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Rakshit T, Melters DP, Dimitriadis EK, Dalal Y. Mechanical properties of nucleoprotein complexes determined by nanoindentation spectroscopy. Nucleus 2021; 11:264-282. [PMID: 32954931 PMCID: PMC7529419 DOI: 10.1080/19491034.2020.1816053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The interplay between transcription factors, chromatin remodelers, 3-D organization, and mechanical properties of the chromatin fiber controls genome function in eukaryotes. Besides the canonical histones which fold the bulk of the chromatin into nucleosomes, histone variants create distinctive chromatin domains that are thought to regulate transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether histone variants translate distinctive biochemical or biophysical properties to their associated chromatin structures, and whether these properties impact chromatin dynamics as the genome undergoes a multitude of transactions, is an important question in biology. Here, we describe single-molecule nanoindentation tools that we developed specifically to determine the mechanical properties of histone variant nucleosomes and their complexes. These methods join an array of cutting-edge new methods that further our quantitative understanding of the response of chromatin to intrinsic and extrinsic forces which act upon it during biological transactions in the nucleus.
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Affiliation(s)
- Tatini Rakshit
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA.,Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Salt Lake, India
| | - Daniël P Melters
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA
| | - Emilios K Dimitriadis
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Cancer Institute, NIH , Bethesda, MD, USA
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA
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2
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Melters DP, Pitman M, Rakshit T, Dimitriadis EK, Bui M, Papoian GA, Dalal Y. Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners. Proc Natl Acad Sci U S A 2019; 116:24066-24074. [PMID: 31712435 PMCID: PMC6883791 DOI: 10.1073/pnas.1911880116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Histone variants fine-tune transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether and how nucleosome variants encode unique mechanical properties to their cognate chromatin structures remains elusive. Here, using in silico and in vitro nanoindentation methods, extending to in vivo dissections, we report that histone variant nucleosomes are intrinsically more elastic than their canonical counterparts. Furthermore, binding proteins, which discriminate between histone variant nucleosomes, suppress this innate elasticity and also compact chromatin. Interestingly, when we overexpress the binding proteins in vivo, we also observe increased compaction of chromatin enriched for histone variant nucleosomes, correlating with diminished access. Taken together, these data suggest a plausible link between innate mechanical properties possessed by histone variant nucleosomes, the adaptability of chromatin states in vivo, and the epigenetic plasticity of the underlying locus.
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Affiliation(s)
- Daniël P Melters
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Mary Pitman
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
- Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742
| | - Tatini Rakshit
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Emilios K Dimitriadis
- Scanning Probe Microscopy Unit, Biomedical Engineering and Physical Science Shared Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Minh Bui
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Garegin A Papoian
- Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742;
| | - Yamini Dalal
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892;
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3
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Ea V, Sexton T, Gostan T, Herviou L, Baudement MO, Zhang Y, Berlivet S, Le Lay-Taha MN, Cathala G, Lesne A, Victor JM, Fan Y, Cavalli G, Forné T. Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains. BMC Genomics 2015; 16:607. [PMID: 26271925 PMCID: PMC4536789 DOI: 10.1186/s12864-015-1786-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/20/2015] [Indexed: 11/25/2022] Open
Abstract
Background In higher eukaryotes, the genome is partitioned into large "Topologically Associating Domains" (TADs) in which the chromatin displays favoured long-range contacts. While a crumpled/fractal globule organization has received experimental supports at higher-order levels, the organization principles that govern chromatin dynamics within these TADs remain unclear. Using simple polymer models, we previously showed that, in mouse liver cells, gene-rich domains tend to adopt a statistical helix shape when no significant locus-specific interaction takes place. Results Here, we use data from diverse 3C-derived methods to explore chromatin dynamics within mouse and Drosophila TADs. In mouse Embryonic Stem Cells (mESC), that possess large TADs (median size of 840 kb), we show that the statistical helix model, but not globule models, is relevant not only in gene-rich TADs, but also in gene-poor and gene-desert TADs. Interestingly, this statistical helix organization is considerably relaxed in mESC compared to liver cells, indicating that the impact of the constraints responsible for this organization is weaker in pluripotent cells. Finally, depletion of histone H1 in mESC alters local chromatin flexibility but not the statistical helix organization. In Drosophila, which possesses TADs of smaller sizes (median size of 70 kb), we show that, while chromatin compaction and flexibility are finely tuned according to the epigenetic landscape, chromatin dynamics within TADs is generally compatible with an unconstrained polymer configuration. Conclusions Models issued from polymer physics can accurately describe the organization principles governing chromatin dynamics in both mouse and Drosophila TADs. However, constraints applied on this dynamics within mammalian TADs have a peculiar impact resulting in a statistical helix organization. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1786-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vuthy Ea
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Tom Sexton
- Institut de Génétique Humaine, UPR 1142, CNRS, Montpellier, France.
| | - Thierry Gostan
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Laurie Herviou
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Marie-Odile Baudement
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Yunzhe Zhang
- School of Biology and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA.
| | - Soizik Berlivet
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Marie-Noëlle Le Lay-Taha
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France.
