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BRG1 Governs Nanog Transcription in Early Mouse Embryos and Embryonic Stem Cells via Antagonism of Histone H3 Lysine 9/14 Acetylation. Mol Cell Biol 2015; 35:4158-69. [PMID: 26416882 DOI: 10.1128/mcb.00546-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/22/2015] [Indexed: 12/19/2022] Open
Abstract
During mouse preimplantation development, the generation of the inner cell mass (ICM) and trophoblast lineages comprises upregulation of Nanog expression in the ICM and its silencing in the trophoblast. However, the underlying epigenetic mechanisms that differentially regulate Nanog in the first cell lineages are poorly understood. Here, we report that BRG1 (Brahma-related gene 1) cooperates with histone deacetylase 1 (HDAC1) to regulate Nanog expression. BRG1 depletion in preimplantation embryos and Cdx2-inducible embryonic stem cells (ESCs) revealed that BRG1 is necessary for Nanog silencing in the trophoblast lineage. Conversely, in undifferentiated ESCs, loss of BRG1 augmented Nanog expression. Analysis of histone H3 within the Nanog proximal enhancer revealed that H3 lysine 9/14 (H3K9/14) acetylation increased in BRG1-depleted embryos and ESCs. Biochemical studies demonstrated that HDAC1 was present in BRG1-BAF155 complexes and BRG1-HDAC1 interactions were enriched in the trophoblast lineage. HDAC1 inhibition triggered an increase in H3K9/14 acetylation and a corresponding rise in Nanog mRNA and protein, phenocopying BRG1 knockdown embryos and ESCs. Lastly, nucleosome-mapping experiments revealed that BRG1 is indispensable for nucleosome remodeling at the Nanog enhancer during trophoblast development. In summary, our data suggest that BRG1 governs Nanog expression via a dual mechanism involving histone deacetylation and nucleosome remodeling.
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Sheinman M, Chung HR. Conditions for positioning of nucleosomes on DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:022704. [PMID: 26382429 DOI: 10.1103/physreve.92.022704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Indexed: 06/05/2023]
Abstract
Positioning of nucleosomes along a eukaryotic genome plays an important role in its organization and regulation. There are many different factors affecting the location of nucleosomes. Some can be viewed as preferential binding of a single nucleosome to different locations along the DNA and some as interactions between neighboring nucleosomes. In this study, we analyze positioning of nucleosomes and derive conditions for their good positioning. Using analytic and numerical approaches we find that, if the binding preferences are very weak, an interplay between the interactions and the binding preferences is essential for a good positioning of nucleosomes, especially on correlated energy landscapes. Analyzing the empirical energy landscape, we conclude that good positioning of nucleosomes in vivo is possible only if they strongly interact. In this case, our model, predicting long-length-scale fluctuations of nucleosomes' occupancy along the DNA, accounts well for the empirical observations.
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Affiliation(s)
- Michael Sheinman
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ho-Ryun Chung
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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Abstract
Allelic imbalance of thymidylate synthase (TYMS) is attributed to polymorphisms in the 5'- and 3'-untranslated region (UTR). These polymorphisms have been related to the risk of suffering different cancers, for example leukemia, breast or gastric cancer, and response to different drugs, among which are methotrexate glutamates, stavudine, and specifically 5-fluorouracil (5-FU), as TYMS is its direct target. A vast literature has been published in relation to 5-FU, even suggesting the sole use of these polymorphisms to effectively manage 5-FU dosage. Estimates of the extent to which these polymorphisms influence in TYMS expression have in the past been based on functional analysis by luciferase assays and quantification of TYMS mRNA, but both these studies, as the association studies with cancer risk or with toxicity or response to 5-FU, are very contradictory. Regarding functional assays, the artificial genetic environment created in luciferase assay and the problems derived from quantitative polymerase chain reactions (qPCRs), for example the use of a reference gene, may have distorted the results. To avoid these sources of interference, we have analyzed the allelic imbalance of TYMS by allelic-specific analysis in peripheral blood mononuclear cells (PBMCs) from patients.Allelic imbalance in PBMCs, taken from 40 patients with suspected myeloproliferative haematological diseases, was determined by fluorescent fragment analysis (for the 3'-UTR polymorphism), Sanger sequencing and allelic-specific qPCR in multiplex (for the 5'-UTR polymorphisms).For neither the 3'- nor the 5'-UTR polymorphisms did the observed allelic imbalance exceed 1.5 fold. None of the TYMS polymorphisms is statistically associated with allelic imbalance.The results acquired allow us to deny the previously established assertion of an influence of 2 to 4 fold of the rs45445694 and rs2853542 polymorphisms in the expression of TYMS and narrow its allelic imbalance to 1.5 fold, in our population. These data circumscribe the influence of these polymorphisms in the clinical outcome of 5-FU and question their use for establishing 5-FU dosage, above all when additional genetic factors are not considered.
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Affiliation(s)
- Emilia Balboa-Beltrán
- From the Grupo de Medicina Xenómica (EB-B, RC, AC), CIBERER, Universidad de Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica (AC, FB), SERGAS, Santiago de Compostela, Spain; and Center of Excellence in Genomic Medicine Research (CEGMR) (AC), King Abdulaziz University, Jeddah, KSA
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Bicknell BA, Dayan P, Goodhill GJ. The limits of chemosensation vary across dimensions. Nat Commun 2015; 6:7468. [PMID: 26088726 PMCID: PMC4557358 DOI: 10.1038/ncomms8468] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 05/13/2015] [Indexed: 01/20/2023] Open
Abstract
Many biological processes rely on the ability of cells to measure local ligand concentration. However, such measurements are constrained by noise arising from diffusion and the stochastic nature of receptor–ligand interactions. It is thus critical to understand how accurately, in principle, concentration measurements can be made. Previous theoretical work has mostly investigated this in 3D under the simplifying assumption of an unbounded domain of diffusion, but many biological problems involve 2D concentration measurement in bounded domains, for which diffusion behaves quite differently. Here we present a theory of the precision of chemosensation that covers bounded domains of any dimensionality. We find that the quality of chemosensation in lower dimensions is controlled by domain size, suggesting a general principle applicable to many biological systems. Applying the theory to biological problems in 2D shows that diffusion-limited signalling is an efficient mechanism on time scales consistent with behaviour. Theoretical studies on chemosensation often invoke a model of three dimensional unbounded diffusion, but many biological problems involve two-dimensional diffusion in a bounded domain. Here Bicknell et al. present a model for chemosensation that covers bounded domains of any dimension, and apply it to biological problems in two dimensions.
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Affiliation(s)
- Brendan A Bicknell
- 1] Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia [2] School of Mathematics and Physics, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Peter Dayan
- Gatsby Computational Neuroscience Unit, University College London, London WC1N 3AR, UK
| | - Geoffrey J Goodhill
- 1] Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia [2] School of Mathematics and Physics, The University of Queensland, St Lucia, Queensland 4072, Australia
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105
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Kotomura N, Harada N, Ishihara S. The Proportion of Chromatin Graded between Closed and Open States Determines the Level of Transcripts Derived from Distinct Promoters in the CYP19 Gene. PLoS One 2015; 10:e0128282. [PMID: 26020632 PMCID: PMC4447357 DOI: 10.1371/journal.pone.0128282] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 04/23/2015] [Indexed: 11/19/2022] Open
Abstract
The human CYP19 gene encodes aromatase, which converts androgens to estrogens. CYP19 mRNA variants are transcribed mainly from three promoters. Quantitative RT-PCR was used to measure the relative amounts of each of the three transcripts and determine the on/off state of the promoters. While some of the promoters were silent, CYP19 mRNA production differed among the other promoters, whose estimated transcription levels were 0.001% to 0.1% of that of the TUBB control gene. To investigate the structural aspects of chromatin that were responsible for this wide range of activity of the CYP19 promoters, we used a fractionation protocol, designated SEVENS, which sequentially separates densely packed nucleosomes from dispersed nucleosomes. The fractional distribution of each inactive promoter showed a similar pattern to that of the repressed reference loci; the inactive regions were distributed toward lower fractions, in which closed chromatin comprising packed nucleosomes was enriched. In contrast, active CYP19 promoters were raised toward upper fractions, including dispersed nucleosomes in open chromatin. Importantly, these active promoters were moderately enriched in the upper fractions as compared to active reference loci, such as the TUBB promoter; the proportion of open chromatin appeared to be positively correlated to the promoter strength. These results, together with ectopic transcription accompanied by an increase in the proportion of open chromatin in cells treated with an H3K27me inhibitor, indicate that CYP19 mRNA could be transcribed from a promoter in which chromatin is shifted toward an open state in the equilibrium between closed and open chromatin.
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Affiliation(s)
- Naoe Kotomura
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Nobuhiro Harada
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoru Ishihara
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- * E-mail:
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106
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Veluchamy A, Rastogi A, Lin X, Lombard B, Murik O, Thomas Y, Dingli F, Rivarola M, Ott S, Liu X, Sun Y, Rabinowicz PD, McCarthy J, Allen AE, Loew D, Bowler C, Tirichine L. An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum. Genome Biol 2015; 16:102. [PMID: 25990474 PMCID: PMC4504042 DOI: 10.1186/s13059-015-0671-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/11/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Nucleosomes are the building blocks of chromatin where gene regulation takes place. Chromatin landscapes have been profiled for several species, providing insights into the fundamental mechanisms of chromatin-mediated transcriptional regulation of gene expression. However, knowledge is missing for several major and deep-branching eukaryotic groups, such as the Stramenopiles, which include the diatoms. Diatoms are highly diverse and ubiquitous species of phytoplankton that play a key role in global biogeochemical cycles. Dissecting chromatin-mediated regulation of genes in diatoms will help understand the ecological success of these organisms in contemporary oceans. RESULTS Here, we use high resolution mass spectrometry to identify a full repertoire of post-translational modifications on histones of the marine diatom Phaeodactylum tricornutum, including eight novel modifications. We map five histone marks coupled with expression data and show that P. tricornutum displays both unique and broadly conserved chromatin features, reflecting the chimeric nature of its genome. Combinatorial analysis of histone marks and DNA methylation demonstrates the presence of an epigenetic code defining activating or repressive chromatin states. We further profile three specific histone marks under conditions of nitrate depletion and show that the histone code is dynamic and targets specific sets of genes. CONCLUSIONS This study is the first genome-wide characterization of the histone code from a stramenopile and a marine phytoplankton. The work represents an important initial step for understanding the evolutionary history of chromatin and how epigenetic modifications affect gene expression in response to environmental cues in marine environments.
