201
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Cui F, Cole HA, Clark DJ, Zhurkin VB. Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing. Nucleic Acids Res 2012; 40:10753-64. [PMID: 23012262 PMCID: PMC3510488 DOI: 10.1093/nar/gks870] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nucleosomes often undergo extensive rearrangement when genes are activated for transcription. We have shown previously, using paired-end sequencing of yeast nucleosomes, that major changes in chromatin structure occur when genes are activated by 3-aminotriazole (3AT), an inducer of the transcriptional activator Gcn4. Here, we provide a global analysis of these data. At the genomic level, nucleosomes are regularly phased relative to the transcription start site. However, for a subset of 234 strongly induced genes, this phasing is much more irregular after induction, consistent with the loss of some nucleosomes and the re-positioning of the remaining nucleosomes. To address the nature of this rearrangement, we developed the inter-nucleosome distance auto-correlation (DAC) function. At long range, DAC analysis indicates that nucleosomes have an average spacing of 162 bp, consistent with the reported repeat length. At short range, DAC reveals a 10.25-bp periodicity, implying that nucleosomes in overlapping positions are rotationally related. DAC analysis of the 3AT-induced genes suggests that transcription activation coincides with rearrangement of nucleosomes into irregular arrays with longer spacing. Sequence analysis of the +1 nucleosomes belonging to the 45 most strongly activated genes reveals a distinctive periodic oscillation in the A/T-dinucleotide occurrence that is present throughout the nucleosome and extends into the linker. This unusual pattern suggests that the +1 nucleosomes might be prone to sliding, thereby facilitating transcription.
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Affiliation(s)
- Feng Cui
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Building 37, Room 3035A, Convent Dr., Bethesda, MD 20892, USA
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202
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Florescu AM, Schiessel H, Blossey R. Kinetic control of nucleosome displacement by ISWI/ACF chromatin remodelers. PHYSICAL REVIEW LETTERS 2012; 109:118103. [PMID: 23005680 DOI: 10.1103/physrevlett.109.118103] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Indexed: 06/01/2023]
Abstract
Chromatin structure is dynamically organized by chromatin remodelers, motor protein complexes which move and remove nucleosomes. The regulation of remodeler action has recently been proposed to underlie a kinetic proofreading scheme which combines the recognition of histone-tail states and the ATP-dependent loosening of DNA around nucleosomes. Members of the ISWI-family of remodelers additionally recognize linker length between nucleosomes. Here, we show that the additional proofreading step involving linker length alone is sufficient to promote the formation of regular arrays of nucleosomes. ATP-dependent remodeling by bidirectional motors is shown to reinforce positioning as compared to statistical positioning.
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Affiliation(s)
- Ana-Maria Florescu
- Max-Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
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203
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Yen K, Vinayachandran V, Batta K, Koerber RT, Pugh BF. Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell 2012; 149:1461-73. [PMID: 22726434 DOI: 10.1016/j.cell.2012.04.036] [Citation(s) in RCA: 239] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 03/30/2012] [Accepted: 04/27/2012] [Indexed: 01/10/2023]
Abstract
How chromatin remodelers cooperate to organize nucleosomes around the start and end of genes is not known. We determined the genome-wide binding of remodeler complexes SWI/SNF, RSC, ISW1a, ISW1b, ISW2, and INO80 to individual nucleosomes in Saccharomyces, and determined their functional contributions to nucleosome positioning through deletion analysis. We applied ultra-high-resolution ChIP-exo mapping to Isw2 to determine its subnucleosomal orientation and organization on a genomic scale. Remodelers interacted with selected nucleosome positions relative to the start and end of genes and produced net directionality in moving nucleosomes either away or toward nucleosome-free regions at the 5' and 3' ends of genes. Isw2 possessed a subnucleosomal organization in accord with biochemical and crystallographic-based models that place its linker binding region within promoters and abutted against Reb1-bound locations. Together, these findings reveal a coordinated position-specific approach taken by remodelers to organize genic nucleosomes into arrays.
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Affiliation(s)
- Kuangyu Yen
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
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204
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Chen H, Monte E, Parvatiyar MS, Rosa-Garrido M, Franklin S, Vondriska TM. Structural considerations for chromatin state models with transcription as a functional readout. FEBS Lett 2012; 586:3548-54. [PMID: 22940112 DOI: 10.1016/j.febslet.2012.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 08/16/2012] [Accepted: 08/16/2012] [Indexed: 02/07/2023]
Abstract
Lacking from the rapidly evolving field of chromatin regulation is a discrete model of chromatin states. We propose that each state in such a model should meet two conditions: a structural component and a quantifiable effect on transcription. The practical benefits to the field of a model with greater than two states (including one with six states, as described herein) would be to improve interpretation of data from disparate organ systems, to reflect temporal and developmental dynamics and to integrate the, at present, conceptually and experimentally disparate analyses of individual genetic loci (in vitro or using single gene approaches) and genome-wide features (including ChlP-seq, chromosomal capture and mRNA expression via microarrays/sequencing).
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Affiliation(s)
- Haodong Chen
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, United States
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205
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Brogaard K, Xi L, Wang JP, Widom J. A map of nucleosome positions in yeast at base-pair resolution. Nature 2012; 486:496-501. [PMID: 22722846 PMCID: PMC3786739 DOI: 10.1038/nature11142] [Citation(s) in RCA: 319] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 04/11/2012] [Indexed: 12/25/2022]
Abstract
The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function, yet existing methods for mapping nucleosomes do not provide the necessary single base pair accuracy to determine these positions. Here we develop and apply a new approach for direct mapping of nucleosome centers based on chemical modification of engineered histones. The resulting map locates nucleosome positions genome-wide in unprecedented detail and accuracy. It reveals novel aspects of the in vivo nucleosome organization that are linked to transcription factor binding, RNA polymerase pausing, and the higher order structure of the chromatin fiber.