| | - Guy Cathala
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France. .,CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France.
| | - Annick Lesne
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France. .,CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France. .,Laboratoire de Physique de la Matière Condensée, CNRS UMR 7600, UPMC, Sorbonne universités, Paris, France.
| | - Jean-Marc Victor
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France. .,CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France. .,Laboratoire de Physique de la Matière Condensée, CNRS UMR 7600, UPMC, Sorbonne universités, Paris, France.
| | - Yuhong Fan
- School of Biology and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA.
| | - Giacomo Cavalli
- Institut de Génétique Humaine, UPR 1142, CNRS, Montpellier, France. .,CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France.
| | - Thierry Forné
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, Cedex 5, France. .,CNRS GDR 3536 UPMC, Sorbonne universités, Paris, France.
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4
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Athwal RK, Walkiewicz MP, Baek S, Fu S, Bui M, Camps J, Ried T, Sung MH, Dalal Y. CENP-A nucleosomes localize to transcription factor hotspots and subtelomeric sites in human cancer cells. Epigenetics Chromatin 2015; 8:2. [PMID: 25788983 PMCID: PMC4363203 DOI: 10.1186/1756-8935-8-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 12/21/2022] Open
Abstract
Background The histone H3 variant CENP-A is normally tightly regulated to ensure only one centromere exists per chromosome. Native CENP-A is often found overexpressed in human cancer cells and a range of human tumors. Consequently, CENP-A misregulation is thought to contribute to genome instability in human cancers. However, the consequences of such overexpression have not been directly elucidated in human cancer cells. Results To investigate native CENP-A overexpression, we sought to uncover CENP-A-associated defects in human cells. We confirm that CENP-A is innately overexpressed in several colorectal cancer cell lines. In such cells, we report that a subset of structurally distinct CENP-A-containing nucleosomes associate with canonical histone H3, and with the transcription-coupled chaperones ATRX and DAXX. Furthermore, such hybrid CENP-A nucleosomes localize to DNase I hypersensitive and transcription factor binding sites, including at promoters of genes across the human genome. A distinct class of CENP-A hotspots also accumulates at subtelomeric chromosomal locations, including at the 8q24/Myc region long-associated with genomic instability. We show this 8q24 accumulation of CENP-A can also be seen in early stage primary colorectal tumors. Conclusions Our data demonstrate that excess CENP-A accumulates at noncentromeric locations in the human cancer genome. These findings suggest that ectopic CENP-A nucleosomes could alter the state of the chromatin fiber, potentially impacting gene regulation and chromosome fragility. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-8-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rajbir K Athwal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Marcin P Walkiewicz
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Song Fu
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Minh Bui
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Jordi Camps
- Genetics Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health, 50 South Drive, Bethesda, MD 20892 USA
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health, 50 South Drive, Bethesda, MD 20892 USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Yamini Dalal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
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5
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Walkiewicz MP, Dimitriadis EK, Dalal Y. CENP-A octamers do not confer a reduction in nucleosome height by AFM. Nat Struct Mol Biol 2014; 21:2-3. [PMID: 24389541 PMCID: PMC6756849 DOI: 10.1038/nsmb.2742] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Marcin P Walkiewicz
- National Cancer Institute, National Institutes of Health,
Bethesda Maryland, USA
| | - Emilios K Dimitriadis
- National Institute for BioImaging and BioEngineering,
National Institutes of Health, Bethesda, Maryland, USA
| | - Yamini Dalal
- National Cancer Institute, National Institutes of Health,
Bethesda Maryland, USA
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6
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Bui M, Walkiewicz MP, Dimitriadis EK, Dalal Y. The CENP-A nucleosome: a battle between Dr Jekyll and Mr Hyde. Nucleus 2013; 4:37-42. [PMID: 23324462 PMCID: PMC3585026 DOI: 10.4161/nucl.23588] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The structure of the centromere-specific histone centromeric protein A (CENP-A) nucleosome has been a hot topic of debate for the past five years. Structures proposed include octamers, hexamers, homotypic and heterotypic tetramers. This controversy has led to the proposal that CENP-A nucleosomes undergo cell-cycle dependent transitions between the multiple states previously documented to exist in vivo and in vitro. In recent work from our laboratory, we sought to test this hypothesis. We discovered that CENP-A nucleosomes undergo unique oscillations in human cells, a finding mirrored in a parallel study performed in budding yeast. This review provides additional insights into the potential mechanisms for the interconversion of CENP-A nucleosomal species, and speculates on a biological role for oscillations in vivo.