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Affiliation(s)
- Alaguraj Veluchamy
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France. .,Present address: BESE Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
| | - Achal Rastogi
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France.
| | - Xin Lin
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France. .,Present address: State key lab of Marine Environmental Science, Xiamen University, Xiamen, 361005, China.
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Cedex 05 Paris, France.
| | - Omer Murik
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France.
| | - Yann Thomas
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France.
| | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Cedex 05 Paris, France.
| | - Maximo Rivarola
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Present address: Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA Castelar), CC 25, Castelar, B1712WAA, Argentina.
| | - Sandra Ott
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Xinyue Liu
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Yezhou Sun
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Pablo D Rabinowicz
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - James McCarthy
- J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, 92121, USA.
| | - Andrew E Allen
- J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, 92121, USA. .,Scripps Institution of Oceanography, Integrative Oceanography Division, University of California, San Diego, CA, 92093, USA.
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Cedex 05 Paris, France.
| | - Chris Bowler
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France.
| | - Leïla Tirichine
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d'Ulm, 75005, Paris, France.
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107
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Peng H, Zhu QS, Zhong S, Levy D. Transcription of the Human Microsomal Epoxide Hydrolase Gene (EPHX1) Is Regulated by PARP-1 and Histone H1.2. Association with Sodium-Dependent Bile Acid Transport. PLoS One 2015; 10:e0125318. [PMID: 25992604 PMCID: PMC4439041 DOI: 10.1371/journal.pone.0125318] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/18/2015] [Indexed: 01/06/2023] Open
Abstract
Microsomal epoxide hydrolase (mEH) is a bifunctional protein that plays a central role in the metabolism of numerous xenobiotics as well as mediating the sodium-dependent transport of bile acids into hepatocytes. These compounds are involved in cholesterol homeostasis, lipid digestion, excretion of xenobiotics and the regulation of several nuclear receptors and signaling transduction pathways. Previous studies have demonstrated the critical role of GATA-4, a C/EBPα-NF/Y complex and an HNF-4α/CAR/RXR/PSF complex in the transcriptional regulation of the mEH gene (EPHX1). Studies also identified heterozygous mutations in human EPHX1 that resulted in a 95% decrease in mEH expression levels which was associated with a decrease in bile acid transport and severe hypercholanemia. In the present investigation we demonstrate that EPHX1 transcription is significantly inhibited by two heterozygous mutations observed in the Old Order Amish population that present numerous hypercholanemic subjects in the absence of liver damage suggesting a defect in bile acid transport into the hepatocyte. The identity of the regulatory proteins binding to these sites, established using biotinylated oligonucleotides in conjunction with mass spectrometry was shown to be poly(ADP-ribose)polymerase-1 (PARP-1) bound to the EPHX1 proximal promoter and a linker histone complex, H1.2/Aly, bound to a regulatory intron 1 site. These sites exhibited 71% homology and may represent potential nucleosome positioning domains. The high frequency of the H1.2 site polymorphism in the Amish population results in a potential genetic predisposition to hypercholanemia and in conjunction with our previous studies, further supports the critical role of mEH in mediating bile acid transport into hepatocytes.
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Affiliation(s)
- Hui Peng
- University of Southern California, Keck School of Medicine, Department of Biochemistry and Molecular Biology, Los Angeles, California, United States of America
| | - Qin-shi Zhu
- University of Southern California, Keck School of Medicine, Department of Biochemistry and Molecular Biology, Los Angeles, California, United States of America
| | - Shuping Zhong
- University of Southern California, Keck School of Medicine, Department of Biochemistry and Molecular Biology, Los Angeles, California, United States of America
| | - Daniel Levy
- University of Southern California, Keck School of Medicine, Department of Biochemistry and Molecular Biology, Los Angeles, California, United States of America
- * E-mail:
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108
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Stable Phenotypic Changes of the Host T Cells Are Essential to the Long-Term Stability of Latent HIV-1 Infection. J Virol 2015; 89:6656-72. [PMID: 25878110 DOI: 10.1128/jvi.00571-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/10/2015] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED The extreme stability of the latent HIV-1 reservoir in the CD4(+) memory T cell population prevents viral eradication with current antiretroviral therapy. It has been demonstrated that homeostatic T cell proliferation and clonal expansion of latently infected T cells due to viral integration into specific genes contribute to this extraordinary reservoir stability. Nevertheless, given the constant exposure of the memory T cell population to specific antigen or bystander activation, this reservoir stability seems remarkable, unless it is assumed that latent HIV-1 resides exclusively in memory T cells that recognize rare antigens. Another explanation for the stability of the reservoir could be that the latent HIV-1 reservoir is associated with an unresponsive T cell phenotype. We demonstrate here that host cells of latent HIV-1 infection events were functionally altered in ways that are consistent with the idea of an anergic, unresponsive T cell phenotype. Manipulations that induced or mimicked an anergic T cell state promoted latent HIV-1 infection. Kinome analysis data reflected this altered host cell phenotype at a system-wide level and revealed how the stable kinase activity changes networked to stabilize latent HIV-1 infection. Protein-protein interaction networks generated from kinome data could further be used to guide targeted genetic or pharmacological manipulations that alter the stability of latent HIV-1 infection. In summary, our data demonstrate that stable changes to the signal transduction and transcription factor network of latently HIV-1 infected host cells are essential to the ability of HIV-1 to establish and maintain latent HIV-1 infection status. IMPORTANCE The extreme stability of the latent HIV-1 reservoir allows the infection to persist for the lifetime of a patient, despite completely suppressive antiretroviral therapy. This extreme reservoir stability is somewhat surprising, since the latently HIV-1 infected CD4(+) memory T cells that form the structural basis of the viral reservoir should be exposed to cognate antigen over time. Antigen exposure would trigger a recall response and should deplete the reservoir, likely over a relatively short period. Our data demonstrate that stable and system-wide phenotypic changes to host cells are a prerequisite for the establishment and maintenance of latent HIV-1 infection events. The changes observed are consistent with an unresponsive, anergy-like T cell phenotype of latently HIV-1 infected host cells. An anergy-like, unresponsive state of the host cells of latent HIV-1 infection events would explain the stability of the HIV-1 reservoir in the face of continuous antigen exposure.
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109
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Belsky JA, MacAlpine HK, Lubelsky Y, Hartemink AJ, MacAlpine DM. Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly. Genes Dev 2015; 29:212-24. [PMID: 25593310 PMCID: PMC4298139 DOI: 10.1101/gad.247924.114] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Start sites of DNA replication are marked by the origin recognition complex (ORC), which coordinates Mcm2–7 helicase loading to form the prereplicative complex (pre-RC). Belsky et al. “footprinted” nucleosomes, transcription factors, and replication proteins at multiple points during the Saccharomyces cerevisiae cell cycle. This revealed a precise ORC-dependent footprint at 269 origins in G2. A separate class of inefficient origins exhibited protein occupancy only in G1. The local chromatin environment restricts the loading of the Mcm2–7 double hexamer either upstream of or downstream from the ACS. Start sites of DNA replication are marked by the origin recognition complex (ORC), which coordinates Mcm2–7 helicase loading to form the prereplicative complex (pre-RC). Although pre-RC assembly is well characterized in vitro, the process is poorly understood within the local chromatin environment surrounding replication origins. To reveal how the chromatin architecture modulates origin selection and activation, we “footprinted” nucleosomes, transcription factors, and replication proteins at multiple points during the Saccharomyces cerevisiae cell cycle. Our nucleotide-resolution protein occupancy profiles resolved a precise ORC-dependent footprint at 269 origins in G2. A separate class of inefficient origins exhibited protein occupancy only in G1, suggesting that stable ORC chromatin association in G2 is a determinant of origin efficiency. G1 nucleosome remodeling concomitant with pre-RC assembly expanded the origin nucleosome-free region and enhanced activation efficiency. Finally, the local chromatin environment restricts the loading of the Mcm2–7 double hexamer either upstream of or downstream from the ARS consensus sequence (ACS).
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Affiliation(s)
- Jason A Belsky
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA; Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA
| | - Heather K MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA;
| | - Yoav Lubelsky
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Alexander J Hartemink
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA; Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA;
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110
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Osberg B, Nuebler J, Korber P, Gerland U. Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays. Nucleic Acids Res 2014; 42:13633-45. [PMID: 25428353 PMCID: PMC4267636 DOI: 10.1093/nar/gku1190] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 11/13/2022] Open
Abstract
The first level of genome packaging in eukaryotic cells involves the formation of dense nucleosome arrays, with DNA coverage near 90% in yeasts. How cells achieve such high coverage within a short time, e.g. after DNA replication, remains poorly understood. It is known that random sequential adsorption of impenetrable particles on a line reaches high density extremely slowly, due to a jamming phenomenon. The nucleosome-shifting action of remodeling enzymes has been proposed as a mechanism to resolve such jams. Here, we suggest two biophysical mechanisms which assist rapid filling of DNA with nucleosomes, and we quantitatively characterize these mechanisms within mathematical models. First, we show that the 'softness' of nucleosomes, due to nucleosome breathing and stepwise nucleosome assembly, significantly alters the filling behavior, speeding up the process relative to 'hard' particles with fixed, mutually exclusive DNA footprints. Second, we explore model scenarios in which the progression of the replication fork could eliminate nucleosome jamming, either by rapid filling in its wake or via memory of the parental nucleosome positions. Taken together, our results suggest that biophysical effects promote rapid nucleosome filling, making the reassembly of densely packed nucleosomes after DNA replication a simpler task for cells than was previously thought.