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Affiliation(s)
- Kristin Brogaard
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
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206
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Hughes AL, Jin Y, Rando OJ, Struhl K. A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol Cell 2012; 48:5-15. [PMID: 22885008 DOI: 10.1016/j.molcel.2012.07.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 06/11/2012] [Accepted: 07/06/2012] [Indexed: 11/18/2022]
Abstract
Although the genomic pattern of nucleosome positioning is broadly conserved, quantitative aspects vary over evolutionary timescales. We identify the cis and trans determinants of nucleosome positioning using a functional evolutionary approach involving S. cerevisiae strains containing large genomic regions from other yeast species. In a foreign species, nucleosome depletion at promoters is maintained over poly(dA:dT) tracts, whereas internucleosome spacing and all other aspects of nucleosome positioning tested are not. Interestingly, the locations of the +1 nucleosome and RNA start sites shift in concert. Strikingly, in a foreign species, nucleosome-depleted regions occur fortuitously in coding regions, and they often act as promoters that are associated with a positioned nucleosome array linked to the length of the transcription unit. We suggest a three-step model in which nucleosome remodelers, general transcription factors, and the transcriptional elongation machinery are primarily involved in generating the nucleosome positioning pattern in vivo.
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Affiliation(s)
- Amanda L Hughes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School,Worcester, MA 01605, USA
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207
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Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution. Biochem Soc Trans 2012; 40:377-82. [PMID: 22435815 DOI: 10.1042/bst20110730] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Genome-wide nucleosome maps revealed well-positioned nucleosomes as a major theme in eukaryotic genome organization. Promoter regions often show a conserved pattern with an NDR (nucleosome-depleted region) from which regular nucleosomal arrays emanate. Three mechanistic contributions to such NDR-array-organization and nucleosome positioning in general are discussed: DNA sequence, DNA binders and DNA-templated processes. Especially, intrinsic biophysics of DNA sequence preferences for nucleosome formation was prominently suggested to explain the majority of nucleosome positions ('genomic code for nucleosome positioning'). Nonetheless, non-histone factors that bind DNA with high or low specificity, such as transcription factors or remodelling enzymes respectively and processes such as replication, transcription and the so-called 'statistical positioning' may be involved too. Recently, these models were tested for yeast by genome-wide reconstitution. DNA sequence preferences as probed by SGD (salt gradient dialysis) reconstitution generated many NDRs, but only few individual nucleosomes, at their proper positions, and no arrays. Addition of a yeast extract and ATP led to dramatically more in vivo-like nucleosome positioning, including regular arrays for the first time. This improvement depended essentially on the extract and ATP but not on transcription or replication. Nucleosome occupancy and close spacing were maintained around promoters, even at lower histone density, arguing for active packing of nucleosomes against the 5' ends of genes rather than statistical positioning. A first extract fractionation identified a direct, specific, necessary, but not sufficient role for the RSC (remodels the structure of chromatin) remodelling enzyme. Collectively, nucleosome positioning in yeast is actively determined by factors beyond intrinsic biophysics, and in steady-state rather than at equilibrium.
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208
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DNA structure, nucleosome placement and chromatin remodelling: a perspective. Biochem Soc Trans 2012; 40:335-40. [PMID: 22435808 DOI: 10.1042/bst20110757] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A major question in chromatin biology is to what extent the sequence of DNA directly determines the genetic and chromatin organization of a eukaryotic genome? We consider two aspects to this question: the DNA sequence-specified positioning of nucleosomes and the determination of NDRs (nucleosome-depleted regions) or barriers. We argue that, in budding yeast, while DNA sequence-specified nucleosome positioning may contribute to positions flanking the regions lacking nucleosomes, DNA thermodynamic stability is a major component determinant of the genetic organization of this organism.
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209
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Liu S, Tao Y. Interplay between chromatin modifications and paused RNA polymerase II in dynamic transition between stalled and activated genes. Biol Rev Camb Philos Soc 2012; 88:40-8. [PMID: 22765520 DOI: 10.1111/j.1469-185x.2012.00237.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The dynamic interplay between chromatin modification (e.g. DNA methylation) and RNA polymerase II (Pol II) plays a critical role in gene transcription during stem cell development, establishment, and maintenance and in the cellular response to extracellular stimuli such as those that cause DNA damage. Pol II is recruited to the promoter-proximal regions of numerous inactive genes at high conentrations in a process called Pol II stalling. This is a key process prior to gene activation and it involves many interacting factors. Chromatin modification including nucleosome position is dependent on chromatin structure. Stalled genes create a particular structural conformation of chromatin, which acts as a target for chromatin modification. In this way, Pol II stalling may be regarded as a type of signal for chromatin modification in these regions during the dynamic transition between stalled and activated genes.
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Affiliation(s)
- Shuang Liu
- Cancer Research Institute, Central South University, Changsha, Hunan 410078, China
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210
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Cole HA, Nagarajavel V, Clark DJ. Perfect and imperfect nucleosome positioning in yeast. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1819:639-43. [PMID: 22306662 PMCID: PMC3358424 DOI: 10.1016/j.bbagrm.2012.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 01/05/2012] [Accepted: 01/11/2012] [Indexed: 11/17/2022]
Abstract
Numerous studies of nucleosome positioning have shown that nucleosomes almost invariably adopt one of several alternative overlapping positions on a short DNA fragment in vitro. We define such a set of overlapping positions as a "position cluster", and the 5S RNA gene positioning sequence is presented as an example. The notable exception is the synthetic 601-sequence, which can position a nucleosome perfectly in vitro, though not in vivo. Many years ago, we demonstrated that nucleosome position clusters are present on the CUP1 and HIS3 genes in native yeast chromatin. Recently, using genome-wide paired-end sequencing of nucleosomes, we have shown that position clusters are the general rule in yeast chromatin, not the exception. We argue that, within a cell population, one of several alternative nucleosomal arrays is formed on each gene. We show how position clusters and alternative arrays can give rise to typical nucleosome occupancy profiles, and that position clusters are disrupted by transcriptional activation. The centromeric nucleosome is a rare example of perfect positioning in vivo. It is, however, a special case, since it contains the centromeric histone H3 variant instead of normal H3. Perfect positioning might be due to centromeric sequence-specific DNA binding proteins. Finally, we point out that the existence of position clusters implies that the putative nucleosome code is degenerate. We suggest that degeneracy might be a crucial point in the debate concerning the code. This article is part of a Special Issue entitled: Chromatin in time and space.
