19104
- Kyungpook National University, Daegu, South Korea
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1359
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Yeo JC, Ng HH. Transcriptomic analysis of pluripotent stem cells: insights into health and disease. Genome Med 2011; 3:68. [PMID: 22035782 PMCID: PMC3239230 DOI: 10.1186/gm284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) hold tremendous clinical potential because of their ability to self-renew, and to differentiate into all cell types of the body. This unique capacity of ESCs and iPSCs to form all cell lineages is termed pluripotency. While ESCs and iPSCs are pluripotent and remarkably similar in appearance, whether iPSCs truly resemble ESCs at the molecular level is still being debated. Further research is therefore needed to resolve this issue before iPSCs may be safely applied in humans for cell therapy or regenerative medicine. Nevertheless, the use of iPSCs as an in vitro human genetic disease model has been useful in studying the molecular pathology of complex genetic diseases, as well as facilitating genetic or drug screens. Here, we review recent progress in transcriptomic approaches in the study of ESCs and iPSCs, and discuss how deregulation of these pathways may be involved in the development of disease. Finally, we address the importance of these advances for developing new therapeutics, and the future challenges facing the clinical application of ESCs and iPSCs.
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Affiliation(s)
- Jia-Chi Yeo
- Gene Regulation Laboratory, Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672.
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1360
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Majumder P, Boss JM. Cohesin regulates MHC class II genes through interactions with MHC class II insulators. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2011; 187:4236-44. [PMID: 21911605 PMCID: PMC3186872 DOI: 10.4049/jimmunol.1100688] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cohesin is a multiprotein, ringed complex that is most well-known for its role in stabilizing the association of sister chromatids between S phase and M. More recently, cohesin was found to be associated with transcriptional insulators, elements that are associated with the organization of chromatin into regulatory domains. The human MHC class II (MHC-II) locus contains 10 intergenic elements, termed MHC-II insulators, which bind the transcriptional insulator protein CCCTC-binding factor. MHC-II insulators interact with each other, forming a base architecture of discrete loops and potential regulatory domains. When MHC-II genes are expressed, their proximal promoter regulatory regions reorganize to the foci established by the interacting MHC-II insulators. MHC-II insulators also bind cohesin, but the functional role of cohesin in regulating this system is not known. In this article, we show that the binding of cohesin to MHC-II insulators occurred irrespective of MHC-II expression but was required for optimal expression of the HLA-DR and HLA-DQ genes. In a DNA-dependent manner, cohesin subunits interacted with CCCTC-binding factor and the MHC-II-specific transcription factors regulatory factor X and CIITA. Intriguingly, cohesin subunits were important for DNA looping interactions between the HLA-DRA promoter region and a 5' MHC-II insulator but were not required for interactions between the MHC-II insulators themselves. This latter observation introduces cohesin as a regulator of MHC-II expression by initiating or stabilizing MHC-II promoter regulatory element interactions with the MHC-II insulator elements, events that are required for maximal MHC-II transcription.
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Affiliation(s)
- Parimal Majumder
- Department of Microbiology & Immunology, 1510 Clifton Rd, Emory University School of Medicine, Atlanta, GA 30322
| | - Jeremy M. Boss
- Department of Microbiology & Immunology, 1510 Clifton Rd, Emory University School of Medicine, Atlanta, GA 30322
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1361
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Fay A, Misulovin Z, Li J, Schaaf CA, Gause M, Gilmour DS, Dorsett D. Cohesin selectively binds and regulates genes with paused RNA polymerase. Curr Biol 2011; 21:1624-34. [PMID: 21962715 PMCID: PMC3193539 DOI: 10.1016/j.cub.2011.08.036] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/07/2011] [Accepted: 08/16/2011] [Indexed: 11/24/2022]
Abstract
BACKGROUND The cohesin complex mediates sister chromatid cohesion and regulates gene transcription. Prior studies show that cohesin preferentially binds and regulates genes that control growth and differentiation and that even mild disruption of cohesin function alters development. Here we investigate how cohesin specifically recognizes and regulates genes that control development in Drosophila. RESULTS Genome-wide analyses show that cohesin selectively binds genes in which RNA polymerase II (Pol II) pauses just downstream of the transcription start site. These genes often have GAGA factor (GAF) binding sites 100 base pairs (bp) upstream of the start site, and GT dinucleotide repeats 50 to 800 bp downstream in the plus strand. They have low levels of histone H3 lysine 36 trimethylation (H3K36me3) associated with transcriptional elongation, even when highly transcribed. Cohesin depletion does not reduce polymerase pausing, in contrast to depletion of the NELF (negative elongation factor) pausing complex. Cohesin, NELF, and Spt5 pausing and elongation factor knockdown experiments indicate that cohesin does not inhibit binding of polymerase to promoters or physically block transcriptional elongation, but at genes that it strongly represses, it hinders transition of paused polymerase to elongation at a step distinct from those controlled by Spt5 and NELF. CONCLUSIONS Our findings argue that cohesin and pausing factors are recruited independently to the same genes, perhaps by GAF and the GT repeats, and that their combined action determines the level of actively elongating RNA polymerase.
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Affiliation(s)
- Avery Fay
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, USA 63108
| | - Ziva Misulovin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, USA 63108
| | - Jian Li
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA 16802
| | - Cheri A. Schaaf
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, USA 63108
| | - Maria Gause
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, USA 63108
| | - David S. Gilmour
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA 16802
| | - Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, USA 63108
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1362
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Lin JJ, Lehmann LW, Bonora G, Sridharan R, Vashisht AA, Tran N, Plath K, Wohlschlegel JA, Carey M. Mediator coordinates PIC assembly with recruitment of CHD1. Genes Dev 2011; 25:2198-209. [PMID: 21979373 DOI: 10.1101/gad.17554711] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Murine Chd1 (chromodomain helicase DNA-binding protein 1), a chromodomain-containing chromatin remodeling protein, is necessary for embryonic stem (ES) cell pluripotency. Chd1 binds to nucleosomes trimethylated at histone 3 Lys 4 (H3K4me3) near the beginning of active genes but not to bivalent domains also containing H3K27me3. To address the mechanism of this specificity, we reproduced H3K4me3- and CHD1-stimulated gene activation in HeLa extracts. Multidimensional protein identification technology (MuDPIT) and immunoblot analyses of purified preinitiation complexes (PICs) revealed the recruitment of CHD1 to naive chromatin but enhancement on H3K4me3 chromatin. Studies in depleted extracts showed that the Mediator coactivator complex, which controls PIC assembly, is also necessary for CHD1 recruitment. MuDPIT analyses of CHD1-associated proteins support the recruitment data and reveal numerous components of the PIC, including Mediator. In vivo, CHD1 and Mediator are recruited to an inducible gene, and genome-wide binding of the two proteins correlates well with active gene transcription in mouse ES cells. Finally, coimmunoprecipitation of CHD1 and Mediator from cell extracts can be ablated by shRNA knockdown of a specific Mediator subunit. Our data support a model in which the Mediator coordinates PIC assembly along with the recruitment of CHD1. The combined action of the PIC and H3K4me3 provides specificity in targeting CHD1 to active genes.