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Affiliation(s)
- Brendan Osberg
- Theory of Complex Biosystems, Physik-Department, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany
| | - Johannes Nuebler
- Theory of Complex Biosystems, Physik-Department, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany
| | - Philipp Korber
- Adolf-Butenandt-Institut, University of Munich, Schillerstrasse 44, 80336 Munich, Germany
| | - Ulrich Gerland
- Theory of Complex Biosystems, Physik-Department, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany
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111
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Andersson R. Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model. Bioessays 2014; 37:314-23. [PMID: 25450156 DOI: 10.1002/bies.201400162] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Gene transcription is strictly controlled by the interplay of regulatory events at gene promoters and gene-distal regulatory elements called enhancers. Despite extensive studies of enhancers, we still have a very limited understanding of their mechanisms of action and their restricted spatio-temporal activities. A better understanding would ultimately lead to fundamental insights into the control of gene transcription and the action of regulatory genetic variants involved in disease. Here, I review and discuss pros and cons of state-of-the-art genomics methods to localize and infer the activity of enhancers. Among the different approaches, profiling of enhancer RNAs yields the highest specificity and may be superior in detecting in vivo activity. I discuss their apparent similarities to promoters, which challenge the established view of enhancers and promoters as distinct entities, and present a unifying model of regulatory elements in transcriptional regulation, in which activity, transcriptional output and regulatory function is context specific.
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Affiliation(s)
- Robin Andersson
- The Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Denmark
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112
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McGann JC, Oyer JA, Garg S, Yao H, Liu J, Feng X, Liao L, Yates JR, Mandel G. Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype. eLife 2014; 3:e04235. [PMID: 25250711 PMCID: PMC4371837 DOI: 10.7554/elife.04235] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 09/22/2014] [Indexed: 12/17/2022] Open
Abstract
The bivalent hypothesis posits that genes encoding developmental regulators required
for early lineage decisions are poised in stem/progenitor cells by the balance
between a repressor histone modification (H3K27me3), mediated by the Polycomb
Repressor Complex 2 (PRC2), and an activator modification (H3K4me3). In this study,
we test whether this mechanism applies equally to genes that are not required until
terminal differentiation. We focus on the RE1 Silencing Transcription Factor (REST)
because it is expressed highly in stem cells and is an established global repressor
of terminal neuronal genes. Elucidation of the REST complex, and comparison of
chromatin marks and gene expression levels in control and REST-deficient stem cells,
shows that REST target genes are poised by a mechanism independent of Polycomb, even
at promoters which bear the H3K27me3 mark. Specifically, genes under REST control are
actively repressed in stem cells by a balance of the H3K4me3 mark and a repressor
complex that relies on histone deacetylase activity. Thus, chromatin distinctions
between pro-neural and terminal neuronal genes are established at the embryonic stem
cell stage by two parallel, but distinct, repressor pathways. DOI:http://dx.doi.org/10.7554/eLife.04235.001 When an embryo is developing, genes are switched on or off at different times, for
many different reasons. Many of these genes are switched off, or repressed, by making
the DNA inaccessible to the various proteins and molecules that control gene
activity. This is achieved by altering the way that the DNA is packaged into a
compacted structure called chromatin. A host of proteins modify the structure of
chromatin: it can be made more tightly packaged, which keeps genes switched off; or
it can be made more loosely packaged, which allows the genes within to be accessed
and switched on. The stem cells in an embryo are able to give rise to many different types of
specialized cell. Genes that determine which cell type a stem cell will eventually
become are often kept in a so-called ‘poised’ state, and have chromatin modifications
that encourage genes to be switch on, as well as modifications that switch genes off.
Current thinking is that this poised state allows these genes to be switched on or
off rapidly in response to the signals that the cell receives during development. The only known protein complex that causes the chromatin to become more compacted in
this poised state is the Polycomb complex. This complex binds to specific regions of
DNA and is thought to allow stem cells to remain able to become different cell types
by repressing the genes required for adopting a specialized cell fate. However, it is
unclear if this poised state also regulates those genes that control the final stages
of a cell becoming a specific cell type. McGann et al. investigated genes that are involved in the final stages of a nerve
cell's development. These genes are regulated by another protein called REST, which
acts to repress the genes in non-neuronal cells. McGann et al. found that the genes
that are regulated by REST in embryonic stem cells from mice also have their
chromatin modified in two contrasting ways. Some of the modifications are linked to
switching genes on, while others are linked to keeping genes switched off. Thus these
genes are also in a poised state. However, for these genes, this state is acquired
without the activity of the Polycomb complex. The results of McGann et al. show that two similar, but distinct, mechanisms keep the
genes required for the early and the late stages of nerve cell development in a
poised state. If this poised state aids the development of other cell types (for
example muscle or fat cells), uncovering how it is achieved could improve our ability
to direct stem cells to develop into specific cell types and tissues. DOI:http://dx.doi.org/10.7554/eLife.04235.002
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Affiliation(s)
- James C McGann
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Jon A Oyer
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Saurabh Garg
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Huilan Yao
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Jun Liu
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Xin Feng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Lujian Liao
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Gail Mandel
- Vollum Institute, Oregon Health and Science University, Portland, United States
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A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking. PLoS One 2014; 9:e107765. [PMID: 25247414 PMCID: PMC4172637 DOI: 10.1371/journal.pone.0107765] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/08/2014] [Indexed: 12/27/2022] Open
Abstract
Chromatin insulators of higher eukaryotes functionally divide the genome into active and inactive domains. Furthermore, insulators regulate enhancer/promoter communication, which is evident from the Drosophila bithorax locus in which a multitude of regulatory elements control segment specific gene activity. Centrosomal protein 190 (CP190) is targeted to insulators by CTCF or other insulator DNA-binding factors. Chromatin analyses revealed that insulators are characterized by open and nucleosome depleted regions. Here, we wanted to identify chromatin modification and remodelling factors required for an enhancer blocking function. We used the well-studied Fab-8 insulator of the bithorax locus to apply a genome-wide RNAi screen for factors that contribute to the enhancer blocking function of CTCF and CP190. Among 78 genes required for optimal Fab-8 mediated enhancer blocking, all four components of the NURF complex as well as several subunits of the dREAM complex were most evident. Mass spectrometric analyses of CTCF or CP190 bound proteins as well as immune precipitation confirmed NURF and dREAM binding. Both co-localise with most CP190 binding sites in the genome and chromatin immune precipitation showed that CP190 recruits NURF and dREAM. Nucleosome occupancy and histone H3 binding analyses revealed that CP190 mediated NURF binding results in nucleosomal depletion at CP190 binding sites. Thus, we conclude that CP190 binding to CTCF or to other DNA binding insulator factors mediates recruitment of NURF and dREAM. Furthermore, the enhancer blocking function of insulators is associated with nucleosomal depletion and requires NURF and dREAM.
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114
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Kraushaar DC, Jin W, Maunakea A, Abraham B, Ha M, Zhao K. Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3. Genome Biol 2014; 14:R121. [PMID: 24176123 PMCID: PMC3983652 DOI: 10.1186/gb-2013-14-10-r121] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/31/2013] [Indexed: 11/16/2022] Open
Abstract
Background Nucleosomes are present throughout the genome and must be dynamically regulated to accommodate binding of transcription factors and RNA polymerase machineries by various mechanisms. Despite the development of protocols and techniques that have enabled us to map nucleosome occupancy genome-wide, the dynamic properties of nucleosomes remain poorly understood, particularly in mammalian cells. The histone variant H3.3 is incorporated into chromatin independently of DNA replication and requires displacement of existing nucleosomes for its deposition. Here, we measure H3.3 turnover at high resolution in the mammalian genome in order to present a genome-wide characterization of replication-independent H3.3-nucleosome dynamics. Results We developed a system to study the DNA replication-independent turnover of nucleosomes containing the histone variant H3.3 in mammalian cells. By measuring the genome-wide incorporation of H3.3 at different time points following epitope-tagged H3.3 expression, we find three categories of H3.3-nucleosome turnover in vivo: rapid turnover, intermediate turnover and, specifically at telomeres, slow turnover. Our data indicate that H3.3-containing nucleosomes at enhancers and promoters undergo rapid turnover that is associated with active histone modification marks including H3K4me1, H3K4me3, H3K9ac, H3K27ac and the histone variant H2A.Z. The rate of turnover is negatively correlated with H3K27me3 at regulatory regions and with H3K36me3 at gene bodies. Conclusions We have established a reliable approach to measure turnover rates of H3.3-containing nucleosomes on a genome-wide level in mammalian cells. Our results suggest that distinct mechanisms control the dynamics of H3.3 incorporation at functionally different genomic regions.
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115
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Hettiarachchi N, Kryukov K, Sumiyama K, Saitou N. Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning. Genome Biol Evol 2014; 6:2527-42. [PMID: 25364802 PMCID: PMC4202324 DOI: 10.1093/gbe/evu188] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2014] [Indexed: 01/01/2023] Open
Abstract
Many studies on conserved noncoding sequences (CNSs) have found that CNSs are enriched significantly in regulatory sequence elements. We conducted whole-genome analysis on plant CNSs to identify lineage-specific CNSs in eudicots, monocots, angiosperms,and vascular plants based on the premise that lineage-specific CNSs define lineage-specific characters and functions in groups of organisms. We identified 27 eudicot, 204 monocot, 6,536 grass, 19 angiosperm, and 2 vascular plant lineage-specific CNSs(lengths range from 16 to 1,517 bp) that presumably originated in their respective common ancestors. A stronger constraint on the CNSs located in the untranslated regions was observed. The CNSs were often flanked by genes involved in transcription regulation. A drop of A+T content near the border of CNSs was observed and CNS regions showed a higher nucleosome occupancy probability. These CNSs are candidate regulatory elements, which are expected to define lineage-specific features of various plant groups.
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Affiliation(s)
- Nilmini Hettiarachchi
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kirill Kryukov
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kenta Sumiyama
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
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Abstract
Combined with TCR stimuli, extracellular cytokine signals initiate the differentiation of naive CD4(+) T cells into specialized effector T-helper (Th) and regulatory T (Treg) cell subsets. The lineage specification and commitment process occurs through the combinatorial action of multiple transcription factors (TFs) and epigenetic mechanisms that drive lineage-specific gene expression programs. In this article, we review recent studies on the transcriptional and epigenetic regulation of distinct Th cell lineages. Moreover, we review current study linking immune disease-associated single-nucleotide polymorphisms with distal regulatory elements and their potential role in the disease etiology.