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Affiliation(s)
- Hope A. Cole
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda MD
| | - V. Nagarajavel
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda MD
| | - David J. Clark
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda MD
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211
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Abstract
The persistence of a reservoir of transcriptionally competent but latent virus in the presence of antiviral regimens presents the main impediment to a curative therapy against HIV. Therefore it is critical to understand the molecular mechanisms, which lead to the establishment and maintenance of HIV latency, and which contribute to the reversal of this process and mediate HIV transcriptional activation in response to T cell activation signals. Here I discuss features of the nucleosomal landscape of the HIV promoter or 5'LTR in controlling HIV transcription. I emphasize on the emerging understanding of the role of the ATP dependent SWI/SNF chromatin remodelling complexes in modulating the chromatin architecture at the HIV LTR and how this leads to a tight regulation of LTR transcription.
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Affiliation(s)
- Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands.
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212
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Zhang Z, Ma X, Zhang MQ. Bivalent-like chromatin markers are predictive for transcription start site distribution in human. PLoS One 2012; 7:e38112. [PMID: 22768038 PMCID: PMC3387189 DOI: 10.1371/journal.pone.0038112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/01/2012] [Indexed: 11/24/2022] Open
Abstract
Deep sequencing of 5′ capped transcripts has revealed a variety of transcription initiation patterns, from narrow, focused promoters to wide, broad promoters. Attempts have already been made to model empirically classified patterns, but virtually no quantitative models for transcription initiation have been reported. Even though both genetic and epigenetic elements have been associated with such patterns, the organization of regulatory elements is largely unknown. Here, linear regression models were derived from a pool of regulatory elements, including genomic DNA features, nucleosome organization, and histone modifications, to predict the distribution of transcription start sites (TSS). Importantly, models including both active and repressive histone modification markers, e.g. H3K4me3 and H4K20me1, were consistently found to be much more predictive than models with only single-type histone modification markers, indicating the possibility of “bivalent-like” epigenetic control of transcription initiation. The nucleosome positions are proposed to be coded in the active component of such bivalent-like histone modification markers. Finally, we demonstrated that models trained on one cell type could successfully predict TSS distribution in other cell types, suggesting that these models may have a broader application range.
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Affiliation(s)
- Zhihua Zhang
- Department of Molecular Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America
- Center for Computational Biology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Laboratory of Disease Genomics and Personalized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xiaotu Ma
- Department of Molecular Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Michael Q. Zhang
- Department of Molecular Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America
- Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing, China
- * E-mail:
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213
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New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 2012; 13:436-47. [PMID: 22722606 DOI: 10.1038/nrm3382] [Citation(s) in RCA: 473] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The compaction of genomic DNA into chromatin has profound implications for the regulation of key processes such as transcription, replication and DNA repair. Nucleosomes, the repeating building blocks of chromatin, vary in the composition of their histone protein components. This is the result of the incorporation of variant histones and post-translational modifications of histone amino acid side chains. The resulting changes in nucleosome structure, stability and dynamics affect the compaction of nucleosomal arrays into higher-order structures. It is becoming clear that chromatin structures are not nearly as uniform and regular as previously assumed. This implies that chromatin structure must also be viewed in the context of specific biological functions.
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214
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Gossett AJ, Lieb JD. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 2012; 8:e1002771. [PMID: 22737086 PMCID: PMC3380831 DOI: 10.1371/journal.pgen.1002771] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Accepted: 05/01/2012] [Indexed: 11/23/2022] Open
Abstract
Previous studies in Saccharomyces cerevisiae established that depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds of genes. To probe the mechanism of this transcriptional de-repression, we depleted nucleosomes in vivo by conditional repression of histone H3 transcription. We then measured the resulting changes in transcription by RNA–seq and in chromatin organization by MNase–seq. This experiment also bears on the degree to which trans-acting factors and DNA–encoded elements affect nucleosome position and occupancy in vivo. We identified ∼60,000 nucleosomes genome wide, and we classified ∼2,000 as having preferentially reduced occupancy following H3 depletion and ∼350 as being preferentially retained. We found that the in vivo influence of DNA sequences that favor or disfavor nucleosome occupancy increases following histone H3 depletion, demonstrating that nucleosome density contributes to moderating the influence of DNA sequence on nucleosome formation in vivo. To identify factors important for influencing nucleosome occupancy and position, we compared our data to 40 existing whole-genome data sets. Factors associated with promoters, such as histone acetylation and H2A.z incorporation, were enriched at sites of nucleosome loss. Nucleosome retention was linked to stabilizing marks such as H3K36me2. Notably, the chromatin remodeler Isw2 was uniquely associated with retained occupancy and altered positioning, consistent with Isw2 stabilizing histone–DNA contacts and centering nucleosomes on available DNA in vivo. RNA–seq revealed a greater number of de-repressed genes (∼2,500) than previous studies, and these genes exhibited reduced nucleosome occupancy in their promoters. In summary, we identify factors likely to influence nucleosome stability under normal growth conditions and the specific genomic locations at which they act. We find that DNA–encoded nucleosome stability and chromatin composition dictate which nucleosomes will be lost under conditions of limiting histone protein and that this, in turn, governs which genes are susceptible to a loss of regulatory fidelity. Chromatin is formed by wrapping 146 bp of DNA around a disc-shaped complex of proteins called histones. These protein–DNA structures are known as nucleosomes. Nucleosomes help to regulate gene transcription, because nucleosomes compete with transcription factors for access to DNA. The precise positioning and level of nucleosome occupancy are known to be vital for transcriptional regulation, but the mechanisms that regulate the position and occupancy of nucleosomes are not fully understood. Recently, many studies have focused on the role of DNA sequence and chromatin remodeling proteins. Here, we manipulate the concentration of histone proteins in the cell to determine which nucleosomes are most susceptible to changes in occupancy and position. We find that the chromatin-associated proteins Sir2 and Tup1, and the chromatin remodelers Isw2 and Rsc8, are associated with stabilized nucleosomes. Histone acetylation and incorporation of the histone variant H2A.z are the factors most highly associated with destabilized nucleosomes. Certain DNA sequence properties also contribute to stability. The data identify factors likely to influence nucleosome stability and show a direct link between changes in chromatin and changes in transcription upon histone depletion.
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Affiliation(s)
- Andrea J. Gossett
- Department of Biology, Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jason D. Lieb
- Department of Biology, Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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215
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Abstract
Understanding the mechanisms by which chromatin structure controls eukaryotic transcription has been an intense area of investigation for the past 25 years. Many of the key discoveries that created the foundation for this field came from studies of Saccharomyces cerevisiae, including the discovery of the role of chromatin in transcriptional silencing, as well as the discovery of chromatin-remodeling factors and histone modification activities. Since that time, studies in yeast have continued to contribute in leading ways. This review article summarizes the large body of yeast studies in this field.