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Affiliation(s)
- Justin J Lin
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
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1363
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Das S, Jena S, Levasseur DN. Alternative splicing produces Nanog protein variants with different capacities for self-renewal and pluripotency in embryonic stem cells. J Biol Chem 2011; 286:42690-42703. [PMID: 21969378 DOI: 10.1074/jbc.m111.290189] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Embryonic stem (ES) cells are distinguished by their ability to undergo unlimited self-renewal although retaining pluripotency, the capacity to specify cells of all germ layers. Alternative splicing contributes to these biological processes by vastly increasing the protein coding repertoire, enabling genes to code for novel variants that may confer different biological functions. The homeodomain transcription factor Nanog acts collaboratively with core factors Oct4 and Sox2 to govern the maintenance of pluripotency. We have discovered that Nanog is regulated by alternative splicing. Two novel exons and six subexons have been identified that extend the known Nanog gene structure and protein coding capacity. Alternative splicing results in two novel Nanog protein variants with attenuated capacities for self-renewal and pluripotency in ES cells. Our previous results have implicated the C-terminal domain, including the tryptophan-rich (WR) domain of Nanog, to be important for the function of Nanog (Wang, J., Levasseur, D. N., and Orkin, S. H. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 6326-6331). Using point mutation analyses, serine 2 (Ser-2) of Nanog has been identified as critical for ES cell self-renewal and for stabilizing a pluripotent gene signature. An inducible conditional knock-out was created to test the ability of new Nanog variants to genetically complement Nanog null ES cells. These results reveal for the first time an expanded Nanog protein coding capacity. We further reveal that a short region of the N-terminal domain and a single phosphorylatable Ser-2 is essential for the maintenance of self-renewal and pluripotency, demonstrating that this region of the protein is highly regulated.
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Affiliation(s)
- Satyabrata Das
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Snehalata Jena
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Dana N Levasseur
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242; Program in Molecular and Cellular Biology, University of Iowa, Iowa City, Iowa 52242.
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1364
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Chien R, Zeng W, Ball AR, Yokomori K. Cohesin: a critical chromatin organizer in mammalian gene regulation. Biochem Cell Biol 2011; 89:445-58. [PMID: 21851156 PMCID: PMC4056987 DOI: 10.1139/o11-039] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cohesins are evolutionarily conserved essential multi-protein complexes that are important for higher-order chromatin organization. They play pivotal roles in the maintenance of genome integrity through mitotic chromosome regulation, DNA repair and replication, as well as gene regulation critical for proper development and cellular differentiation. In this review, we will discuss the multifaceted functions of mammalian cohesins and their apparent functional hierarchy in the cell, with particular focus on their actions in gene regulation and their relevance to human developmental disorders.
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Affiliation(s)
- Richard Chien
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California 92697-1700, USA
| | - Weihua Zeng
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California 92697-1700, USA
| | - Alexander R. Ball
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California 92697-1700, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California 92697-1700, USA
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1365
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Unraveling framework of the ancestral Mediator complex in human diseases. Biochimie 2011; 94:579-87. [PMID: 21983542 DOI: 10.1016/j.biochi.2011.09.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 09/15/2011] [Indexed: 01/13/2023]
Abstract
Mediator (MED) is a fundamental component of the RNA polymerase II-mediated transcription machinery. This multiprotein complex plays a pivotal role in the regulation of eukaryotic mRNA synthesis. The yeast Mediator complex consists of 26 different subunits. Recent studies indicate additional pathogenic roles for Mediator, for example during transcription elongation and non-coding RNA production. Mediator subunits have been emerging also to have pathophysiological roles suggesting MED-dependent therapeutic targets involving in several diseases, such as cancer, cardiovascular disease (CVD), metabolic and neurological disorders.
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1366
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Muto A, Calof AL, Lander AD, Schilling TF. Multifactorial origins of heart and gut defects in nipbl-deficient zebrafish, a model of Cornelia de Lange Syndrome. PLoS Biol 2011; 9:e1001181. [PMID: 22039349 PMCID: PMC3201921 DOI: 10.1371/journal.pbio.1001181] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 09/13/2011] [Indexed: 12/31/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is the founding member of a class of multi-organ system birth defect syndromes termed cohesinopathies, named for the chromatin-associated protein complex cohesin, which mediates sister chromatid cohesion. Most cases of CdLS are caused by haploinsufficiency for Nipped-B-like (Nipbl), a highly conserved protein that facilitates cohesin loading. Consistent with recent evidence implicating cohesin and Nipbl in transcriptional regulation, both CdLS cell lines and tissues of Nipbl-deficient mice show changes in the expression of hundreds of genes. Nearly all such changes are modest, however--usually less than 1.5-fold--raising the intriguing possibility that, in CdLS, severe developmental defects result from the collective action of many otherwise innocuous perturbations. As a step toward testing this hypothesis, we developed a model of nipbl-deficiency in zebrafish, an organism in which we can quantitatively investigate the combinatorial effects of gene expression changes. After characterizing the structure and embryonic expression of the two zebrafish nipbl genes, we showed that morpholino knockdown of these genes produces a spectrum of specific heart and gut/visceral organ defects with similarities to those in CdLS. Analysis of nipbl morphants further revealed that, as early as gastrulation, expression of genes involved in endodermal differentiation (sox32, sox17, foxa2, and gata5) and left-right patterning (spaw, lefty2, and dnah9) is altered. Experimental manipulation of the levels of several such genes--using RNA injection or morpholino knockdown--implicated both additive and synergistic interactions in causing observed developmental defects. These findings support the view that birth defects in CdLS arise from collective effects of quantitative changes in gene expression. Interestingly, both the phenotypes and gene expression changes in nipbl morphants differed from those in mutants or morphants for genes encoding cohesin subunits, suggesting that the transcriptional functions of Nipbl cannot be ascribed simply to its role in cohesin loading.
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Affiliation(s)
- Akihiko Muto
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
| | - Anne L. Calof
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
- Department of Anatomy and Neurobiology, University of California, Irvine, California, United States of America
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
| | - Thomas F. Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
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1367
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Millau JF, Gaudreau L. CTCF, cohesin, and histone variants: connecting the genome. Biochem Cell Biol 2011; 89:505-13. [PMID: 21970734 DOI: 10.1139/o11-052] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
During the last decades our view of the genome organization has changed. We moved from a linear view to a looped view of the genome. It is now well established that inter- and intra-connections occur between chromosomes and play a major role in gene regulations. These interconnections are mainly orchestrated by the CTCF protein, which is also known as the "master weaver" of the genome. Recent advances in sequencing and genome-wide studies revealed that CTCF binds to DNA at thousands of sites within the human genome, providing the possibility to form thousands of genomic connection hubs. Strikingly, two histone variants, namely H2A.Z and H3.3, strongly co-localize at CTCF binding sites. In this article, we will review the recent advances in CTCF biology and discuss the role of histone variants H2A.Z and H3.3 at CTCF binding sites.
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Affiliation(s)
- Jean-François Millau
- Department of Biology, Faculty of Sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
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1368
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Murrell A. Setting up and maintaining differential insulators and boundaries for genomic imprinting. Biochem Cell Biol 2011; 89:469-78. [PMID: 21936680 DOI: 10.1139/o11-043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
It is becoming increasingly clear that gene expression is strongly regulated by the surrounding chromatin and nuclear environment. Gene regulatory elements can influence expression over long distances and the genome needs mechanisms whereby transcription can be contained. Our current understanding of the mechanisms whereby insulator/boundary elements organise the genome into active and silent domains is based on chromatin looping models that separate genes and regulatory elements. Imprinted genes have parent-of-origin specific chromatin conformation that seems to be maintained in somatic tissues and reprogrammed in the germline. This review focuses on the proteins found to be present at insulator/boundary sequences at imprinted genes and examines the experimental evidence at the IGF2-H19 locus for a model in which CTCF or other proteins determine primary looping scaffolds that are maintained in most cell lineages and speculates how these loops may enable dynamic secondary associations that can activate or silence genes.