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Affiliation(s)
- Subhash K Tripathi
- Turku Centre for Biotechnology, University of Turku and
Åbo Akademi UniversityTurku, Finland
- National Doctoral Programme in Informational and
Structural BiologyTurku, Finland
- Turku Doctoral Programme of Molecular Medicine (TuDMM),
University of TurkuTurku, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and
Åbo Akademi UniversityTurku, Finland
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117
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Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R. Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci 2014; 39:381-99. [PMID: 25129887 DOI: 10.1016/j.tibs.2014.07.002] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/21/2022]
Abstract
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a genome. TFs recognize DNA in a specific manner; the mechanisms underlying this specificity have been identified for many TFs based on 3D structures of protein-DNA complexes. More recently, structural views have been complemented with data from high-throughput in vitro and in vivo explorations of the DNA-binding preferences of many TFs. Together, these approaches have greatly expanded our understanding of TF-DNA interactions. However, the mechanisms by which TFs select in vivo binding sites and alter gene expression remain unclear. Recent work has highlighted the many variables that influence TF-DNA binding, while demonstrating that a biophysical understanding of these many factors will be central to understanding TF function.
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Affiliation(s)
- Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Tianyin Zhou
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Lin Yang
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Ana Carolina Dantas Machado
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Departments of Biostatistics and Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA.
| | - Remo Rohs
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
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118
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Engelhorn J, Blanvillain R, Carles CC. Gene activation and cell fate control in plants: a chromatin perspective. Cell Mol Life Sci 2014; 71:3119-37. [PMID: 24714879 PMCID: PMC11113918 DOI: 10.1007/s00018-014-1609-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 01/02/2023]
Abstract
In plants, environment-adaptable organogenesis extends throughout the lifespan, and iterative development requires repetitive rounds of activation and repression of several sets of genes. Eukaryotic genome compaction into chromatin forms a physical barrier for transcription; therefore, induction of gene expression requires alteration in chromatin structure. One of the present great challenges in molecular and developmental biology is to understand how chromatin is brought from a repressive to permissive state on specific loci and in a very specific cluster of cells, as well as how this state is further maintained and propagated through time and cell division in a cell lineage. In this review, we report recent discoveries implementing our knowledge on chromatin dynamics that modulate developmental gene expression. We also discuss how new data sets highlight plant specificities, likely reflecting requirement for a highly dynamic chromatin.
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Affiliation(s)
- Julia Engelhorn
- Université Grenoble Alpes, UMR5168, 38041, Grenoble, France,
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119
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Nie Y, Cheng X, Chen J, Sun X. Nucleosome organization in the vicinity of transcription factor binding sites in the human genome. BMC Genomics 2014; 15:493. [PMID: 24942981 PMCID: PMC4073502 DOI: 10.1186/1471-2164-15-493] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 06/10/2014] [Indexed: 12/23/2022] Open
Abstract
Background The binding of transcription factors (TFs) to specific DNA sequences is an initial and crucial step of transcription. In eukaryotes, this process is highly dependent on the local chromatin state, which can be modified by recruiting chromatin remodelers. However, previous studies have focused mainly on nucleosome occupancy around the TF binding sites (TFBSs) of a few specific TFs. Here, we investigated the nucleosome occupancy profiles around computationally inferred binding sites, based on 519 TF binding motifs, in human GM12878 and K562 cells. Results Although high nucleosome occupancy is intrinsically encoded at TFBSs in vitro, nucleosomes are generally depleted at TFBSs in vivo, and approximately a quarter of TFBSs showed well-positioned in vivo nucleosomes on both sides. RNA polymerase near the transcription start site (TSS) has a large effect on the nucleosome occupancy distribution around the binding sites located within one kilobase to the nearest TSS; fuzzier nucleosome positioning was thus observed around these sites. In addition, in contrast to yeast, repressors, rather than activators, were more likely to bind to nucleosomal DNA in the human cells, and nucleosomes around repressor sites were better positioned in vivo. Genes with repressor sites exhibiting well-positioned nucleosomes on both sides, and genes with activator sites occupied by nucleosomes had significantly lower expression, suggesting that actions of activators and repressors are associated with the nucleosome occupancy around their binding sites. It was also interesting to note that most of the binding sites, which were not in the DNase I-hypersensitive regions, were cell-type specific, and higher in vivo nucleosome occupancy were observed at these binding sites. Conclusions This study demonstrated that RNA polymerase and the functions of bound TFs affected the local nucleosome occupancy around TFBSs, and nucleosome occupancy patterns around TFBSs were associated with the expression levels of target genes. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-493) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, 210096 Nanjing, China.
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120
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Busslinger M, Tarakhovsky A. Epigenetic control of immunity. Cold Spring Harb Perspect Biol 2014; 6:6/6/a019307. [PMID: 24890513 DOI: 10.1101/cshperspect.a019307] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Immunity relies on the heterogeneity of immune cells and their ability to respond to pathogen challenges. In the adaptive immune system, lymphocytes display a highly diverse antigen receptor repertoire that matches the vast diversity of pathogens. In the innate immune system, the cell's heterogeneity and phenotypic plasticity enable flexible responses to changes in tissue homeostasis caused by infection or damage. The immune responses are calibrated by the graded activity of immune cells that can vary from yeast-like proliferation to lifetime dormancy. This article describes key epigenetic processes that contribute to the function of immune cells during health and disease.
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Affiliation(s)
- Meinrad Busslinger
- Research Institute of Molecular Pathology, Vienna Biocenter, A-1030 Vienna, Austria
| | - Alexander Tarakhovsky
- Laboratory of Lymphocyte Signaling, The Rockefeller University, New York, New York 10021
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121
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Li G, Liu S, Wang J, He J, Huang H, Zhang Y, Xu L. ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:706-14. [PMID: 24606212 DOI: 10.1111/tpj.12499] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/28/2014] [Accepted: 02/24/2014] [Indexed: 05/25/2023]
Abstract
Chromatin is a highly organized structure with repetitive nucleosome subunits. Nucleosome distribution patterns, which contain information on epigenetic controls, are dynamically affected by ATP-dependent chromatin remodeling factors (remodelers). However, whether plants have specific nucleosome distribution patterns and how plant remodelers contribute to the pattern formation are not clear. In this study we used the micrococcal nuclease digestion followed by deep sequencing (MNase-seq) assay to show the genome-wide nucleosome pattern in Arabidopsis thaliana. We demonstrated that the nucleosome distribution patterns of Arabidopsis are associated with the gene expression level, and have several specific characteristics that are different from those of animals and yeast. In addition, we found that remodelers in the A. thaliana imitation switch (AtISWI) subfamily are important for the formation of the nucleosome distribution pattern. Double mutations in the AtISWI genes, CHROMATIN REMODELING 11 (CHR11) and CHR17, resulted in the loss of the evenly spaced nucleosome pattern in gene bodies, but did not affect nucleosome density, supporting a previous idea that the primary role of ISWI is to slide nucleosomes in gene bodies for pattern formation.
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Affiliation(s)
- Guang Li
- National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
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Srivastava R, Rai KM, Srivastava M, Kumar V, Pandey B, Singh SP, Bag SK, Singh BD, Tuli R, Sawant SV. Distinct role of core promoter architecture in regulation of light-mediated responses in plant genes. MOLECULAR PLANT 2014; 7:626-41. [PMID: 24177688 DOI: 10.1093/mp/sst146] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In the present study, we selected four distinct classes of light-regulated promoters. The light-regulated promoters can be distinctly grouped into either TATA-box-containing or TATA-less (initiator-containing) promoters. Further, using either native promoters or their swapped versions of core promoter elements, we established that TATA-box and Inr (Initiator) elements have distinct mechanisms which are involved in light-mediated regulation, and these elements are not swappable. We identified that mutations in either functional TATA-box or Inr elements lead to the formation of nucleosomal structure. The nucleotide diversity in either the TATA-box or Inr element in Arabidopsis ecotypes proposes that the nucleotide variation in core promoters can alter the gene expression. We show that motif overrepresentation in light-activated promoters encompasses different specific regulatory motifs present downstream of TSS (transcription start site), and this might serve as a key factor in regulating light promoters which are parallel with these elements. Finally, we conclude that the TATA-box or Inr element does not act in isolation, but our results clearly suggests the probable involvement of other distinct core promoter elements in concurrence with the TATA-box or Inr element to impart selectivity to light-mediated transcription.
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Affiliation(s)
- Rakesh Srivastava
- Plant Molecular Biology and Genetic Engineering Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001 (U.P.), India
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123
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LeGresley SE, Wilt J, Antonik M. DNA damage may drive nucleosomal reorganization to facilitate damage detection. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:032708. [PMID: 24730875 DOI: 10.1103/physreve.89.032708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Indexed: 06/03/2023]
Abstract
One issue in genome maintenance is how DNA repair proteins find lesions at rates that seem to exceed diffusion-limited search rates. We propose a phenomenon where DNA damage induces nucleosomal rearrangements which move lesions to potential rendezvous points in the chromatin structure. These rendezvous points are the dyad and the linker DNA between histones, positions in the chromatin which are more likely to be accessible by repair proteins engaged in a random search. The feasibility of this mechanism is tested by considering the statistical mechanics of DNA containing a single lesion wrapped onto the nucleosome. We consider lesions which make the DNA either more flexible or more rigid by modeling the lesion as either a decrease or an increase in the bending energy. We include this energy in a partition function model of nucleosome breathing. Our results indicate that the steady state for a breathing nucleosome will most likely position the lesion at the dyad or in the linker, depending on the energy of the lesion. A role for DNA binding proteins and chromatin remodelers is suggested based on their ability to alter the mechanical properties of the DNA and DNA-histone binding, respectively. We speculate that these positions around the nucleosome potentially serve as rendezvous points where DNA lesions may be encountered by repair proteins which may be sterically hindered from searching the rest of the nucleosomal DNA. The strength of the repositioning is strongly dependent on the structural details of the DNA lesion and the wrapping and breathing of the nucleosome. A more sophisticated evaluation of this proposed mechanism will require detailed information about breathing dynamics, the structure of partially wrapped nucleosomes, and the structural properties of damaged DNA.