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216
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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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217
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Machné R, Murray DB. The yin and yang of yeast transcription: elements of a global feedback system between metabolism and chromatin. PLoS One 2012; 7:e37906. [PMID: 22685547 PMCID: PMC3369881 DOI: 10.1371/journal.pone.0037906] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 04/30/2012] [Indexed: 11/19/2022] Open
Abstract
When grown in continuous culture, budding yeast cells tend to synchronize their respiratory activity to form a stable oscillation that percolates throughout cellular physiology and involves the majority of the protein-coding transcriptome. Oscillations in batch culture and at single cell level support the idea that these dynamics constitute a general growth principle. The precise molecular mechanisms and biological functions of the oscillation remain elusive. Fourier analysis of transcriptome time series datasets from two different oscillation periods (0.7 h and 5 h) reveals seven distinct co-expression clusters common to both systems (34% of all yeast ORF), which consolidate into two superclusters when correlated with a compilation of 1,327 unrelated transcriptome datasets. These superclusters encode for cell growth and anabolism during the phase of high, and mitochondrial growth, catabolism and stress response during the phase of low oxygen uptake. The promoters of each cluster are characterized by different nucleotide contents, promoter nucleosome configurations, and dependence on ATP-dependent nucleosome remodeling complexes. We show that the ATP:ADP ratio oscillates, compatible with alternating metabolic activity of the two superclusters and differential feedback on their transcription via activating (RSC) and repressive (Isw2) types of promoter structure remodeling. We propose a novel feedback mechanism, where the energetic state of the cell, reflected in the ATP:ADP ratio, gates the transcription of large, but functionally coherent groups of genes via differential effects of ATP-dependent nucleosome remodeling machineries. Besides providing a mechanistic hypothesis for the delayed negative feedback that results in the oscillatory phenotype, this mechanism may underpin the continuous adaptation of growth to environmental conditions.
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Affiliation(s)
- Rainer Machné
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.
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218
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Owen-Hughes T, Gkikopoulos T. Making sense of transcribing chromatin. Curr Opin Cell Biol 2012; 24:296-304. [PMID: 22410403 PMCID: PMC3432231 DOI: 10.1016/j.ceb.2012.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/16/2012] [Accepted: 02/17/2012] [Indexed: 11/03/2022]
Abstract
Eukaryotic cells package their genomes into a nucleoprotein form called chromatin. The basic unit of chromatin is the nucleosome, formed by the wrapping of ∼147bp of DNA around an octameric complex of core histones. Advances in genomic technologies have enabled the locations of nucleosomes to be mapped across genomes. This has revealed a striking organisation with respect to transcribed genes in a diverse range of eukaryotes. This consists of a nucleosome depleted region upstream of promoters, with an array of well spaced nucleosomes extending into coding regions. This observation reinforces the links between chromatin organisation and transcription. Central to this is the paradox that while chromatin is required by eukaryotes to restrict inappropriate access to DNA, this must be overcome in order for genetic information to be expressed. This conundrum is at its most flagrant when considering the need for nucleic acid polymerase's to transit 1000's of based pairs of DNA wrapped as arrays of nucleosomes.
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Affiliation(s)
- Tom Owen-Hughes
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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219
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Wippo CJ, Korber P. In vitro reconstitution of in vivo-like nucleosome positioning on yeast DNA. Methods Mol Biol 2012; 833:271-87. [PMID: 22183600 DOI: 10.1007/978-1-61779-477-3_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Genome-wide nucleosome mapping in vivo highlighted the extensive degree of well-defined nucleosome positioning. Such positioned nucleosomes, especially in promoter regions, control access to DNA and constitute an important level of genome regulation. However, the molecular mechanisms that lead to nucleosome positioning are far from understood. In order to dissect this mechanism in detail with biochemical tools, an in vitro system is necessary that can generate proper nucleosome positioning de novo. We present a protocol that allows the assembly of nucleosomes with very much in vivo-like positioning on budding yeast DNA, either of single loci or of the whole-genome. Our method combines salt gradient dialysis and incubation with yeast extract in the presence of ATP. It provides an invaluable tool for the study of nucleosome positioning mechanisms, and can be used to assess the relative stability of properly positioned nucleosomes. It may also generate more physiological templates for in vitro studies of, e.g., nucleosome remodeling or transcription through chromatin.
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Affiliation(s)
- Christian J Wippo
- Molecular Biology Unit, Adolf-Butenandt-Institut, University of Munich, Munich, Germany
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220
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He HH, Meyer CA, Chen MW, Jordan VC, Brown M, Liu XS. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res 2012; 22:1015-25. [PMID: 22508765 PMCID: PMC3371710 DOI: 10.1101/gr.133280.111] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Transcription factor cistromes are highly cell-type specific. Chromatin accessibility, histone modifications, and nucleosome occupancy have all been found to play a role in defining these binding locations. Here, we show that hormone-induced DNase I hypersensitivity changes (ΔDHS) are highly predictive of androgen receptor (AR) and estrogen receptor 1 (ESR1) binding in prostate cancer and breast cancer cells, respectively. While chromatin structure prior to receptor binding and nucleosome occupancy after binding are strikingly different for ESR1 and AR, ΔDHS is highly predictive for both. AR binding is associated with changes in both local nucleosome occupancy and DNase I hypersensitivity. In contrast, while global ESR1 binding is unrelated to changes in nucleosome occupancy, DNase I hypersensitivity dynamics are also predictive of the ESR1 cistrome. These findings suggest that AR and ESR1 have distinct modes of interaction with chromatin and that DNase I hypersensitivity dynamics provides a general approach for predicting cell-type specific cistromes.