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1369
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Isolated NIBPL missense mutations that cause Cornelia de Lange syndrome alter MAU2 interaction. Eur J Hum Genet 2011; 20:271-6. [PMID: 21934712 DOI: 10.1038/ejhg.2011.175] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS; or Brachmann-de Lange syndrome) is a dominantly inherited congenital malformation disorder with features that include characteristic facies, cognitive delays, growth retardation and limb anomalies. Mutations in nearly 60% of CdLS patients have been identified in NIPBL, which encodes a regulator of the sister chromatid cohesion complex. NIPBL, also known as delangin, is a homolog of yeast and amphibian Scc2 and C. elegans PQN-85. Although the exact mechanism of NIPBL function in sister chromatid cohesion is unclear, in vivo yeast and C. elegans experiments and in vitro vertebrate cell experiments have demonstrated that NIPBL/Scc2 functionally interacts with the MAU2/Scc4 protein to initiate loading of cohesin onto chromatin. To test the significance of this model in the clinical setting of CdLS, we fine-mapped the NIBPL-MAU2 interaction domain and tested the functional significance of missense mutations and variants in NIPBL and MAU2 identified in these minimal domains in a cohort of patients with CdLS. We demonstrate that specific novel mutations at the N-terminus of the MAU2-interacting domain of NIBPL result in markedly reduced MAU2 binding, although we appreciate no consistent clinical difference in the small group of patients with these mutations. These data suggest that factors in addition to MAU2 are essential in determining the clinical features and severity of CdLS.
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1370
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Carrière L, Graziani S, Alibert O, Ghavi-Helm Y, Boussouar F, Humbertclaude H, Jounier S, Aude JC, Keime C, Murvai J, Foglio M, Gut M, Gut I, Lathrop M, Soutourina J, Gérard M, Werner M. Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells. Nucleic Acids Res 2011; 40:270-83. [PMID: 21911356 PMCID: PMC3245943 DOI: 10.1093/nar/gkr737] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RNA polymerase (Pol) III synthesizes the tRNAs, the 5S ribosomal RNA and a small number of untranslated RNAs. In vitro, it also transcribes short interspersed nuclear elements (SINEs). We investigated the distribution of Pol III and its associated transcription factors on the genome of mouse embryonic stem cells using a highly specific tandem ChIP-Seq method. Only a subset of the annotated class III genes was bound and thus transcribed. A few hundred SINEs were associated with the Pol III transcription machinery. We observed that Pol III and its transcription factors were present at 30 unannotated sites on the mouse genome, only one of which was conserved in human. An RNA was associated with >80% of these regions. More than 2200 regions bound by TFIIIC transcription factor were devoid of Pol III. These sites were associated with cohesins and often located close to CTCF-binding sites, suggesting that TFIIIC might cooperate with these factors to organize the chromatin. We also investigated the genome-wide distribution of the ubiquitous TFIIS variant, TCEA1. We found that, as in Saccharomyces cerevisiae, TFIIS is associated with class III genes and also with SINEs suggesting that TFIIS is a Pol III transcription factor in mammals.
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Affiliation(s)
- Lucie Carrière
- Commissariat à l'Energie Atomique et aux Energies Alternatives, iBiTec-S, F-91191 Gif-sur-Yvette cedex, France
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1371
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Hashimoto S, Boissel S, Zarhrate M, Rio M, Munnich A, Egly JM, Colleaux L. MED23 mutation links intellectual disability to dysregulation of immediate early gene expression. Science 2011; 333:1161-3. [PMID: 21868677 DOI: 10.1126/science.1206638] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MED23 is a subunit of the Mediator complex, a key regulator of protein-coding gene expression. Here, we report a missense mutation (p. R617Q) in MED23 that cosegregates with nonsyndromic autosomal recessive intellectual disability. This mutation specifically impaired the response of JUN and FOS immediate early genes (IEGs) to serum mitogens by altering the interaction between enhancer-bound transcription factors (TCF4 and ELK1, respectively) and Mediator. Transcriptional dysregulation of these genes was also observed in cells derived from patients presenting with other neurological disorders linked to mutations in other Mediator subunits or proteins interacting with MED. These findings highlight the crucial role of Mediator in brain development and functioning and suggest that altered IEG expression might be a common molecular hallmark of cognitive deficit.
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Affiliation(s)
- Satoru Hashimoto
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université de Strasbourg, BP 163, 67404 Illkirch Cedex, C. U. Strasbourg, France
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1372
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Liu Z, Scannell DR, Eisen MB, Tjian R. Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell 2011; 146:720-31. [PMID: 21884934 PMCID: PMC3191068 DOI: 10.1016/j.cell.2011.08.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 06/06/2011] [Accepted: 08/03/2011] [Indexed: 11/26/2022]
Abstract
Deciphering the molecular basis of pluripotency is fundamental to our understanding of development and embryonic stem cell function. Here, we report that TAF3, a TBP-associated core promoter factor, is highly enriched in ES cells. In this context, TAF3 is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. In addition to its role in the core promoter recognition complex TFIID, genome-wide binding studies reveal that TAF3 localizes to a subset of chromosomal regions bound by CTCF/cohesin that are selectively associated with genes upregulated by TAF3. Notably, CTCF directly recruits TAF3 to promoter distal sites and TAF3-dependent DNA looping is observed between the promoter distal sites and core promoters occupied by TAF3/CTCF/cohesin. Together, our findings support a new role of TAF3 in mediating long-range chromatin regulatory interactions that safeguard the finely-balanced transcriptional programs underlying pluripotency.
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Affiliation(s)
- Zhe Liu
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Devin R. Scannell
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael B. Eisen
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert Tjian
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720, USA
- LKS Bio-medical and Health Sciences Center, CIRM Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
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1373
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Kidd BN, Cahill DM, Manners JM, Schenk PM, Kazan K. Diverse roles of the Mediator complex in plants. Semin Cell Dev Biol 2011; 22:741-8. [DOI: 10.1016/j.semcdb.2011.07.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 07/17/2011] [Indexed: 02/06/2023]
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1374
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Keightley MC, Layton JE, Hayman JW, Heath JK, Lieschke GJ. Mediator subunit 12 is required for neutrophil development in zebrafish. PLoS One 2011; 6:e23845. [PMID: 21901140 PMCID: PMC3162013 DOI: 10.1371/journal.pone.0023845] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 07/25/2011] [Indexed: 11/19/2022] Open
Abstract
Hematopoiesis requires the spatiotemporal organization of regulatory factors to successfully orchestrate diverse lineage specificity from stem and progenitor cells. Med12 is a regulatory component of the large Mediator complex that enables contact between the general RNA polymerase II transcriptional machinery and enhancer bound regulatory factors. We have identified a new zebrafish med12 allele, syr, with a single missense mutation causing a valine to aspartic acid change at position 1046. Syr shows defects in hematopoiesis, which predominantly affect the myeloid lineage. Syr has identified a hematopoietic cell-specific requirement for Med12, suggesting a new role for this transcriptional regulator.