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Affiliation(s)
- Sarah E LeGresley
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
| | - Jamie Wilt
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
| | - Matthew Antonik
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
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124
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Flores O, Deniz Ö, Soler-López M, Orozco M. Fuzziness and noise in nucleosomal architecture. Nucleic Acids Res 2014; 42:4934-46. [PMID: 24586063 PMCID: PMC4005669 DOI: 10.1093/nar/gku165] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Nucleosome organization plays a key role in the regulation of gene expression. However, despite the striking advances in the accuracy of nucleosome maps, there are still severe discrepancies on individual nucleosome positioning and how this influences gene regulation. The variability among nucleosome maps, which precludes the fine analysis of nucleosome positioning, might emerge from diverse sources. We have carefully inspected the extrinsic factors that may induce diversity by the comparison of microccocal nuclease (MNase)-Seq derived nucleosome maps generated under distinct conditions. Furthermore, we have also explored the variation originated from intrinsic nucleosome dynamics by generating additional maps derived from cell cycle synchronized and asynchronous yeast cultures. Taken together, our study has enabled us to measure the effect of noise in nucleosome occupancy and positioning and provides insights into the underlying determinants. Furthermore, we present a systematic approach that may guide the standardization of MNase-Seq experiments in order to generate reproducible genome-wide nucleosome patterns.
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Affiliation(s)
- Oscar Flores
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain, Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain and Department of Biochemistry and Molecular Biology. University of Barcelona, 08028 Barcelona, Spain
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125
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Priest HD, Fox SE, Rowley ER, Murray JR, Michael TP, Mockler TC. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress. PLoS One 2014; 9:e87499. [PMID: 24489928 PMCID: PMC3906199 DOI: 10.1371/journal.pone.0087499] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 12/27/2013] [Indexed: 12/01/2022] Open
Abstract
Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.
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Affiliation(s)
- Henry D. Priest
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
- Division of Biology and Biomedical Sciences, Washington University, Saint Louis, Missouri, United States of America
| | - Samuel E. Fox
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Erik R. Rowley
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Jessica R. Murray
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Todd P. Michael
- Waksman Institute and Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
- Division of Biology and Biomedical Sciences, Washington University, Saint Louis, Missouri, United States of America
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS. Canonical nucleosome organization at promoters forms during genome activation. Genome Res 2013; 24:260-6. [PMID: 24285721 PMCID: PMC3912416 DOI: 10.1101/gr.157750.113] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. The mechanisms of formation and the function of canonical promoter nucleosome organization remain unclear. Here we analyze the genome-wide location of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear on thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization is independent of DNA sequence preference, transcriptional elongation, and robust RNA polymerase II (Pol II) binding. Instead, canonical promoter nucleosome organization correlates with the presence of histone H3 lysine 4 trimethylation (H3K4me3) and affects future transcriptional activation. These findings reveal that genome activation is central to the organization of nucleosome arrays during early embryogenesis.
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Affiliation(s)
- Yong Zhang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
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127
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Kinase control of latent HIV-1 infection: PIM-1 kinase as a major contributor to HIV-1 reactivation. J Virol 2013; 88:364-76. [PMID: 24155393 DOI: 10.1128/jvi.02682-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite the clinical relevance of latent HIV-1 infection as a block to HIV-1 eradication, the molecular biology of HIV-1 latency remains incompletely understood. We recently demonstrated the presence of a gatekeeper kinase function that controls latent HIV-1 infection. Using kinase array analysis, we here expand on this finding and demonstrate that the kinase activity profile of latently HIV-1-infected T cells is altered relative to that of uninfected T cells. A ranking of altered kinases generated from these kinome profile data predicted PIM-1 kinase as a key switch involved in HIV-1 latency control. Using genetic and pharmacologic perturbation strategies, we demonstrate that PIM-1 activity is indeed required for HIV-1 reactivation in T cell lines and primary CD4 T cells. The presented results thus confirm that kinases are key contributors to HIV-1 latency control. In addition, through mutational studies we link the inhibitory effect of PIM-1 inhibitor IV (PIMi IV) on HIV-1 reactivation to an AP-1 motif in the CD28-responsive element of the HIV-1 long terminal repeat (LTR). The results expand our conceptual understanding of the dynamic interactions of the host cell and the latent HIV-1 integration event and position kinome profiling as a research tool to reveal novel molecular mechanisms that can eventually be targeted to therapeutically trigger HIV-1 reactivation.
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128
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Nguyen N, Vo A, Won KJ. A wavelet-based method to exploit epigenomic language in the regulatory region. ACTA ACUST UNITED AC 2013; 30:908-14. [PMID: 24096080 DOI: 10.1093/bioinformatics/btt467] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MOTIVATION Epigenetic landscapes in the regulatory regions reflect binding condition of transcription factors and their co-factors. Identifying epigenetic condition and its variation is important in understanding condition-specific gene regulation. Computational approaches to explore complex multi-dimensional landscapes are needed. RESULTS To study epigenomic condition for gene regulation, we developed a method, AWNFR, to classify epigenomic landscapes based on the detected epigenomic landscapes. Assuming mixture of Gaussians for a nucleosome, the proposed method captures the shape of histone modification and identifies potential regulatory regions in the wavelet domain. For accuracy estimation as well as enhanced computational speed, we developed a novel algorithm based on down-sampling operation and footprint in wavelet. We showed the algorithmic advantages of AWNFR using the simulated data. AWNFR identified regulatory regions more effectively and accurately than the previous approaches with the epigenome data in mouse embryonic stem cells and human lung fibroblast cells (IMR90). Based on the detected epigenomic landscapes, AWNFR classified epigenomic status and studied epigenomic codes. We studied co-occurring histone marks and showed that AWNFR captures the epigenomic variation across time. AVAILABILITY AND IMPLEMENTATION The source code and supplemental document of AWNFR are available at http://wonk.med.upenn.edu/AWNFR.
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Affiliation(s)
- Nha Nguyen
- Department of Genetics, Institute for Diabetes, Obesity and Metabolism, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA and Center for Neurosciences, The Feinstein Institute for Medical Research, Manhasset, NY 11030, USA
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Adamik J, Wang KZQ, Unlu S, Su AJA, Tannahill GM, Galson DL, O’Neill LA, Auron PE. Distinct mechanisms for induction and tolerance regulate the immediate early genes encoding interleukin 1β and tumor necrosis factor α. PLoS One 2013; 8:e70622. [PMID: 23936458 PMCID: PMC3731334 DOI: 10.1371/journal.pone.0070622] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/19/2013] [Indexed: 12/16/2022] Open
Abstract
Interleukin-1β and Tumor Necrosis Factor α play related, but distinct, roles in immunity and disease. Our study revealed major mechanistic distinctions in the Toll-like receptor (TLR) signaling-dependent induction for the rapidly expressed genes (IL1B and TNF) coding for these two cytokines. Prior to induction, TNF exhibited pre-bound TATA Binding Protein (TBP) and paused RNA Polymerase II (Pol II), hallmarks of poised immediate-early (IE) genes. In contrast, unstimulated IL1B displayed very low levels of both TBP and paused Pol II, requiring the lineage-specific Spi-1/PU.1 (Spi1) transcription factor as an anchor for induction-dependent interaction with two TLR-activated transcription factors, C/EBPβ and NF-κB. Activation and DNA binding of these two pre-expressed factors resulted in de novo recruitment of TBP and Pol II to IL1B in concert with a permissive state for elongation mediated by the recruitment of elongation factor P-TEFb. This Spi1-dependent mechanism for IL1B transcription, which is unique for a rapidly-induced/poised IE gene, was more dependent upon P-TEFb than was the case for the TNF gene. Furthermore, the dependence on phosphoinositide 3-kinase for P-TEFb recruitment to IL1B paralleled a greater sensitivity to the metabolic state of the cell and a lower sensitivity to the phenomenon of endotoxin tolerance than was evident for TNF. Such differences in induction mechanisms argue against the prevailing paradigm that all IE genes possess paused Pol II and may further delineate the specific roles played by each of these rapidly expressed immune modulators.
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Affiliation(s)
- Juraj Adamik
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Kent Z. Q. Wang
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Sebnem Unlu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - An-Jey A. Su
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | | | - Deborah L. Galson
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Luke A. O’Neill
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Philip E. Auron
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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130
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James SR, Cedeno CD, Sharma A, Zhang W, Mohler JL, Odunsi K, Wilson EM, Karpf AR. DNA methylation and nucleosome occupancy regulate the cancer germline antigen gene MAGEA11. Epigenetics 2013; 8:849-63. [PMID: 23839233 DOI: 10.4161/epi.25500] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
MAGEA11 is a cancer germline (CG) antigen and androgen receptor co-activator. Its expression in cancers other than prostate, and its mechanism of activation, has not been reported. In silico analyses reveal that MAGEA11 is frequently expressed in human cancers, is increased during tumor progression, and correlates with poor prognosis and survival. In prostate and epithelial ovarian cancers (EOC), MAGEA11 expression was associated with promoter and global DNA hypomethylation, and with activation of other CG genes. Pharmacological or genetic inhibition of DNA methyltransferases (DNMTs) and/or histone deacetylases (HDACs) activated MAGEA11 in a cell line specific manner. MAGEA11 promoter activity was directly repressed by DNA methylation, and partially depended on Sp1, as pharmacological or genetic targeting of Sp1 reduced MAGEA11 promoter activity and endogenous gene expression. Importantly, DNA methylation regulated nucleosome occupancy specifically at the -1 positioned nucleosome of MAGEA11. Methylation of a single Ets site near the transcriptional start site (TSS) correlated with -1 nucleosome occupancy and, by itself, strongly repressed MAGEA11 promoter activity. Thus, DNA methylation regulates nucleosome occupancy at MAGEA11, and this appears to function cooperatively with sequence-specific transcription factors to regulate gene expression. MAGEA11 regulation is highly instructive for understanding mechanisms regulating CG antigen genes in human cancer.