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Affiliation(s)
- Housheng Hansen He
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA
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221
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Chang GS, Noegel AA, Mavrich TN, Müller R, Tomsho L, Ward E, Felder M, Jiang C, Eichinger L, Glöckner G, Schuster SC, Pugh BF. Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium. Genome Res 2012; 22:1098-106. [PMID: 22434426 PMCID: PMC3371697 DOI: 10.1101/gr.131649.111] [Citation(s) in RCA: 26] [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]
Abstract
Dictyosteliumdiscoideum is an amoebozoa that exists in both a free-living unicellular and a multicellular form. It is situated in a deep branch in the evolutionary tree and is particularly noteworthy in having a very A/T-rich genome. Dictyostelium provides an ideal system to examine the extreme to which nucleotide bias may be employed in organizing promoters, genes, and nucleosomes across a genome. We find that Dictyostelium genes are demarcated precisely at their 5′ ends by poly-T tracts and precisely at their 3′ ends by poly-A tracts. These tracts are also associated with nucleosome-free regions and are embedded with precisely positioned TATA boxes. Homo- and heteropolymeric tracts of A and T demarcate nucleosome border regions. Together, these findings reveal the presence of a variety of functionally distinct polymeric A/T elements. Strikingly, Dictyostelium chromatin may be organized in di-nucleosome units but is otherwise organized as in animals. This includes a +1 nucleosome in a position that predicts the presence of a paused RNA polymerase II. Indeed, we find a strong phylogenetic relationship between the presence of the NELF pausing factor and positioning of the +1 nucleosome. Pausing and +1 nucleosome positioning may have coevolved in animals.
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Affiliation(s)
- Gue Su Chang
- Center for Eukaryotic Gene Regulation and Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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222
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Iyer VR. Nucleosome positioning: bringing order to the eukaryotic genome. Trends Cell Biol 2012; 22:250-6. [PMID: 22421062 DOI: 10.1016/j.tcb.2012.02.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/07/2012] [Accepted: 02/10/2012] [Indexed: 11/18/2022]
Abstract
Nucleosomes are an essential component of eukaryotic chromosomes. The impact of nucleosomes is seen not just on processes that directly access the genome, such as transcription, but also on an evolutionary timescale. Recent studies in various organisms have provided high-resolution maps of nucleosomes throughout the genome. Computational analysis, in conjunction with many other kinds of data, has shed light on several aspects of nucleosome biology. Nucleosomes are positioned by several means, including intrinsic sequence biases, by stacking against a fixed barrier, by DNA-binding proteins and by chromatin remodelers. These studies underscore the important organizational role of nucleosomes in all eukaryotic genomes. This paper reviews recent genomic studies that have shed light on the determinants of nucleosome positioning and their impact on the genome.
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Affiliation(s)
- Vishwanath R Iyer
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712-0159, USA.
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223
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Yuan GC. Linking genome to epigenome. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:297-309. [PMID: 22344857 DOI: 10.1002/wsbm.1165] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recent epigenomic studies have identified significant differences between developmental stages and cell types. While the importance of epigenetic regulation has been increasingly recognized, it remains unclear how the global epigenetic patterns are established and maintained. Here I review a number of recent studies with the emphasis on the role of the genomic sequence in shaping the epigenetic landscape. These studies strongly suggest that the sequence information is important not just for controlling target specificity but for orchestrating the diversity of epigenetic patterns among different cell types. The epigenome is maintained by the complex network of a large number of interactions. Integrative approaches are needed to gain insights into these networks.
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Affiliation(s)
- Guo-Cheng Yuan
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
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224
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Teif VB, Shkrabkou AV, Egorova VP, Krot VI. Nucleosomes in gene regulation: Theoretical approaches. Mol Biol 2012. [DOI: 10.1134/s002689331106015x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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225
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Jansen A, van der Zande E, Meert W, Fink GR, Verstrepen KJ. Distal chromatin structure influences local nucleosome positions and gene expression. Nucleic Acids Res 2012; 40:3870-85. [PMID: 22241769 PMCID: PMC3351160 DOI: 10.1093/nar/gkr1311] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The positions of nucleosomes across the genome influence several cellular processes, including gene transcription. However, our understanding of the factors dictating where nucleosomes are located and how this affects gene regulation is still limited. Here, we perform an extensive in vivo study to investigate the influence of the neighboring chromatin structure on local nucleosome positioning and gene expression. Using truncated versions of the Saccharomyces cerevisiae URA3 gene, we show that nucleosome positions in the URA3 promoter are at least partly determined by the local DNA sequence, with so-called ‘antinucleosomal elements’ like poly(dA:dT) tracts being key determinants of nucleosome positions. In addition, we show that changes in the nucleosome positions in the URA3 promoter strongly affect the promoter activity. Most interestingly, in addition to demonstrating the effect of the local DNA sequence, our study provides novel in vivo evidence that nucleosome positions are also affected by the position of neighboring nucleosomes. Nucleosome structure may therefore be an important selective force for conservation of gene order on a chromosome, because relocating a gene to another genomic position (where the positions of neighboring nucleosomes are different from the original locus) can have dramatic consequences for the gene's nucleosome structure and thus its expression.
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Affiliation(s)
- An Jansen
- Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, B-3001, Leuven, Belgium
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226
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Singh V, Owen-Hughes T. Evolutionary insights into genome-wide nucleosome positioning. Genome Biol 2012; 13:170. [DOI: 10.1186/gb4046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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227
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Wal M, Pugh BF. Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq. Methods Enzymol 2012; 513:233-50. [PMID: 22929772 DOI: 10.1016/b978-0-12-391938-0.00010-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Eukaryotic DNA is packaged into chromatin where nucleosomes form the basic building unit. Knowing the precise positions of nucleosomes is important because they determine the accessibility of underlying regulatory DNA sequences. Here we describe a detailed method to map on a genomic scale the locations of nucleosomes with very high resolution. Micrococcal nuclease (MNase) digestion followed by chromatin immunoprecipitation and facilitated library construction for deep sequencing provides a simple and accurate map of nucleosome positions.
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Affiliation(s)
- Megha Wal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
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228
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Krietenstein N, Wippo CJ, Lieleg C, Korber P. Genome-wide in vitro reconstitution of yeast chromatin with in vivo-like nucleosome positioning. Methods Enzymol 2012; 513:205-32. [PMID: 22929771 DOI: 10.1016/b978-0-12-391938-0.00009-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recent genome-wide mapping of nucleosome positions revealed that well-positioned nucleosomes are pervasive across eukaryotic genomes, especially in important regulatory regions such as promoters or origins of replication. As nucleosomes impede access to DNA, their positioning is a primary mode of genome regulation. In vivo studies, especially in yeast, shed some light on factors involved in nucleosome positioning, but there is an urgent need for a complementary biochemical approach in order to confirm their direct roles, identify missing factors, and study their mechanisms. Here we describe a method that allows the genome-wide in vitro reconstitution of nucleosomes with very in vivo-like positions by a combination of salt gradient dialysis reconstitution, yeast whole cell extracts, and ATP. This system provides a starting point and positive control for the biochemical dissection of nucleosome positioning mechanisms.