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Affiliation(s)
- Maria-Cristina Keightley
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- Cancer and Haematology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Judith E. Layton
- Cancer and Haematology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - John W. Hayman
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- Cancer and Haematology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Joan K. Heath
- Colon Molecular and Cell Biology Laboratory, Melbourne Branch, Ludwig Institute for Cancer Research, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Graham J. Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- Cancer and Haematology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
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1375
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Prenzel T, Begus-Nahrmann Y, Kramer F, Hennion M, Hsu C, Gorsler T, Hintermair C, Eick D, Kremmer E, Simons M, Beissbarth T, Johnsen SA. Estrogen-dependent gene transcription in human breast cancer cells relies upon proteasome-dependent monoubiquitination of histone H2B. Cancer Res 2011; 71:5739-53. [PMID: 21862633 DOI: 10.1158/0008-5472.can-11-1896] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The estrogen receptor-α (ERα) determines the phenotype of breast cancers where it serves as a positive prognostic indicator. ERα is a well-established target for breast cancer therapy, but strategies to target its function remain of interest to address therapeutic resistance and further improve treatment. Recent findings indicate that proteasome inhibition can regulate estrogen-induced transcription, but how ERα function might be regulated was uncertain. In this study, we investigated the transcriptome-wide effects of the proteasome inhibitor bortezomib on estrogen-regulated transcription in MCF7 human breast cancer cells and showed that bortezomib caused a specific global decrease in estrogen-induced gene expression. This effect was specific because gene expression induced by the glucocorticoid receptor was unaffected by bortezomib. Surprisingly, we observed no changes in ERα recruitment or assembly of its transcriptional activation complex on ERα target genes. Instead, we found that proteasome inhibition caused a global decrease in histone H2B monoubiquitination (H2Bub1), leading to transcriptional elongation defects on estrogen target genes and to decreased chromatin dynamics overall. In confirming the functional significance of this link, we showed that RNA interference-mediated knockdown of the H2B ubiquitin ligase RNF40 decreased ERα-induced gene transcription. Surprisingly, RNF40 knockdown also supported estrogen-independent cell proliferation and activation of cell survival signaling pathways. Most importantly, we found that H2Bub1 levels decrease during tumor progression. H2Bub1 was abundant in normal mammary epithelium and benign breast tumors but absent in most malignant and metastatic breast cancers. Taken together, our findings show how ERα activity is blunted by bortezomib treatment as a result of reducing the downstream ubiquitin-dependent function of H2Bub1. In supporting a tumor suppressor role for H2Bub1 in breast cancer, our findings offer a rational basis to pursue H2Bub1-based therapies for future management of breast cancer.
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Affiliation(s)
- Tanja Prenzel
- Department of Molecular Oncology, Göttingen Center for Molecular Biosciences, Department of Medical Statistics, University Medical Center Göttingen, Germany
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1376
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Solomon DA, Kim T, Diaz-Martinez LA, Fair J, Elkahloun AG, Harris BT, Toretsky JA, Rosenberg SA, Shukla N, Ladanyi M, Samuels Y, James CD, Yu H, Kim JS, Waldman T. Mutational inactivation of STAG2 causes aneuploidy in human cancer. Science 2011; 333:1039-43. [PMID: 21852505 PMCID: PMC3374335 DOI: 10.1126/science.1203619] [Citation(s) in RCA: 333] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Most cancer cells are characterized by aneuploidy, an abnormal number of chromosomes. We have identified a clue to the mechanistic origins of aneuploidy through integrative genomic analyses of human tumors. A diverse range of tumor types were found to harbor deletions or inactivating mutations of STAG2, a gene encoding a subunit of the cohesin complex, which regulates the separation of sister chromatids during cell division. Because STAG2 is on the X chromosome, its inactivation requires only a single mutational event. Studying a near-diploid human cell line with a stable karyotype, we found that targeted inactivation of STAG2 led to chromatid cohesion defects and aneuploidy, whereas in two aneuploid human glioblastoma cell lines, targeted correction of the endogenous mutant alleles of STAG2 led to enhanced chromosomal stability. Thus, genetic disruption of cohesin is a cause of aneuploidy in human cancer.
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Affiliation(s)
- David A. Solomon
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, USA
| | - Taeyeon Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, USA
| | - Laura A. Diaz-Martinez
- Howard Hughes Medical Institute and Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshlean Fair
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, USA
| | - Abdel G. Elkahloun
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brent T. Harris
- Departments of Neurology and Pathology, Georgetown University School of Medicine, Washington, DC 20057, USA
| | - Jeffrey A. Toretsky
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, USA
| | - Steven A. Rosenberg
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neerav Shukla
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Yardena Samuels
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - C. David James
- Department of Neurological Surgery, Brain Tumor Research Center, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Hongtao Yu
- Howard Hughes Medical Institute and Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jung-Sik Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, USA
| | - Todd Waldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC 20057, USA
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1377
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Roy AL, Sen R, Roeder RG. Enhancer-promoter communication and transcriptional regulation of Igh. Trends Immunol 2011; 32:532-9. [PMID: 21855411 DOI: 10.1016/j.it.2011.06.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/23/2011] [Accepted: 06/23/2011] [Indexed: 12/18/2022]
Abstract
Transcriptional regulation of eukaryotic protein-coding genes requires the participation of site-specific transcription factors that bind distal regulatory elements, as well as factors that, together with RNA polymerase II, form the basal transcription machinery at the core promoter. Gene regulation requires proper communication between promoters and enhancers, often over great distances. Therefore, it is important to understand the potentially inter-related transcription factor interactions at both of these elements. How this is achieved on tissue-specific genes, such as the immunoglobulin heavy chain (IgH) in B cells remains unclear. Here, we review known interactions at the Igh variable region (V(H)) promoters and present our perspective on promoter-enhancer interactions that are likely important for Ig gene regulation in B cells.
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Affiliation(s)
- Ananda L Roy
- Program in Immunology, Department of Pathology, Tufts University School of Medicine, Boston, MA, USA.
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1378
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Recillas-Targa F, de la Rosa-Velázquez IA, Soto-Reyes E. Insulation of tumor suppressor genes by the nuclear factor CTCF. Biochem Cell Biol 2011; 89:479-88. [PMID: 21846316 DOI: 10.1139/o11-031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
One of the most outstanding nuclear factors, which has chromatin insulator and transcriptional properties and also contribute to genomic organization, is the zinc-finger protein CCCTC-binding factor (CTCF). Among its multiple functions, a growing amount of evidence implicates CTCF in the epigenetic regulation of genes responsible for the control of the cell cycle, and its mis-regulation can lead to aberrant epigenetic silencing of genes involved in cancer development. Detailed studies are now revealing that CTCF can serve as a barrier against the spread of DNA methylation and histone repressive marks over promoter regions of tumor suppressor genes. Moreover, new evidences points out to the capacity of CTCF to be covalently modified, in particular, through poly(ADP-ribosyl)ation with regulatory consequences. An unexplored aspect of CTCF is its intergenic and intragenic distribution in certain loci. Such distribution seems to facilitate the formation of an optimal chromatin structure and the recruitment of chromatin remodelers with the possible incorporation of RNA polymerase II. Therefore, in the context of tumor suppressor genes and cancer development, CTCF appears to play a relevant role by incorporating a combination of mechanisms involved in the protection against epigenetic silencing components and the maintenance of optimal higher-order organization of the corresponding loci.
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Affiliation(s)
- Félix Recillas-Targa
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, México.
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1379
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Poon BP, Mekhail K. Cohesin and related coiled-coil domain-containing complexes physically and functionally connect the dots across the genome. Cell Cycle 2011; 10:2669-82. [PMID: 21822055 PMCID: PMC3219537 DOI: 10.4161/cc.10.16.17113] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 07/05/2011] [Indexed: 12/17/2022] Open
Abstract
Interactions between genetic regions located across the genome maintain its three-dimensional organization and function. Recent studies point to key roles for a set of coiled-coil domain-containing complexes (cohibin, cohesin, condensin and monopolin) and related factors in the regulation of DNA-DNA connections across the genome. These connections are critical to replication, recombination, gene expression as well as chromosome segregation.
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Affiliation(s)
- Betty P.K Poon
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine; University of Toronto; Toronto, ON Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine; University of Toronto; Toronto, ON Canada
- Canada Research Chairs Program; Faculty of Medicine; University of Toronto; Toronto, ON Canada
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1380
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Ries D, Meisterernst M. Control of gene transcription by Mediator in chromatin. Semin Cell Dev Biol 2011; 22:735-40. [PMID: 21864698 DOI: 10.1016/j.semcdb.2011.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 08/02/2011] [Accepted: 08/08/2011] [Indexed: 01/07/2023]
Abstract
The Mediator complex serves as an adaptor for regulatory factors, recruits and controls RNA polymerase II promotes preinitiation complex formation and functions post initiation. There is increasing evidence for further coordinating roles of the Mediator complex in chromatin. Here we summarize interactions with regulatory, general and accessory factors that function in transcription and chromatin.