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Affiliation(s)
- Smitha R James
- Department of Pharmacology and Therapeutics; Roswell Park Cancer Institute; Buffalo, NY USA
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131
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Bravo S, Núñez F, Cruzat F, Cafferata EG, De Ferrari GV, Montecino M, Podhajcer OL. Enhanced CRAd activity using enhancer motifs driven by a nucleosome positioning sequence. Mol Ther 2013; 21:1403-12. [PMID: 23712038 PMCID: PMC3702098 DOI: 10.1038/mt.2013.93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 04/10/2013] [Indexed: 01/13/2023] Open
Abstract
Cancer development involves changes driven by the epigenetic machinery, including nucleosome positioning. Recently, the concept that adenoviral replication may be driven by tumor specific promoters (TSPs) gained support, and several conditionally replicative adenoviruses (CRAd) exhibited therapeutic efficacy in clinical trials. Here, we show for the first time that placing a nucleosome positioning sequence (NPS) upstream of a TSP combined with Wnt-responsive motifs (pART enhancer) enhanced the TSP transcriptional activity and increased the lytic activity of a CRAd. pART enhanced the transcriptional activity of the gastrointestinal cancer (GIC)-specific REG1A promoter (REG1A-pr); moreover, pART also increased the in vitro lytic activity of a CRAd whose replication was driven by REG1A-Pr. The pART enhancer effect in vitro and in vivo was strictly dependent on the presence of the NPS. Indeed, deletion of the NPS was strongly deleterious for the in vivo antitumor efficacy of the CRAd on orthotopically established pancreatic xenografts. pART also enhanced the specific activity of other heterologous promoters; moreover, the NPS was also able to enhance the responsiveness of hypoxia- and NFκB-response elements. We conclude that NPS could be useful for gene therapy approaches in cancer as well as other diseases.
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Affiliation(s)
- Soraya Bravo
- Centro de Investigaciones Biomédicas and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - Felipe Núñez
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Fernando Cruzat
- Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | | | - Giancarlo V De Ferrari
- Centro de Investigaciones Biomédicas and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - Martín Montecino
- Centro de Investigaciones Biomédicas and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
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Abstract
Histone-DNA complexes, so-called nucleosomes, are the building blocks of DNA packaging in eukaryotic cells. The histone-binding affinity of a local DNA segment depends on its elastic properties and determines its accessibility within the nucleus, which plays an important role in the regulation of gene expression. Here, we derive a fitness landscape for intergenic DNA segments in yeast as a function of two molecular phenotypes: their elasticity-dependent histone affinity and their coverage with transcription factor binding sites. This landscape reveals substantial selection against nucleosome formation over a wide range of both phenotypes. We use it as the core component of a quantitative evolutionary model for intergenic DNA segments. This model consistently predicts the observed diversity of histone affinities within wild Saccharomyces paradoxus populations, as well as the affinity divergence between neighboring Saccharomyces species. Our analysis establishes histone binding and transcription factor binding as two separable modes of sequence evolution, each of which is a direct target of natural selection.
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133
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Sandovici I, Hammerle CM, Ozanne SE, Constância M. Developmental and environmental epigenetic programming of the endocrine pancreas: consequences for type 2 diabetes. Cell Mol Life Sci 2013; 70:1575-95. [PMID: 23463236 PMCID: PMC11113912 DOI: 10.1007/s00018-013-1297-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 02/05/2013] [Accepted: 02/05/2013] [Indexed: 12/26/2022]
Abstract
The development of the endocrine pancreas is controlled by a hierarchical network of transcriptional regulators. It is increasingly evident that this requires a tightly interconnected epigenetic "programme" to drive endocrine cell differentiation and maintain islet function. Epigenetic regulators such as DNA and histone-modifying enzymes are now known to contribute to determination of pancreatic cell lineage, maintenance of cellular differentiation states, and normal functioning of adult pancreatic endocrine cells. Persistent effects of an early suboptimal environment, known to increase risk of type 2 diabetes in later life, can alter the epigenetic control of transcriptional master regulators, such as Hnf4a and Pdx1. Recent genome-wide analyses also suggest that an altered epigenetic landscape is associated with the β cell failure observed in type 2 diabetes and aging. At the cellular level, epigenetic mechanisms may provide a mechanistic link between energy metabolism and stable patterns of gene expression. Key energy metabolites influence the activity of epigenetic regulators, which in turn alter transcription to maintain cellular homeostasis. The challenge is now to understand the detailed molecular mechanisms that underlie these diverse roles of epigenetics, and the extent to which they contribute to the pathogenesis of type 2 diabetes. In-depth understanding of the developmental and environmental epigenetic programming of the endocrine pancreas has the potential to lead to novel therapeutic approaches in diabetes.
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Affiliation(s)
- Ionel Sandovici
- Department of Obstetrics and Gynaecology, Metabolic Research Laboratories, University of Cambridge, Cambridge, CB2 0SW UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG UK
- Cambridge Biomedical Research Centre, National Institute for Health Research, Cambridge, CB2 0QQ UK
| | - Constanze M. Hammerle
- Department of Obstetrics and Gynaecology, Metabolic Research Laboratories, University of Cambridge, Cambridge, CB2 0SW UK
| | - Susan E. Ozanne
- Cambridge Biomedical Research Centre, National Institute for Health Research, Cambridge, CB2 0QQ UK
- Metabolic Research Laboratories, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Miguel Constância
- Department of Obstetrics and Gynaecology, Metabolic Research Laboratories, University of Cambridge, Cambridge, CB2 0SW UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG UK
- Cambridge Biomedical Research Centre, National Institute for Health Research, Cambridge, CB2 0QQ UK
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134
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Abstract
HIV-1 can establish a state of latent infection at the level of individual T cells. Latently infected cells are rare in vivo and appear to arise when activated CD4(+) T cells, the major targets cells for HIV-1, become infected and survive long enough to revert back to a resting memory state, which is nonpermissive for viral gene expression. Because latent virus resides in memory T cells, it persists indefinitely even in patients on potent antiretroviral therapy. This latent reservoir is recognized as a major barrier to curing HIV-1 infection. The molecular mechanisms of latency are complex and include the absence in resting CD4(+) T cells of nuclear forms of key host transcription factors (e.g., NFκB and NFAT), the absence of Tat and associated host factors that promote efficient transcriptional elongation, epigenetic changes inhibiting HIV-1 gene expression, and transcriptional interference. The presence of a latent reservoir for HIV-1 helps explain the presence of very low levels of viremia in patients on antiretroviral therapy. These viruses are released from latently infected cells that have become activated and perhaps from other stable reservoirs but are blocked from additional rounds of replication by the drugs. Several approaches are under exploration for reactivating latent virus with the hope that this will allow elimination of the latent reservoir.
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Affiliation(s)
- Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Baltimore, Maryland 21205, USA.
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135
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Nie Y, Liu H, Sun X. The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines. PLoS One 2013; 8:e60002. [PMID: 23527292 PMCID: PMC3602107 DOI: 10.1371/journal.pone.0060002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 02/25/2013] [Indexed: 01/12/2023] Open
Abstract
Transcription factor (TF) binding at specific DNA sequences is the fundamental step in transcriptional regulation and is highly dependent on the chromatin structure context, which may be affected by specific histone modifications and variants, known as histone marks. The lack of a global binding map for hundreds of TFs means that previous studies have focused mainly on histone marks at binding sites for several specific TFs. We therefore studied 11 histone marks around computationally-inferred and experimentally-determined TF binding sites (TFBSs), based on 164 and 34 TFs, respectively, in human lymphoblastoid cell lines. For H2A.Z, methylation of H3K4, and acetylation of H3K27 and H3K9, the mark patterns exhibited bimodal distributions and strong pairwise correlations in the 600-bp region around enriched TFBSs, suggesting that these marks mainly coexist within the two nucleosomes proximal to the TF sites. TFs competing with nucleosomes to access DNA at most binding sites, contributes to the bimodal distribution, which is a common feature of histone marks for TF binding. Mark H3K79me2 showed a unimodal distribution on one side of TFBSs and the signals extended up to 4000 bp, indicating a longer-distance pattern. Interestingly, H4K20me1, H3K27me3, H3K36me3 and H3K9me3, which were more diffuse and less enriched surrounding TFBSs, showed unimodal distributions around the enriched TFBSs, suggesting that some TFs may bind to nucleosomal DNA. Besides, asymmetrical distributions of H3K36me3 and H3K9me3 indicated that repressors might establish a repressive chromatin structure in one direction to repress gene expression. In conclusion, this study demonstrated the ranges of histone marks associated with TF binding, and the common features of these marks around the binding sites. These findings have epigenetic implications for future analysis of regulatory elements.
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Affiliation(s)
- Yumin Nie
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
- * E-mail:
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136
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Xi S, Xu H, Shan J, Tao Y, Hong JA, Inchauste S, Zhang M, Kunst TF, Mercedes L, Schrump DS. Cigarette smoke mediates epigenetic repression of miR-487b during pulmonary carcinogenesis. J Clin Invest 2013; 123:1241-61. [PMID: 23426183 PMCID: PMC3582115 DOI: 10.1172/jci61271] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 01/03/2013] [Indexed: 02/03/2023] Open
Abstract
MicroRNAs are critical mediators of stem cell pluripotency, differentiation, and malignancy. Limited information exists regarding microRNA alterations that facilitate initiation and progression of human lung cancers. In this study, array techniques were used to evaluate microRNA expression in normal human respiratory epithelia and lung cancer cells cultured in the presence or absence of cigarette smoke condensate (CSC). Under relevant exposure conditions, CSC significantly repressed miR-487b. Subsequent experiments demonstrated that miR-487b directly targeted SUZ12, BMI1, WNT5A, MYC, and KRAS. Repression of miR-487b correlated with overexpression of these targets in primary lung cancers and coincided with DNA methylation, de novo nucleosome occupancy, and decreased H2AZ and TCF1 levels within the miR-487b genomic locus. Deoxy-azacytidine derepressed miR-487b and attenuated CSC-mediated silencing of miR-487b. Constitutive expression of miR-487b abrogated Wnt signaling, inhibited in vitro proliferation and invasion of lung cancer cells mediated by CSC or overexpression of miR-487b targets, and decreased growth and metastatic potential of lung cancer cells in vivo. Collectively, these findings indicate that miR-487b is a tumor suppressor microRNA silenced by epigenetic mechanisms during tobacco-induced pulmonary carcinogenesis and suggest that DNA demethylating agents may be useful for activating miR-487b for lung cancer therapy.