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Affiliation(s)
- Nils Krietenstein
- Adolf-Butenandt-Institut, Molecular Biology Unit, University of Munich, Munich, Germany
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229
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Zaret KS, Carroll JS. Pioneer transcription factors: establishing competence for gene expression. Genes Dev 2011; 25:2227-41. [PMID: 22056668 DOI: 10.1101/gad.176826.111] [Citation(s) in RCA: 1131] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transcription factors are adaptor molecules that detect regulatory sequences in the DNA and target the assembly of protein complexes that control gene expression. Yet much of the DNA in the eukaryotic cell is in nucleosomes and thereby occluded by histones, and can be further occluded by higher-order chromatin structures and repressor complexes. Indeed, genome-wide location analyses have revealed that, for all transcription factors tested, the vast majority of potential DNA-binding sites are unoccupied, demonstrating the inaccessibility of most of the nuclear DNA. This raises the question of how target sites at silent genes become bound de novo by transcription factors, thereby initiating regulatory events in chromatin. Binding cooperativity can be sufficient for many kinds of factors to simultaneously engage a target site in chromatin and activate gene expression. However, in cases in which the binding of a series of factors is sequential in time and thus not initially cooperative, special "pioneer transcription factors" can be the first to engage target sites in chromatin. Such initial binding can passively enhance transcription by reducing the number of additional factors that are needed to bind the DNA, culminating in activation. In addition, pioneer factor binding can actively open up the local chromatin and directly make it competent for other factors to bind. Passive and active roles for the pioneer factor FoxA occur in embryonic development, steroid hormone induction, and human cancers. Herein we review the field and describe how pioneer factors may enable cellular reprogramming.
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Affiliation(s)
- Kenneth S Zaret
- Epigenetics Program, Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, USA.
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230
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Abstract
Two recent studies mapped nucleosomes across the yeast and human genomes, teasing apart the relative contributions of DNA sequence and chromatin remodelers to nucleosome organization. These data suggest two emerging models: chromatin remodelers position nucleosomes around transcriptional start sites in yeast, and a few "locked" nucleosomes may serve as barriers from which nucleosome arrays emanate in human genomes.
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Affiliation(s)
- Ronen Sadeh
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
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231
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Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner. Mol Cell Biol 2011; 32:675-88. [PMID: 22124157 DOI: 10.1128/mcb.06365-11] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The nucleosome is the fundamental repeating unit of eukaryotic chromatin. Here, we assessed the interplay between DNA sequence and ATP-dependent chromatin-remodeling factors (remodelers) in the nucleosomal organization of a eukaryotic genome. We compared the genome-wide distribution of Drosophila NURD, (P)BAP, INO80, and ISWI, representing the four major remodeler families. Each remodeler has a unique set of genomic targets and generates distinct chromatin signatures. Remodeler loci have characteristic DNA sequence features, predicted to influence nucleosome formation. Strikingly, remodelers counteract DNA sequence-driven nucleosome distribution in two distinct ways. NURD, (P)BAP, and INO80 increase histone density at their target sequences, which intrinsically disfavor positioned nucleosome formation. In contrast, ISWI promotes open chromatin at sites that are propitious for precise nucleosome placement. Remodelers influence nucleosome organization genome-wide, reflecting their high genomic density and the propagation of nucleosome redistribution beyond remodeler binding sites. In transcriptionally silent early embryos, nucleosome organization correlates with intrinsic histone-DNA sequence preferences. Following differential expression of the genome, however, this relationship diminishes and eventually disappears. We conclude that the cellular nucleosome landscape is the result of the balance between DNA sequence-driven nucleosome placement and active nucleosome repositioning by remodelers and the transcription machinery.
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232
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Afek A, Sela I, Musa-Lempel N, Lukatsky DB. Nonspecific transcription-factor-DNA binding influences nucleosome occupancy in yeast. Biophys J 2011; 101:2465-75. [PMID: 22098745 DOI: 10.1016/j.bpj.2011.10.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 10/05/2011] [Accepted: 10/12/2011] [Indexed: 01/16/2023] Open
Abstract
Quantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model organism. We perform a genome-wide computational analysis of the nonspecific transcription factor (TF)-DNA binding free-energy landscape and compare this landscape with experimentally determined nucleosome-binding preferences. We show that DNA regions with enhanced nonspecific TF-DNA binding are statistically significantly depleted of nucleosomes. We suggest therefore that the competition between TFs with histones for nonspecific binding to genomic sequences might be an important mechanism influencing nucleosome-binding preferences in vivo. We also predict that poly(dA:dT) and poly(dC:dG) tracts represent genomic elements with the strongest propensity for nonspecific TF-DNA binding, thus allowing TFs to outcompete nucleosomes at these elements. Our results suggest that nonspecific TF-DNA binding might provide a barrier for statistical positioning of nucleosomes throughout the yeast genome. We predict that the strength of this barrier increases with the concentration of DNA binding proteins in a cell. We discuss the connection of the proposed mechanism with the recently discovered pathway of active nucleosome reconstitution.
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Affiliation(s)
- Ariel Afek
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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233
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Yang Z, Hayes JJ. The divalent cations Ca2+ and Mg2+ play specific roles in stabilizing histone-DNA interactions within nucleosomes that are partially redundant with the core histone tail domains. Biochemistry 2011; 50:9973-81. [PMID: 22007636 DOI: 10.1021/bi201377x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We previously reported that reconstituted nucleosomes undergo sequence-dependent translational repositioning upon removal of the core histone tail domains under physiological conditions, indicating that the tails influence the choice of position. We report here that removal of the core histone tail domains increases the exposure of the DNA backbone in nucleosomes to hydroxyl radicals, a nonbiased chemical cleavage reagent, indicative of an increase in the motility of the DNA on the histone surface. Moreover, we demonstrate that the divalent cations Mg(2+) and Ca(2+) can replace the role of the tail domains with regard to stabilization of histone-DNA interactions within the nucleosome core and restrict repositioning of nucleosomes upon tail removal. However, when nucleosomes were incubated with Mg(2+) after tail removal, the original distribution of translational positions was not re-established, indicating that divalent cations increase the energy barrier between translational positions rather than altering the free energy differences between positions. Interestingly, other divalent cations such as Zn(2+), Fe(2+), Co(2+), and Mn(2+) had little or no effect on the stability of histone-DNA interactions within tailless nucleosomes. These results support the idea that specific binding sites for Mg(2+) and Ca(2+) ions exist within the nucleosome and play a critical role in nucleosome stability that is partially redundant with the core histone tail domains.