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Affiliation(s)
- David Ries
- Institute of Molecular Tumor Biology, Westfalian Wilhelms University, Münster, Germany, Robert-Koch Strasse 43, 48149 Münster, Germany
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1381
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Chen W, Roeder RG. Mediator-dependent nuclear receptor function. Semin Cell Dev Biol 2011; 22:749-58. [PMID: 21854863 DOI: 10.1016/j.semcdb.2011.07.026] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 12/24/2022]
Abstract
As gene-specific transcription factors, nuclear receptors are broadly involved in many important biological processes. Their function on target genes requires the stepwise assembly of different coactivator complexes that facilitate chromatin remodeling and subsequent preinitiation complex (PIC) formation and function. Mediator has proved to be a crucial, and general, nuclear receptor-interacting coactivator, with demonstrated functions in transcription steps ranging from chromatin remodeling to subsequent PIC formation and function. Here we discuss our current understanding of (i) pathways involved in Mediator recruitment and function through nuclear receptor target gene enhancers and promoters, (ii) conditional requirements for the strong nuclear receptor-Mediator interactions mediated by NR AF2 domains and the MED1 LXXLL motifs, (iii) Mediator functions, through different nuclear receptor-interacting subunits, in different metabolic pathways, (iv) emerging functions of Mediator as a corepressor in addition to its major role as a coactivator and (v) mechanisms by which Mediator acts to transmit signals from enhancer-bound nuclear receptors to the general transcription machinery at core promoters to effect PIC formation and function. As a nuclear receptor coregulator with increasingly diverse functions, Mediator may thus modulate nuclear receptor signaling through several different mechanisms.
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Affiliation(s)
- Wei Chen
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA.
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1382
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Seitan VC, Hao B, Tachibana-Konwalski K, Lavagnolli T, Mira-Bontenbal H, Brown KE, Teng G, Carroll T, Terry A, Horan K, Marks H, Adams DJ, Schatz DG, Aragon L, Fisher AG, Krangel MS, Nasmyth K, Merkenschlager M. A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation. Nature 2011; 476:467-71. [PMID: 21832993 PMCID: PMC3179485 DOI: 10.1038/nature10312] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 06/20/2011] [Indexed: 12/14/2022]
Abstract
Cohesin enables post-replicative DNA repair and chromosome segregation by holding sister chromatids together from the time of DNA replication in S phase until mitosis. There is growing evidence that cohesin also forms long-range chromosomal cis-interactions and may regulate gene expression in association with CTCF, mediator or tissue-specific transcription factors. Human cohesinopathies such as Cornelia de Lange syndrome are thought to result from impaired non-canonical cohesin functions, but a clear distinction between the cell-division-related and cell-division-independent functions of cohesion--as exemplified in Drosophila--has not been demonstrated in vertebrate systems. To address this, here we deleted the cohesin locus Rad21 in mouse thymocytes at a time in development when these cells stop cycling and rearrange their T-cell receptor (TCR) α locus (Tcra). Rad21-deficient thymocytes had a normal lifespan and retained the ability to differentiate, albeit with reduced efficiency. Loss of Rad21 led to defective chromatin architecture at the Tcra locus, where cohesion-binding sites flank the TEA promoter and the Eα enhancer, and demarcate Tcra from interspersed Tcrd elements and neighbouring housekeeping genes. Cohesin was required for long-range promoter-enhancer interactions, Tcra transcription, H3K4me3 histone modifications that recruit the recombination machinery and Tcra rearrangement. Provision of pre-rearranged TCR transgenes largely rescued thymocyte differentiation, demonstrating that among thousands of potential target genes across the genome, defective Tcra rearrangement was limiting for the differentiation of cohesin-deficient thymocytes. These findings firmly establish a cell-division-independent role for cohesin in Tcra locus rearrangement and provide a comprehensive account of the mechanisms by which cohesin enables cellular differentiation in a well-characterized mammalian system.
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MESH Headings
- Animals
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Chromosomal Proteins, Non-Histone/deficiency
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA-Binding Proteins
- Gene Expression Regulation
- Gene Rearrangement, T-Lymphocyte/genetics
- Genes, RAG-1/genetics
- Mice
- Nuclear Proteins/deficiency
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phosphoproteins/deficiency
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Recombinases/metabolism
- Thymus Gland/cytology
- Thymus Gland/metabolism
- Transcription, Genetic
- Cohesins
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Affiliation(s)
- Vlad C. Seitan
- Lymphocyte Development Group, Imperial College London, Du Cane Road, London W12 0NN, UK
- Cell Cycle Group, Imperial College London, Du Cane Road, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Bingtao Hao
- Department of Immunology, Duke University Medical Center, Durham NC, USA
| | | | - Thais Lavagnolli
- Lymphocyte Development Group, Imperial College London, Du Cane Road, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Hegias Mira-Bontenbal
- Lymphocyte Development Group, Imperial College London, Du Cane Road, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Karen E Brown
- Lymphocyte Development Group, Imperial College London, Du Cane Road, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Grace Teng
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, USA
| | - Tom Carroll
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Anna Terry
- Lymphocyte Development Group, Imperial College London, Du Cane Road, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Katie Horan
- Central Biological Services, Imperial College London, Du Cane Road, London, UK
| | - Hendrik Marks
- Department of Molecular Biology. Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, USA
| | - Luis Aragon
- Cell Cycle Group, Imperial College London, Du Cane Road, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Amanda G Fisher
- Lymphocyte Development Group, Imperial College London, Du Cane Road, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham NC, USA
| | - Kim Nasmyth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, Imperial College London, Du Cane Road, London W12 0NN, UK
- Epigenetics Section, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
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1383
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Noncoding RNAs and enhancers: complications of a long-distance relationship. Trends Genet 2011; 27:433-9. [PMID: 21831473 DOI: 10.1016/j.tig.2011.06.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 06/22/2011] [Accepted: 06/22/2011] [Indexed: 01/30/2023]
Abstract
Spatial and temporal regulation of gene expression is achieved through instructions provided by the distal transcriptional regulatory elements known as enhancers. How enhancers transmit such information to their targets has been the subject of intense investigation. Recent advances in high throughput analysis of the mammalian transcriptome have revealed a surprising result indicating that a large number of enhancers are transcribed to noncoding RNAs. Although long noncoding RNAs were initially shown to confer epigenetic transcriptional repression, recent studies have uncovered a role for a class of such transcripts in gene-specific activation, often from distal genomic regions. In this review, we discuss recent findings on the role of long noncoding RNAs in transcriptional regulation, with an emphasis on new developments on the functional links between long noncoding RNAs and enhancers.
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1384
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Interactions between subunits of the Mediator complex with gene-specific transcription factors. Semin Cell Dev Biol 2011; 22:759-68. [PMID: 21839847 DOI: 10.1016/j.semcdb.2011.07.022] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 07/26/2011] [Accepted: 07/28/2011] [Indexed: 11/24/2022]
Abstract
The Mediator complex forms the bridge between gene-specific transcription factors and the RNA polymerase II (RNAP II) machinery. Mediator is a large polypetide complex consisting of about thirty polypeptides that are mostly conserved from yeast to human. Mediator coordinates RNAP II recruitment, phosphorylation of the C-terminal domain of RNAP II, enhancer-loop formation and post-initiation events. The focus of the review is to summarize the current knowledge of transcription factor/Mediator interactions in higher eukaryotes and illuminate the physiological and gene-selective roles of Mediator.