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Affiliation(s)
- Sichuan Xi
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
Laboratory of Cancer Prevention, National Cancer Institute, Frederick, Maryland, USA.
Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, USA
| | - Hong Xu
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
Laboratory of Cancer Prevention, National Cancer Institute, Frederick, Maryland, USA.
Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, USA
| | - Jigui Shan
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
Laboratory of Cancer Prevention, National Cancer Institute, Frederick, Maryland, USA.
Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, USA
| | - Yongguang Tao
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
Laboratory of Cancer Prevention, National Cancer Institute, Frederick, Maryland, USA.
Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, USA
| | - Julie A. Hong
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
Laboratory of Cancer Prevention, National Cancer Institute, Frederick, Maryland, USA.
Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, USA
| | - Suzanne Inchauste
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
Laboratory of Cancer Prevention, National Cancer Institute, Frederick, Maryland, USA.
Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, USA
| | - Mary Zhang
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
Laboratory of Cancer Prevention, National Cancer Institute, Frederick, Maryland, USA.
Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, USA
| | - Tricia F. Kunst
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
Laboratory of Cancer Prevention, National Cancer Institute, Frederick, Maryland, USA.
Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, USA
| | - Leandro Mercedes
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
Laboratory of Cancer Prevention, National Cancer Institute, Frederick, Maryland, USA.
Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, USA
| | - David S. Schrump
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
Laboratory of Cancer Prevention, National Cancer Institute, Frederick, Maryland, USA.
Advanced Biomedical Computing Center, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, USA
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Urayama S, Semi K, Sanosaka T, Hori Y, Namihira M, Kohyama J, Takizawa T, Nakashima K. Chromatin accessibility at a STAT3 target site is altered prior to astrocyte differentiation. Cell Struct Funct 2013; 38:55-66. [PMID: 23439558 DOI: 10.1247/csf.12034] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
DNA demethylation of astrocyte-specific gene promoters and STAT3 activation in neural precursor cells (NPCs) are essential for astrogliogenesis in the developing brain. To date, it remains unclear whether DNA methylation is the sole epigenetic determinant responsible for suppressing astrocyte-specific genes. Here, we used mouse embryonic stem cells (TKO ESCs) that lacked all 3 DNA methyltransferase genes, Dnmt1, Dnmt3a, and Dnmt3b, and thereby exhibit complete demethylation of the astrocyte-specific glial fibrillary acidic protein (Gfap) gene promoter. We found that although the Gfap promoter was demethylated, STAT3 failed to bind to its cognate element to induce Gfap transcription, whereas it induced transcription of a different target gene, Socs3. Moreover, although the Gfap promoter region containing the STAT3-binding site (GSBS) is enriched with transcription-repressive histone modifications, such as methylation of H3 at lysine 9 (H3K9me3) and H3K27me3, the reduction of these modifications in TKO ESCs was not sufficient for binding of STAT3 at GSBS. Furthermore, GSBS was digested by micrococcal nuclease in late-gestational NPCs that express GFAP upon LIF stimulation, but not in cells that show no expression of GFAP even in the presence of LIF, indicating that STAT3 can access GSBS in the former cells. We further showed that expression of NF-1A, which is known to potentiate differentiation of mid-gestational NPCs into astrocytes, increased its accessibility. Taken together, our results suggest that chromatin accessibility of GSBS plays a critical role in the regulation of Gfap expression.
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Affiliation(s)
- Satoshi Urayama
- Laboratory of Molecular Neuroscience, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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138
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Pandiyan K, You JS, Yang X, Dai C, Zhou XJ, Baylin SB, Jones PA, Liang G. Functional DNA demethylation is accompanied by chromatin accessibility. Nucleic Acids Res 2013; 41:3973-85. [PMID: 23408854 PMCID: PMC3627572 DOI: 10.1093/nar/gkt077] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA methylation inhibitors such as 5-aza-2′-deoxycytidine (5-Aza-CdR) are currently used for the treatment of myelodysplastic syndrome. Although global DNA demethylation has been observed after treatment, it is unclear to what extent demethylation induces changes in nucleosome occupancy, a key determinant of gene expression. We use the colorectal cancer cell line HCT116 as a model to address this question and determine that <2% of regions demethylated by 5-Aza-CdR treatment assume an open configuration. Consolidating our findings, we detect nucleosome retention at sites of global DNA methylation loss in DKO1, an HCT116-derived non-tumorigenic cell-line engineered for DNA methyltransferase disruption. Notably, regions that are open in both HCT116 cells after treatment and in DKO1 cells include promoters belonging to tumor suppressors and genes under-expressed in colorectal cancers. Our results indicate that only a minority of demethylated promoters are associated with nucleosome remodeling, and these could potentially be the epigenetic drivers causing the loss of tumorigenicity. Furthermore, we show that the chromatin opening induced by the histone deacetylase inhibitor suberoylanilide hydroxamic acid has strikingly distinct targets compared with those of 5-Aza-CdR, providing a mechanistic explanation for the importance of combinatorial therapy in eliciting maximal de-repression of the cancer epigenome.
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Affiliation(s)
- Kurinji Pandiyan
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033 USA
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139
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Becker J, Yau C, Hancock JM, Holmes CC. NucleoFinder: a statistical approach for the detection of nucleosome positions. Bioinformatics 2013; 29:711-6. [PMID: 23297036 PMCID: PMC3597142 DOI: 10.1093/bioinformatics/bts719] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Motivation: The identification of nucleosomes along the chromatin is key to understanding their role in the regulation of gene expression and other DNA-related processes. However, current experimental methods (MNase-ChIP, MNase-Seq) sample nucleosome positions from a cell population and contain biases, making thus the precise identification of individual nucleosomes not straightforward. Recent works have only focused on the first point, where noise reduction approaches have been developed to identify nucleosome positions. Results: In this article, we propose a new approach, termed NucleoFinder, that addresses both the positional heterogeneity across cells and experimental biases by seeking nucleosomes consistently positioned in a cell population and showing a significant enrichment relative to a control sample. Despite the absence of validated dataset, we show that our approach (i) detects fewer false positives than two other nucleosome calling methods and (ii) identifies two important features of the nucleosome organization (the nucleosome spacing downstream of active promoters and the enrichment/depletion of GC/AT dinucleotides at the centre of in vitro nucleosomes) with equal or greater ability than the other two methods. Availability: The R code of NucleoFinder, an example datafile and instructions are available for download from https://sites.google.com/site/beckerjeremie/ Contact: cholmes@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jeremie Becker
- Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
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140
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NucVoter: A Voting Algorithm for Reliable Nucleosome Prediction Using Next-Generation Sequencing Data. ISRN BIOINFORMATICS 2013; 2013:174064. [PMID: 25937943 PMCID: PMC4393064 DOI: 10.1155/2013/174064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/08/2013] [Indexed: 11/17/2022]
Abstract
Nucleosomes, which consist of DNA wrapped around histone octamers, are dynamic, and their structure, including their location, size, and occupancy, can be transformed. Nucleosomes can regulate gene expression by controlling the DNA accessibility of proteins. Using next-generation sequencing techniques along with such laboratory methods as micrococcal nuclease digestion, predicting the genomic locations of nucleosomes is possible. However, the true locations of nucleosomes are unknown, and it is difficult to determine their exact locations using next-generation sequencing data. This paper proposes a novel voting algorithm, NucVoter, for the reliable prediction of nucleosome locations. Multiple models verify the consensus areas in which nucleosomes are placed by the model with the highest priority. NucVoter significantly improves the performance of nucleosome prediction.
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141
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Impact of methylation on the physical properties of DNA. Biophys J 2012; 102:2140-8. [PMID: 22824278 DOI: 10.1016/j.bpj.2012.03.056] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 03/13/2012] [Accepted: 03/22/2012] [Indexed: 11/19/2022] Open
Abstract
There is increasing evidence for the presence of an alternative code imprinted in the genome that might contribute to gene expression regulation through an indirect reading mechanism. In mammals, components of this coarse-grained regulatory mechanism include chromatin structure and epigenetic signatures, where d(CpG) nucleotide steps are key players. We report a comprehensive experimental and theoretical study of d(CpG) steps that provides a detailed description of their physical characteristics and the impact of cytosine methylation on these properties. We observed that methylation changes the physical properties of d(CpG) steps, having a dramatic effect on enriched CpG segments, such as CpG islands. We demonstrate that methylation reduces the affinity of DNA to assemble into nucleosomes, and can affect nucleosome positioning around transcription start sites. Overall, our results suggest a mechanism by which the basic physical properties of the DNA fiber can explain parts of the cellular epigenetic regulatory mechanisms.
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142
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Kamiya H, Miyamoto S, Goto H, Kanda GN, Kobayashi M, Matsuoka I, Harashima H. Enhanced transgene expression from chromatinized plasmid DNA in mouse liver. Int J Pharm 2012; 441:146-50. [PMID: 23247018 DOI: 10.1016/j.ijpharm.2012.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 10/30/2012] [Accepted: 12/05/2012] [Indexed: 01/22/2023]
Abstract
Plasmid DNA was chromatinized with core histones (H2A, H2B, H3, and H4) in vitro and was delivered into mouse liver by hydrodynamics-based administration. Transgene expression from the chromatinized plasmid DNA was more efficient than that from plasmid DNA delivered in the naked form. The use of acetylation-enriched histones isolated from cells treated with a histone deacetylase inhibitor (trichostatin A) seemed to be more effective. These results indicated that chromatinized plasmid DNA is useful for efficient transgene expression in vivo.
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Affiliation(s)
- Hiroyuki Kamiya
- Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan.