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Affiliation(s)
- Zungyoon Yang
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
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234
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Nucleosomes and the accessibility problem. Trends Genet 2011; 27:487-92. [PMID: 22019336 DOI: 10.1016/j.tig.2011.09.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 09/07/2011] [Accepted: 09/08/2011] [Indexed: 11/21/2022]
Abstract
Eukaryotic DNA is packaged in nucleosomes. How does this sequestration affect the ability of transcription regulators to access their sites? We cite evidence against the idea that nucleosome positioning is determined primarily by the intrinsic propensities of DNA sequences to form nucleosomes--such that, for example, regulatory sites would be 'nucleosome-free'. Instead, studies in yeast show that nucleosome positioning is primarily determined by specific DNA-binding proteins. Where nucleosomes would otherwise compete with regulatory protein binding (a modest but potentially biologically important effect), this obstacle can be relieved by at least two strategies for exposing regulatory sites. In contrast to their lack of effect on nucleosome positioning, DNA sequence differences do directly affect both the efficiencies with which nucleosomes form in regions flanking regulatory sites before induction, and the extent of their removal upon induction. These nucleosomes, evidently, inhibit basal transcription but are poised to be removed quickly upon command.
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235
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Deniz O, Flores O, Battistini F, Pérez A, Soler-López M, Orozco M. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC Genomics 2011; 12:489. [PMID: 21981773 PMCID: PMC3224377 DOI: 10.1186/1471-2164-12-489] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 10/07/2011] [Indexed: 01/13/2023] Open
Abstract
Background In eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. DNA compaction and nucleosome positioning have clear functional implications, since they modulate the accessibility of genomic regions to regulatory proteins. Despite the intensive research effort focused in this area, the rules defining nucleosome positioning and the location of DNA regulatory regions still remain elusive. Results Naked (histone-free) and nucleosomal DNA from yeast were digested by microccocal nuclease (MNase) and sequenced genome-wide. MNase cutting preferences were determined for both naked and nucleosomal DNAs. Integration of their sequencing profiles with DNA conformational descriptors derived from atomistic molecular dynamic simulations enabled us to extract the physical properties of DNA on a genomic scale and to correlate them with chromatin structure and gene regulation. The local structure of DNA around regulatory regions was found to be unusually flexible and to display a unique pattern of nucleosome positioning. Ab initio physical descriptors derived from molecular dynamics were used to develop a computational method that accurately predicts nucleosome enriched and depleted regions. Conclusions Our experimental and computational analyses jointly demonstrate a clear correlation between sequence-dependent physical properties of naked DNA and regulatory signals in the chromatin structure. These results demonstrate that nucleosome positioning around TSS (Transcription Start Site) and TTS (Transcription Termination Site) (at least in yeast) is strongly dependent on DNA physical properties, which can define a basal regulatory mechanism of gene expression.
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Affiliation(s)
- Ozgen Deniz
- Institute for Research in Biomedicine and Barcelona Supercomputing Center Joint Research Program on Computational Biology, Baldiri i Reixac 10, Barcelona 08028, Spain
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236
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Piatti P, Zeilner A, Lusser A. ATP-dependent chromatin remodeling factors and their roles in affecting nucleosome fiber composition. Int J Mol Sci 2011; 12:6544-65. [PMID: 22072904 PMCID: PMC3210995 DOI: 10.3390/ijms12106544] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 09/20/2011] [Accepted: 09/28/2011] [Indexed: 01/03/2023] Open
Abstract
ATP-dependent chromatin remodeling factors of the SNF2 family are key components of the cellular machineries that shape and regulate chromatin structure and function. Members of this group of proteins have broad and heterogeneous functions ranging from controlling gene activity, facilitating DNA damage repair, promoting homologous recombination to maintaining genomic stability. Several chromatin remodeling factors are critical components of nucleosome assembly processes, and recent reports have identified specific functions of distinct chromatin remodeling factors in the assembly of variant histones into chromatin. In this review we will discuss the specific roles of ATP-dependent chromatin remodeling factors in determining nucleosome composition and, thus, chromatin fiber properties.
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Affiliation(s)
- Paolo Piatti
- Division of Molecular Biology, Innsbruck Medical University, Biocenter, Fritz-Pregl Strasse 3, 6020 Innsbruck, Austria; E-Mails: (P.P.); (A.Z.)
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237
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Gkikopoulos T, Schofield P, Singh V, Pinskaya M, Mellor J, Smolle M, Workman JL, Barton G, Owen-Hughes T. A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science 2011; 333:1758-60. [PMID: 21940898 PMCID: PMC3428865 DOI: 10.1126/science.1206097] [Citation(s) in RCA: 216] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here, we show that the combined action of Isw1 and Chd1 nucleosome-spacing enzymes is required to maintain this organization. In the absence of these enzymes, regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome, and a subset of locations distributed throughout coding regions where other factors are likely to be involved. These observations indicate that adenosine triphosphate-dependent remodeling enzymes are responsible for directing the positioning of the majority of nucleosomes within the Saccharomyces cerevisiae genome.
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Affiliation(s)
- Triantaffyllos Gkikopoulos
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Pieta Schofield
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Division of Biological Chemistry and Drug discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Vijender Singh
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marina Pinskaya
- Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU
| | - Jane Mellor
- Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU
| | - Michaela Smolle
- Stowers Institute for Medical Research, 1000E. 50 Street, Kansas City, MO 64110, USA
| | - Jerry L. Workman
- Stowers Institute for Medical Research, 1000E. 50 Street, Kansas City, MO 64110, USA
| | - Geoffrey Barton
- Division of Biological Chemistry and Drug discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tom Owen-Hughes
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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238
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Tirosh I, Barkai N. Inferring regulatory mechanisms from patterns of evolutionary divergence. Mol Syst Biol 2011; 7:530. [PMID: 21915117 PMCID: PMC3202799 DOI: 10.1038/msb.2011.60] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 07/07/2011] [Indexed: 12/31/2022] Open
Abstract
The number of sequenced species is increasing at a staggering rate, calling for new approaches for incorporating evolutionary information in the study of biological mechanisms. Evolutionary conservation is widely used for assigning a function to new proteins and for predicting functional coding or non-coding sequences. Here, we argue for a complementary approach that focuses on the divergence of regulatory programs. Regulatory mechanisms can be learned from patterns of evolutionary divergence in regulatory properties such as gene expression, transcription factor binding or nucleosome positioning. We review examples of this concept using yeast as a model system, and highlight a hybrid-based approach that is highly instrumental in this analysis.