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1385
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Zou H. The sister bonding of duplicated chromosomes. Semin Cell Dev Biol 2011; 22:566-71. [PMID: 21497666 PMCID: PMC3142318 DOI: 10.1016/j.semcdb.2011.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/23/2011] [Accepted: 03/30/2011] [Indexed: 11/21/2022]
Abstract
Sister chromatid cohesion and separation are two fundamental chromosome dynamics that are essential to equal chromosome segregation during cell proliferation. In this review, I will discuss the major steps that regulate these dynamics during mitosis, with an emphasis on vertebrate cells. The implications of these machineries outside of sister chromatid cohesion and separation are also discussed.
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Affiliation(s)
- Hui Zou
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75252-9148, United States.
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1386
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George CL, Lightman SL, Biddie SC. Transcription factor interactions in genomic nuclear receptor function. Epigenomics 2011; 3:471-85. [DOI: 10.2217/epi.11.66] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Transcription factors (TF) regulate gene expression acting as DNA sequence-specific binding factors, orchestrating cofactor recruitment and assembly of the transcriptional machinery. Nuclear receptors, a ligand-inducible TF class, regulate a large proportion of the genome, yet achieve highly cell-specific and context-dependent transcription, despite their widespread expression. High-throughput genome-wide profiling of TF binding reveals a startling proportion of colocalized cell- and context-specific TF-binding patterns, implying TF interactions play a critical role in transcription. These interactions depend on the chromatin architecture, that predominantly acts to predetermine accessibility of TF-binding sites at regulatory elements. Here, we summarize recent findings that highlight the importance of combinatorial TF interactions in determining diverse nuclear receptor-mediated transcriptional responses, emphasizing the significance of chromatin structure in directing TF and nuclear receptor recruitment. Interactions between TFs are likely to be a general mechanism of regulatory factors, contributing to transcriptional control in health and disease.
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Affiliation(s)
- Charlotte L George
- Henry Wellcome Laboratories for Integrative Neuroscience & Endocrinology, Faculty of Medicine & Dentistry, University of Bristol, Bristol, BS1 3NY, UK
| | - Stafford L Lightman
- Henry Wellcome Laboratories for Integrative Neuroscience & Endocrinology, Faculty of Medicine & Dentistry, University of Bristol, Bristol, BS1 3NY, UK
| | - Simon C Biddie
- Dorothy Hodgkin Building, Whitson Street, University of Bristol, Bristol, BS1 3NY, UK
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1387
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Manning AL, Dyson NJ. pRB, a tumor suppressor with a stabilizing presence. Trends Cell Biol 2011; 21:433-41. [PMID: 21664133 PMCID: PMC3149724 DOI: 10.1016/j.tcb.2011.05.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 05/04/2011] [Accepted: 05/05/2011] [Indexed: 01/19/2023]
Abstract
The product of the retinoblastoma tumor-susceptibility gene (RB1) is a key regulator of cell proliferation and this function is thought to be central to its tumor suppressive activity. Several studies have demonstrated that inactivation of pRB not only allows inappropriate proliferation but also undermines mitotic fidelity, leading to genome instability and ploidy changes. Such properties promote tumor evolution and correlate with increased resistance to therapeutics and tumor relapse. These observations suggest that inactivation of pRB could contribute to both tumor initiation and progression. Further characterization of the role of pRB in chromosome segregation will provide insight into processes that are misregulated in human tumors and could reveal new therapeutic targets to kill or stall these chromosomally unstable lesions. We review the evidence that pRB promotes genome stability and discuss the mechanisms that probably contribute to this effect.
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Affiliation(s)
- Amity L Manning
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, USA.
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1388
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Lin S, Ferguson-Smith AC, Schultz RM, Bartolomei MS. Nonallelic transcriptional roles of CTCF and cohesins at imprinted loci. Mol Cell Biol 2011; 31:3094-104. [PMID: 21628529 PMCID: PMC3147605 DOI: 10.1128/mcb.01449-10] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 01/29/2011] [Accepted: 05/17/2011] [Indexed: 11/20/2022] Open
Abstract
The cohesin complex holds sister chromatids together and is essential for chromosome segregation. Recently, cohesins have been implicated in transcriptional regulation and insulation through genome-wide colocalization with the insulator protein CTCF, including involvement at the imprinted H19/Igf2 locus. CTCF binds to multiple imprinted loci and is required for proper imprinted expression at the H19/Igf2 locus. Here we report that cohesins colocalize with CTCF at two additional imprinted loci, the Dlk1-Dio3 and the Kcnq1/Kcnq1ot1 loci. Similar to the H19/Igf2 locus, CTCF and cohesins preferentially bind to the Gtl2 differentially methylated region (DMR) on the unmethylated maternal allele. To determine the functional importance of the binding of CTCF and cohesins at the three imprinted loci, CTCF and cohesins were depleted in mouse embryonic fibroblast cells. The monoallelic expression of imprinted genes at these three loci was maintained. However, mRNA levels for these genes were typically increased; for H19 and Igf2 the increased level of expression was independent of the CTCF-binding sites in the imprinting control region. Results of these experiments demonstrate an unappreciated role for CTCF and cohesins in the repression of imprinted genes in somatic cells.
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Affiliation(s)
- Shu Lin
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Anne C. Ferguson-Smith
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Richard M. Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
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1389
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Integrated Gene Regulatory Circuits: Celebrating the 50th Anniversary of the Operon Model. Mol Cell 2011; 43:505-14. [DOI: 10.1016/j.molcel.2011.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/02/2011] [Accepted: 08/02/2011] [Indexed: 12/17/2022]
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1390
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Kang H, Wiedmer A, Yuan Y, Robertson E, Lieberman PM. Coordination of KSHV latent and lytic gene control by CTCF-cohesin mediated chromosome conformation. PLoS Pathog 2011; 7:e1002140. [PMID: 21876668 PMCID: PMC3158054 DOI: 10.1371/journal.ppat.1002140] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 05/10/2011] [Indexed: 12/22/2022] Open
Abstract
Herpesvirus persistence requires a dynamic balance between latent and lytic cycle gene expression, but how this balance is maintained remains enigmatic. We have previously shown that the Kaposi's Sarcoma-Associated Herpesvirus (KSHV) major latency transcripts encoding LANA, vCyclin, vFLIP, v-miRNAs, and Kaposin are regulated, in part, by a chromatin organizing element that binds CTCF and cohesins. Using viral genome-wide chromatin conformation capture (3C) methods, we now show that KSHV latency control region is physically linked to the promoter regulatory region for ORF50, which encodes the KSHV immediate early protein RTA. Other linkages were also observed, including an interaction between the 5' and 3' end of the latency transcription cluster. Mutation of the CTCF-cohesin binding site reduced or eliminated the chromatin conformation linkages, and deregulated viral transcription and genome copy number control. siRNA depletion of CTCF or cohesin subunits also disrupted chromosomal linkages and deregulated viral latent and lytic gene transcription. Furthermore, the linkage between the latent and lytic control region was subject to cell cycle fluctuation and disrupted during lytic cycle reactivation, suggesting that these interactions are dynamic and regulatory. Our findings indicate that KSHV genomes are organized into chromatin loops mediated by CTCF and cohesin interactions, and that these inter-chromosomal linkages coordinate latent and lytic gene control.