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143
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Nishida H. Nucleosome Positioning. ISRN MOLECULAR BIOLOGY 2012; 2012:245706. [PMID: 27335664 PMCID: PMC4890889 DOI: 10.5402/2012/245706] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Accepted: 09/17/2012] [Indexed: 02/05/2023]
Abstract
Nucleosome positioning is not only related to genomic DNA compaction but also to other biological functions. After the chromatin is digested by micrococcal nuclease, nucleosomal (nucleosome-bound) DNA fragments can be sequenced and mapped on the genomic DNA sequence. Due to the development of modern DNA sequencing technology, genome-wide nucleosome mapping has been performed in a wide range of eukaryotic species. Comparative analyses of the nucleosome positions have revealed that the nucleosome is more frequently formed in exonic than intronic regions, and that most of transcription start and translation (or transcription) end sites are located in nucleosome linker DNA regions, indicating that nucleosome positioning influences transcription initiation, transcription termination, and gene splicing. In addition, nucleosomal DNA contains guanine and cytosine (G + C)-rich sequences and a high level of cytosine methylation. Thus, the nucleosome positioning system has been conserved during eukaryotic evolution.
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Affiliation(s)
- Hiromi Nishida
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
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144
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Soukup AA, Chiang YM, Bok JW, Reyes-Dominguez Y, Oakley BR, Wang CCC, Strauss J, Keller NP. Overexpression of the Aspergillus nidulans histone 4 acetyltransferase EsaA increases activation of secondary metabolite production. Mol Microbiol 2012; 86:314-30. [PMID: 22882998 PMCID: PMC3514908 DOI: 10.1111/j.1365-2958.2012.08195.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2012] [Indexed: 01/07/2023]
Abstract
Regulation of secondary metabolite (SM) gene clusters in Aspergillus nidulans has been shown to occur through cluster-specific transcription factors or through global regulators of chromatin structure such as histone methyltransferases, histone deacetylases, or the putative methyltransferase LaeA. A multicopy suppressor screen for genes capable of returning SM production to the SM deficient ΔlaeA mutant resulted in identification of the essential histone acetyltransferase EsaA, able to complement an esa1 deletion in Saccharomyces cereviseae. Here we report that EsaA plays a novel role in SM cluster activation through histone 4 lysine 12 (H4K12) acetylation in four examined SM gene clusters (sterigmatocystin, penicillin, terrequinone and orsellinic acid), in contrast to no increase in H4K12 acetylation of the housekeeping tubA promoter. This augmented SM cluster acetylation requires LaeA for full effect and correlates with both increased transcript levels and metabolite production relative to wild type. H4K12 levels may thus represent a unique indicator of relative production potential, notably of SMs.
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Affiliation(s)
- Alexandra A. Soukup
- Department of Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706
| | - Yi-Ming Chiang
- Graduate Institute of Pharmaceutical Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan, ROC 71710,Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033
| | - Jin Woo Bok
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706
| | - Yazmid Reyes-Dominguez
- Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna, and Austrian Institute of Technology GmbH, University and Research Center Campus Tulln, Konrad Lorenz Strasse 24, Tulln/Donau, Austria A-3430
| | - Berl R. Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, USA 66045
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033,Department of Chemistry, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033
| | - Joseph Strauss
- Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna, and Austrian Institute of Technology GmbH, University and Research Center Campus Tulln, Konrad Lorenz Strasse 24, Tulln/Donau, Austria A-3430
| | - Nancy P. Keller
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706,Corresponding author: 3476 Microbial Sciences, 1550 Linden Drive, Madison, WI, USA 53706 Phone: (608) 262-9795 Fax: (608)262-8418
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145
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146
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Xu Z, Li H, Jin P. Epigenetics-Based Therapeutics for Neurodegenerative Disorders. CURRENT GERIATRICS REPORTS 2012; 1:229-236. [PMID: 23526405 DOI: 10.1007/s13670-012-0027-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Epigenetic regulation, such as DNA methylation and histone modification, is implicated in the aberrant changes in gene expression that occur during the progression of neurodegeneration. Many epigenetics-based drugs have been developed recently for the treatment of some neurodegenerative disorders, including Alzheimer's, Parkinson's, and Huntington's diseases. Here we review recent studies that highlight the role of epigenetic modifications in neurodegeneration, among them DNA methylation and demethylation and histone acetylation and deacetylation; we also explore the possibility of using epigenetics-based therapeutics to treat neurodegenerative disorders.
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Affiliation(s)
- Zihui Xu
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA ; Division of Histology and Embryology, Department of Anatomy, Tongji Medical College, Huazhong University of Science and Technology, P. R. China
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147
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Lelli KM, Slattery M, Mann RS. Disentangling the many layers of eukaryotic transcriptional regulation. Annu Rev Genet 2012; 46:43-68. [PMID: 22934649 DOI: 10.1146/annurev-genet-110711-155437] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Regulation of gene expression in eukaryotes is an extremely complex process. In this review, we break down several critical steps, emphasizing new data and techniques that have expanded current gene regulatory models. We begin at the level of DNA sequence where cis-regulatory modules (CRMs) provide important regulatory information in the form of transcription factor (TF) binding sites. In this respect, CRMs function as instructional platforms for the assembly of gene regulatory complexes. We discuss multiple mechanisms controlling complex assembly, including cooperative DNA binding, combinatorial codes, and CRM architecture. The second section of this review places CRM assembly in the context of nucleosomes and condensed chromatin. We discuss how DNA accessibility and histone modifications contribute to TF function. Lastly, new advances in chromosomal mapping techniques have provided increased understanding of intra- and interchromosomal interactions. We discuss how these topological maps influence gene regulatory models.
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Affiliation(s)
- Katherine M Lelli
- Department of Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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148
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Li R, Guo W, Gu J, Zhang MQ, Wang X. Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics 2012; 100:297-302. [PMID: 22824656 DOI: 10.1016/j.ygeno.2012.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 07/03/2012] [Accepted: 07/12/2012] [Indexed: 10/28/2022]
Abstract
Gene expression is a dynamic process, and what factors influence gene expression changes upon external stimulus have not been clearly understood. We studied gene expression profiles in human umbilical vein endothelial cells (HUVEC) after the Tumor Necrosis Factor (TNF) stimulus, and found that: the promoters of fast-response up-regulated genes were enriched with several "active" chromatin markers like H3K27ac and H3K4me3, and also preferentially bound by Pol II and c-Myc; the core-promoter regions of slow-response up-regulated genes were frequently occupied by nucleosomes; down-regulated genes were more intensively regulated by microRNAs. Moreover, the Gene Ontology and motif analysis of the promoter regions revealed that gene clusters with different response behaviors had different functions and were regulated by different sets of transcription factors. Our observations suggested that the different gene expression patterns upon external stimulus were regulated by a combination of multi-layer regulators.
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Affiliation(s)
- Ruijuan Li
- MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
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149
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Schizosaccharomyces pombe Hat1 (Kat1) is associated with Mis16 and is required for telomeric silencing. EUKARYOTIC CELL 2012; 11:1095-103. [PMID: 22771823 DOI: 10.1128/ec.00123-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Hat1 histone acetyltransferase has been implicated in the acetylation of histone H4 during chromatin assembly. In this study, we have characterized the Hat1 complex from the fission yeast Schizosaccharomyces pombe and have examined its role in telomeric silencing. Hat1 is found associated with the RbAp46 homologue Mis16, an essential protein. The Hat1 complex acetylates lysines 5 and 12 of histone H4, the sites that are acetylated in newly synthesized H4 in a wide range of eukaryotes. Deletion of hat1 in S. pombe is itself sufficient to cause the loss of silencing at telomeres. This is in contrast to results obtained with an S. cerevisiae hat1Δ strain, which must also carry mutations of specific acetylatable lysines in the H3 tail domain for loss of telomeric silencing to occur. Notably, deletion of hat1 from S. pombe resulted in an increase of acetylation of histone H4 in subtelomeric chromatin, concomitant with derepression of this region. A similar loss of telomeric silencing was also observed after growing cells in the presence of the deacetylase inhibitor trichostatin A. However, deleting hat1 did not cause loss of silencing at centromeres or the silent mating type locus. These results point to a direct link between Hat1, H4 acetylation, and the establishment of repressed telomeric chromatin in fission yeast.
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150
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Reamon-Buettner SM, Borlak J. Dissecting epigenetic silencing complexity in the mouse lung cancer suppressor gene Cadm1. PLoS One 2012; 7:e38531. [PMID: 22701659 PMCID: PMC3368868 DOI: 10.1371/journal.pone.0038531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 05/07/2012] [Indexed: 11/19/2022] Open
Abstract
Disease-oriented functional analysis of epigenetic factors and their regulatory mechanisms in aberrant silencing is a prerequisite for better diagnostics and therapy. Yet, the precise mechanisms are still unclear and complex, involving the interplay of several effectors including nucleosome positioning, DNA methylation, histone variants and histone modifications. We investigated the epigenetic silencing complexity in the tumor suppressor gene Cadm1 in mouse lung cancer progenitor cell lines, exhibiting promoter hypermethylation associated with transcriptional repression, but mostly unresponsive to demethylating drug treatments. After predicting nucleosome positions and transcription factor binding sites along the Cadm1 promoter, we carried out single-molecule mapping with DNA methyltransferase M.SssI, which revealed in silent promoters high nucleosome occupancy and occlusion of transcription factor binding sites. Furthermore, M.SssI maps of promoters varied within and among the different lung cancer cell lines. Chromatin analysis with micrococcal nuclease also indicated variations in nucleosome positioning to have implications in the binding of transcription factors near nucleosome borders. Chromatin immunoprecipitation showed that histone variants (H2A.Z and H3.3), and opposing histone modification marks (H3K4me3 and H3K27me3) all colocalized in the same nucleosome positions that is reminiscent of epigenetic plasticity in embryonic stem cells. Altogether, epigenetic silencing complexity in the promoter region of Cadm1 is not only defined by DNA hypermethylation, but high nucleosome occupancy, altered nucleosome positioning, and ‘bivalent’ histone modifications, also likely contributed in the transcriptional repression of this gene in the lung cancer cells. Our results will help define therapeutic intervention strategies using epigenetic drugs in lung cancer.
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Affiliation(s)
- Stella Marie Reamon-Buettner
- Toxicology and Environmental Hygiene, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany.
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