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Affiliation(s)
- Itay Tirosh
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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239
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Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns. Mol Cell Biol 2011; 31:4348-55. [PMID: 21896781 DOI: 10.1128/mcb.05276-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
To examine the role of nucleosome occupancy in the evolution of gene expression, we measured the genome-wide nucleosome profiles of four yeast species, three belonging to the Saccharomyces sensu stricto lineage and the more distantly related Candida glabrata. Nucleosomes and associated promoter elements at C. glabrata genes are typically shifted upstream by ∼20 bp, compared to their orthologs from sensu stricto species. Nonetheless, all species display the same global organization features first described for Saccharomyces cerevisiae: a stereotypical nucleosome organization along genes and a division of promoters into those that contain or lack a pronounced nucleosome-depleted region (NDR), with the latter displaying a more dynamic pattern of gene expression. Despite this global similarity, however, nucleosome occupancy at specific genes diverged extensively between sensu stricto and C. glabrata orthologs (∼50 million years). Orthologs with dynamic expression patterns tend to maintain their lack of NDR, but apart from that, sensu stricto and C. glabrata orthologs are nearly as similar in nucleosome occupancy patterns as nonorthologous genes. This extensive divergence in nucleosome occupancy contrasts with a conserved pattern of gene expression. Thus, while some evolutionary changes in nucleosome occupancy contribute to gene expression divergence, nucleosome occupancy often diverges extensively with apparently little impact on gene expression.
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OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes. Proc Natl Acad Sci U S A 2011; 108:14497-502. [PMID: 21844352 DOI: 10.1073/pnas.1111309108] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recent epigenome-wide mapping studies describe nucleosome-depleted regions (NDRs) at transcription start sites and enhancers. However, these static maps do not address causality or the roles of NDRs in gene control, and their relationship to transcription factors and DNA methylation is not well understood. Using a high-resolution single-molecule mapping approach to simultaneously investigate endogenous DNA methylation and nucleosome occupancies on individual DNA molecules, we show that the unmethylated OCT4 distal enhancer has an NDR, whereas NANOG has a clear NDR at its proximal promoter. These NDRs are maintained by binding of OCT4 and are required for OCT4 and NANOG expression. Differentiation causes a rapid loss of both NDRs accompanied by nucleosome occupancy, which precedes de novo DNA methylation. NDRs can be restored by forced expression of OCT4 in somatic cells but only when there is no cytosine methylation. These data show the central role of the NDRs, established by OCT4, in ensuring the autoregulatory loop of pluripotency and, furthermore, that de novo methylation follows the loss of NDRs and stabilizes the suppressed state.
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Abstract
Precise positioning of nucleosomes along DNA is important for a variety of gene regulatory processes. Among the factors directing nucleosome positioning, the DNA sequence is highly important. Two main classes of nucleosome positioning sequence (NPS) patterns have previously been described. In the first class, AA, TT, and other WW dinucleotides (where W is A or T) tend to occur together (in-phase) in the major groove of DNA closest to the histone octamer surface, while SS dinucleotides (where S is G or C) are predominantly positioned in the major groove facing outward. In the second class, AA and TT are structurally separated (AA backbone near the histone octamer, and TT backbone further away), but grouped with other RR (where R is purine A or G) and YY (where Y is pyrimidine C or T) dinucleotides. As a result, the RR/YY pattern includes counter-phase AA/TT distributions. We describe here anti-NPS patterns, which are inverse to the conventional NPS patterns: WW runs inverse to SS, and RR inverse to YY. Evidence for the biological relevance of anti-NPS patterns is presented.
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Abstract
In eukaryotes, all DNA-templated reactions occur in the context of chromatin. Nucleosome packaging inherently restricts DNA accessibility for regulatory proteins but also provides an opportunity to regulate DNA-based processes through modulating nucleosome positions and local chromatin structure. Recent advances in genome-scale methods are yielding increasingly detailed profiles of the genomic distribution of nucleosomes, their modifications and their modifiers. The picture now emerging is one in which the dynamic control of genome accessibility is governed by contributions from DNA sequence, ATP-dependent chromatin remodelling and nucleosome modifications. Here we discuss the interplay of these processes by reviewing our current understanding of how chromatin access contributes to the regulation of transcription, replication and repair.
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Muers M. Positioning the players. Nat Rev Genet 2011; 12:454. [DOI: 10.1038/nrg3018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Erdel F, Krug J, Längst G, Rippe K. Targeting chromatin remodelers: signals and search mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:497-508. [PMID: 21704204 DOI: 10.1016/j.bbagrm.2011.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 06/02/2011] [Accepted: 06/06/2011] [Indexed: 12/26/2022]
Abstract
Chromatin remodeling complexes are ATP-driven molecular machines that change chromatin structure by translocating nucleosomes along the DNA, evicting nucleosomes, or changing the nucleosomal histone composition. They are highly abundant in the cell and numerous different complexes exist that display distinct activity patterns. Here we review chromatin-associated signals that are recognized by remodelers. It is discussed how these regulate the remodeling reaction via changing the nucleosome substrate/product binding affinity or the catalytic translocation rate. Finally, we address the question of how chromatin remodelers operate in the cell nucleus to find specifically marked nucleosome substrates via a diffusion driven target location mechanism, and estimate the search times of this process. This article is part of a Special Issue entitled:Snf2/Swi2 ATPase structure and function.
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Affiliation(s)
- Fabian Erdel
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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Chevereau G, Arneodo A, Vaillant C. Influence of the genomic sequence on the primary structure of chromatin. FRONTIERS IN LIFE SCIENCE 2011. [DOI: 10.1080/21553769.2012.708882] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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246
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Flaus A. Principles and practice of nucleosome positioningin vitro. FRONTIERS IN LIFE SCIENCE 2011. [DOI: 10.1080/21553769.2012.702667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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