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Affiliation(s)
- Hyojeung Kang
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
- The Kyungpook National University, College of Pharmacy, Daegu, Korea
| | - Andreas Wiedmer
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Yan Yuan
- The University of Pennsylvania, School of Dentistry, Philadelphia, Pennsylvania, United States of America
| | - Erle Robertson
- The University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Paul M. Lieberman
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
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1391
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Tempera I, Klichinsky M, Lieberman PM. EBV latency types adopt alternative chromatin conformations. PLoS Pathog 2011; 7:e1002180. [PMID: 21829357 PMCID: PMC3145795 DOI: 10.1371/journal.ppat.1002180] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 06/09/2011] [Indexed: 12/18/2022] Open
Abstract
Epstein-Barr Virus (EBV) can establish latent infections with distinct gene expression patterns referred to as latency types. These different latency types are epigenetically stable and correspond to different promoter utilization. Here we explore the three-dimensional conformations of the EBV genome in different latency types. We employed Chromosome Conformation Capture (3C) assay to investigate chromatin loop formation between the OriP enhancer and the promoters that determine type I (Qp) or type III (Cp) gene expression. We show that OriP is in close physical proximity to Qp in type I latency, and to Cp in type III latency. The cellular chromatin insulator and boundary factor CTCF was implicated in EBV chromatin loop formation. Combining 3C and ChIP assays we found that CTCF is physically associated with OriP-Qp loop formation in type I and OriP-Cp loop formation in type III latency. Mutations in the CTCF binding site located at Qp disrupt loop formation between Qp and OriP, and lead to the activation of Cp transcription. Mutation of the CTCF binding site at Cp, as well as siRNA depletion of CTCF eliminates both OriP-associated loops, indicating that CTCF plays an integral role in loop formation. These data indicate that epigenetically stable EBV latency types adopt distinct chromatin architectures that depend on CTCF and mediate alternative promoter targeting by the OriP enhancer. Epstein-Barr Virus (EBV) latent infection is associated with several human malignancies. The viral genes expressed during latent infection can vary depending on host cell or tumor type. The different gene expression programs, referred to as latency types, are determined by alternative viral promoter usage. In this work, we investigate how differential DNA loop formation regulates viral promoter selection in different latency types. We use chromatin conformation capture methods to demonstrate that the transcriptional enhancer at OriP forms a stable loop with one of two different promoters, depending on the latency type. In type I latency, OriP forms a loop with the active Q promoter (Qp). In type III latency, OriP forms a loop with the active C promoter (Cp). Loop formation was mediated, in part, by CTCF binding sites located within the loops. Mutation in the CTCF binding site located at Qp caused a loss of OriP-Qp loop formation, a loss of Qp transcription, and a reactivation of Cp transcription from an alternative loop formed with OriP-Cp. These findings indicate that OriP loop formation is an integral component of promoter selection, and that chromatin conformation may determine EBV latency type.
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Affiliation(s)
- Italo Tempera
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Michael Klichinsky
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Paul M. Lieberman
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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1392
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Abstract
Cohesin is a member of the Smc family of protein complexes that mediates higher-order chromosome structure by tethering different regions of chromatin. We present a new in vitro system that assembles cohesin-DNA complexes with in vivo properties. The assembly of these physiological salt-resistant complexes requires the cohesin holo-complex, its ability to bind ATP, the cohesin loader Scc2p and a closed DNA topology. Both the number of cohesin molecules bound to the DNA substrate and their distribution on the DNA substrate are limited. Cohesin and Scc2p bind preferentially to cohesin associated regions (CARs), DNA sequences with enriched cohesin binding in vivo. A subsequence of CARC1 promotes cohesin binding to neighboring sequences within CARC1. The enhancer-like function of this sequence is validated by in vivo deletion analysis. By demonstrating the physiological relevance of these in vitro assembled cohesin-DNA complexes, we establish our in vitro system as a powerful tool to elucidate the mechanism of cohesin and other Smc complexes.
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Affiliation(s)
- Itay Onn
- Howard Hughes Medical Institute
- Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, MD 21218; and
| | - Douglas Koshland
- Howard Hughes Medical Institute
- Department of Molecular and Cell Biology, University of California, Berkeley, 16 Barker Hall #3202, Berkeley, CA 94720-3202
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1393
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Abstract
Pluripotency and self-renewal are the hallmarks of embryonic stem cells. This state is maintained by a network of transcription factors and is influenced by specific signalling pathways. Current evidence indicates that multiple pluripotent states can exist in vitro. Here we review the recent advances in studying the transcriptional regulatory networks that define pluripotency, and elaborate on how manipulation of signalling pathways can modulate pluripotent states to varying degrees.
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1394
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Choreographing pluripotency and cell fate with transcription factors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:337-49. [DOI: 10.1016/j.bbagrm.2011.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/15/2011] [Accepted: 06/15/2011] [Indexed: 01/12/2023]
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1395
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Stephens AD, Haase J, Vicci L, Taylor RM, Bloom K. Cohesin, condensin, and the intramolecular centromere loop together generate the mitotic chromatin spring. J Cell Biol 2011; 193:1167-80. [PMID: 21708976 PMCID: PMC3216333 DOI: 10.1083/jcb.201103138] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 05/25/2011] [Indexed: 01/18/2023] Open
Abstract
Sister chromatid cohesion provides the mechanistic basis, together with spindle microtubules, for generating tension between bioriented chromosomes in metaphase. Pericentric chromatin forms an intramolecular loop that protrudes bidirectionally from the sister chromatid axis. The centromere lies on the surface of the chromosome at the apex of each loop. The cohesin and condensin structural maintenance of chromosomes (SMC) protein complexes are concentrated within the pericentric chromatin, but whether they contribute to tension-generating mechanisms is not known. To understand how pericentric chromatin is packaged and resists tension, we map the position of cohesin (SMC3), condensin (SMC4), and pericentric LacO arrays within the spindle. Condensin lies proximal to the spindle axis and is responsible for axial compaction of pericentric chromatin. Cohesin is radially displaced from the spindle axis and confines pericentric chromatin. Pericentric cohesin and condensin contribute to spindle length regulation and dynamics in metaphase. Together with the intramolecular centromere loop, these SMC complexes constitute a molecular spring that balances spindle microtubule force in metaphase.
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Affiliation(s)
- Andrew D. Stephens
- Department of Biology and Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Julian Haase
- Department of Biology and Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Leandra Vicci
- Department of Biology and Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Russell M. Taylor
- Department of Biology and Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kerry Bloom
- Department of Biology and Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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1396
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Holdorf MM, Cooper SB, Yamamoto KR, Miranda JJL. Occupancy of chromatin organizers in the Epstein-Barr virus genome. Virology 2011; 415:1-5. [PMID: 21550623 PMCID: PMC3808970 DOI: 10.1016/j.virol.2011.04.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Revised: 02/11/2011] [Accepted: 04/15/2011] [Indexed: 01/02/2023]
Abstract
The human CCCTC-binding factor, CTCF, regulates transcription of the double-stranded DNA genomes of herpesviruses. The architectural complex cohesin and RNA Polymerase II also contribute to this organization. We profiled the occupancy of CTCF, cohesin, and RNA Polymerase II on the episomal genome of the Epstein-Barr virus in a cell culture model of latent infection. CTCF colocalizes with cohesin but not RNA Polymerase II. CTCF and cohesin bind specific sequences throughout the genome that are found not just proximal to the regulatory elements of latent genes, but also near lytic genes. In addition to tracking with known transcripts, RNA Polymerase II appears at two unannotated positions, one of which lies within the latent origin of replication. The widespread occupancy profile of each protein reveals binding near or at a myriad of regulatory elements and suggests context-dependent functions.
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MESH Headings
- Base Sequence
- CCCTC-Binding Factor
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Immunoprecipitation
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA, Viral/genetics
- DNA, Viral/metabolism
- DNA-Binding Proteins/metabolism
- Epstein-Barr Virus Nuclear Antigens/genetics
- Epstein-Barr Virus Nuclear Antigens/metabolism
- Gene Expression Regulation, Viral
- Genome, Viral
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/metabolism
- Herpesvirus 4, Human/physiology
- Humans
- Plasmids/genetics
- Promoter Regions, Genetic
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- Replication Origin/genetics
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Sequence Analysis, DNA
- Virus Latency
- Cohesins
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Affiliation(s)
- Meghan M. Holdorf
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158
| | - Samantha B. Cooper
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158
- Graduate Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA 94158
| | - Keith R. Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158
| | - JJL Miranda
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158
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1397
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Splinter E, de Wit E, Nora EP, Klous P, van de Werken HJG, Zhu Y, Kaaij LJT, van Ijcken W, Gribnau J, Heard E, de Laat W. The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev 2011; 25:1371-83. [PMID: 21690198 DOI: 10.1101/gad.633311] [Citation(s) in RCA: 257] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Three-dimensional topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between the transcriptional activity and the spatial environment of a gene, we used allele-specific chromosome conformation capture-on-chip (4C) technology to produce high-resolution topology maps of the active and inactive X chromosomes in female cells. We found that loci on the active X form multiple long-range interactions, with spatial segregation of active and inactive chromatin. On the inactive X, silenced loci lack preferred interactions, suggesting a unique random organization inside the inactive territory. However, escapees, among which is Xist, are engaged in long-range contacts with each other, enabling identification of novel escapees. Deletion of Xist results in partial refolding of the inactive X into a conformation resembling the active X without affecting gene silencing or DNA methylation. Our data point to a role for Xist RNA in shaping the conformation of the inactive X chromosome at least partially independent of transcription.
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Affiliation(s)
- Erik Splinter
- Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
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1398
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Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CWH, Ye C, Ping JLH, Mulawadi F, Wong E, Sheng J, Zhang Y, Poh T, Chan CS, Kunarso G, Shahab A, Bourque G, Cacheux-Rataboul V, Sung WK, Ruan Y, Wei CL. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011; 43:630-8. [PMID: 21685913 PMCID: PMC3436933 DOI: 10.1038/ng.857] [Citation(s) in RCA: 492] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/16/2011] [Indexed: 12/13/2022]
Abstract
Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. However, little is known about CTCF-associated higher-order chromatin structures at a global scale. Here we applied chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing to elucidate the CTCF-chromatin interactome in pluripotent cells. From this analysis, we identified 1,480 cis- and 336 trans-interacting loci with high reproducibility and precision. Associating these chromatin interaction loci with their underlying epigenetic states, promoter activities, enhancer binding and nuclear lamina occupancy, we uncovered five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive cross-talk between promoters and regulatory elements. This highly complex nuclear organization offers insights toward the unifying principles that govern genome plasticity and function.
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Affiliation(s)
| | - Han Xu
- Genome Institute of Singapore, Singapore 138672
| | - Guoliang Li
- Genome Institute of Singapore, Singapore 138672
| | | | - Elaine Chew
- Genome Institute of Singapore, Singapore 138672
| | | | | | - Chaopeng Ye
- Genome Institute of Singapore, Singapore 138672
| | | | | | - Eleanor Wong
- Genome Institute of Singapore, Singapore 138672
- National University of Singapore, Singapore 117543
| | | | - Yubo Zhang
- Genome Institute of Singapore, Singapore 138672
| | | | | | - Galih Kunarso
- Duke-NUS Graduate Medical School Singapore, Singapore 169857
| | - Atif Shahab
- Genome Institute of Singapore, Singapore 138672
| | | | | | - Wing-Kin Sung
- Genome Institute of Singapore, Singapore 138672
- National University of Singapore, Singapore 117543
| | - Yijun Ruan
- Genome Institute of Singapore, Singapore 138672
| | - Chia-Lin Wei
- Genome Institute of Singapore, Singapore 138672
- National University of Singapore, Singapore 117543
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1399
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Chatterjee S, Ju Z, Hassan R, Volpi SA, Emelyanov AV, Birshtein BK. Dynamic changes in binding of immunoglobulin heavy chain 3' regulatory region to protein factors during class switching. J Biol Chem 2011; 286:29303-29312. [PMID: 21685395 DOI: 10.1074/jbc.m111.243543] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The 3' regulatory region (3' RR) of the Igh locus works at long distances on variable region (V(H)) and switch region (I) region promoters to initiate germ line (non-coding) transcription (GT) and promote class switch recombination (CSR). The 3' RR contains multiple elements, including enhancers (hs3a, hs1.2, hs3b, and hs4) and a proposed insulator region containing CTCF (CCCTC-binding factor) binding sites, i.e. hs5/6/7 and the downstream region ("38"). Notably, deletion of each individual enhancer (hs3a-hs4) has no significant phenotypic consequence, suggesting that the 3' RR has considerable structural flexibility in its function. To better understand how the 3' RR functions, we identified transcription factor binding sites and used chromatin immunoprecipitation (ChIP) assays to monitor their occupancy in splenic B cells that initiate GT and undergo CSR (LPS±IL4), are deficient in GT and CSR (p50(-/-)), or do not undergo CSR despite efficient GT (anti-IgM+IL4). Like 3' RR enhancers, hs5-7 and the 38 region were observed to contain multiple Pax5 binding sites (in addition to multiple CTCF sites). We found that the Pax5 binding profile to the 3' RR dynamically changed during CSR independent of the specific isotype to which switching was induced, and binding focused on hs1.2, hs4, and hs7. CTCF-associated and CTCF-independent cohesin interactions were also identified. Our observations are consistent with a scaffold model in which a platform of active protein complexes capable of facilitating GT and CSR can be formed by varying constellations of 3' RR elements.
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Affiliation(s)
- Sanjukta Chatterjee
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Zhongliang Ju
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Rabih Hassan
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Sabrina A Volpi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Alexander V Emelyanov
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Barbara K Birshtein
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461.
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1400
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Lin W, Jin H, Liu X, Hampton K, Yu HG. Scc2 regulates gene expression by recruiting cohesin to the chromosome as a transcriptional activator during yeast meiosis. Mol Biol Cell 2011; 22:1985-96. [PMID: 21508318 PMCID: PMC3113765 DOI: 10.1091/mbc.e10-06-0545] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 04/08/2011] [Accepted: 04/12/2011] [Indexed: 11/11/2022] Open
Abstract
To tether sister chromatids, a protein-loading complex, including Scc2, recruits cohesin to the chromosome at discrete loci. Cohesin facilitates the formation of a higher-order chromosome structure that could also influence gene expression. How cohesin directly regulates transcription remains to be further elucidated. We report that in budding yeast Scc2 is required for sister-chromatid cohesion during meiosis for two reasons. First, Scc2 is required for activating the expression of REC8, which encodes a meiosis-specific cohesin subunit; second, Scc2 is necessary for recruiting meiotic cohesin to the chromosome to generate sister-chromatid cohesion. Using a heterologous reporter assay, we have found that Scc2 increases the activity of its target promoters by recruiting cohesin to establish an upstream cohesin-associated region in a position-dependent manner. Rec8-associated meiotic cohesin is required for the full activation of the REC8 promoter, revealing that cohesin has a positive feedback on transcriptional regulation. Finally, we provide evidence that chromosomal binding of cohesin is sufficient for target-gene activation during meiosis. Our data support a noncanonical role for cohesin as a transcriptional activator during cell differentiation.
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Affiliation(s)
- Weiqiang Lin
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4370
| | - Hui Jin
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4370
| | - Xiuwen Liu
- Department of Computer Science, Florida State University, Tallahassee, FL 32306-4370
| | - Kristin Hampton
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4370
| | - Hong-Guo Yu
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4370
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