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Affiliation(s)
- Minh Bui
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
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7
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Bui M, Dimitriadis EK, Hoischen C, An E, Quénet D, Giebe S, Nita-Lazar A, Diekmann S, Dalal Y. Cell-cycle-dependent structural transitions in the human CENP-A nucleosome in vivo. Cell 2012; 150:317-26. [PMID: 22817894 PMCID: PMC3592566 DOI: 10.1016/j.cell.2012.05.035] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/19/2011] [Accepted: 05/18/2012] [Indexed: 12/21/2022]
Abstract
In eukaryotes, DNA is packaged into chromatin by canonical histone proteins. The specialized histone H3 variant CENP-A provides an epigenetic and structural basis for chromosome segregation by replacing H3 at centromeres. Unlike exclusively octameric canonical H3 nucleosomes, CENP-A nucleosomes have been shown to exist as octamers, hexamers, and tetramers. An intriguing possibility reconciling these observations is that CENP-A nucleosomes cycle between octamers and tetramers in vivo. We tested this hypothesis by tracking CENP-A nucleosomal components, structure, chromatin folding, and covalent modifications across the human cell cycle. We report that CENP-A nucleosomes alter from tetramers to octamers before replication and revert to tetramers after replication. These structural transitions are accompanied by reversible chaperone binding, chromatin fiber folding changes, and previously undescribed modifications within the histone fold domains of CENP-A and H4. Our results reveal a cyclical nature to CENP-A nucleosome structure and have implications for the maintenance of epigenetic memory after centromere replication.
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Affiliation(s)
- Minh Bui
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Emilios K. Dimitriadis
- Laboratory of Biomedical Engineering and Physical Sciences, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892, USA
| | | | - Eunkyung An
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Delphine Quénet
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Aleksandra Nita-Lazar
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | | | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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8
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Huang WH, Huang XY, Sun FZ. Modified agarose gel for high-performance Southern blotting of short DNA fragments. Biotechniques 2010; 49:580-1. [DOI: 10.2144/000113465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Southern blotting is a common method used for the study of gene organization. Current methods of DNA transfer for Southern blotting, however, can be inefficient for high concentration agarose gels. Here, we report a method for high-performance Southern blotting of short DNA fragments such as nucleosomal DNAs by using a discontinuous agarose zone gel. The results show that sharp and well-resolved fractionation of short DNA fragments comparable to that from a high-concentration agarose gel could be obtained using a low-concentration agarose gel with a small zone of high-concentration agarose, and that the resulting DNA transfer is highly efficient and rapid.
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Affiliation(s)
- Wei-Hong Huang
- Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiu-Ying Huang
- Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fang-Zhen Sun
- Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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9
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Hebert C, Roest Crollius H. Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes. Genome Biol 2010; 11:R51. [PMID: 20462404 PMCID: PMC2898081 DOI: 10.1186/gb-2010-11-5-r51] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 02/24/2010] [Accepted: 05/12/2010] [Indexed: 01/09/2023] Open
Abstract
Human genes contain a 10 bp repeat of RR dinucleotides focused around the first nucleosome position suggesting a role in transcriptional control. Background The position of a nucleosome, both translational along the DNA molecule and rotational between the histone core and the DNA, is controlled by many factors, including the regular occurrence of specific dinucleotides with a period of approximately 10 bp, important for the rotational setting of the DNA around the histone octamer. Results We show that such a 10 bp periodic signal of purine-purine dinucleotides occurs in phase with the transcription start site (TSS) of human genes and is centered on the position of the first (+1) nucleosome downstream of the TSS. These data support a direct link between transcription and the rotational setting of the nucleosome. The periodic signal is most prevalent in genes that contain CpG islands that are expressed at low levels in a tissue-specific manner and are involved in the control of transcription. Conclusions These results, together with several lines of evidence from the recent literature, support a new model whereby the +1 nucleosome could be more efficiently disassembled from gene promoters by H3K56 acetylation marks if the periodic signal specifies an optimal rotational setting.
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Affiliation(s)
- Charles Hebert
- Dyogen Group, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), 46 rue d'Ulm, CNRS UMR8197, INSERM U1024, 75005 Paris Cedex 05, France.
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10
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Takasuka TE, Stein A. Direct measurements of the nucleosome-forming preferences of periodic DNA motifs challenge established models. Nucleic Acids Res 2010; 38:5672-80. [PMID: 20460457 PMCID: PMC2943623 DOI: 10.1093/nar/gkq279] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Several periodic motifs have been implicated in facilitating the bending of DNA around the histone core of the nucleosome. For example, di-nucleotides AA/TT/TA and GC at ∼10-bp periods, but offset by 5 bp, are found with higher-than-expected occurrences in aligned nucleosomal DNAs in vitro and in vivo. Additionally, regularly oscillating period-10 trinucleotide motifs non-T, A/T, G and their complements have been implicated in the formation of regular nucleosome arrays. The effects of these periodic motifs on nucleosome formation have not been systematically tested directly by competitive reconstitution assays. We show that, in general, none of these period-10 motifs, except TA, in certain sequence contexts, facilitates nucleosome formation. The influence of periodic TAs on nucleosome formation is appreciable; with some of the 200-bp DNAs out-competing bulk nucleosomal DNA by more than 400-fold. Only the nucleotides immediately flanking TA influence its nucleosome-forming ability. Period-10 TA, when flanked by a pair of permissive nucleotides, facilitates DNA bending through compression of the minor groove. The free energy change for nucleosome formation decreases linearly with the number of consecutive TAs, up to eight. We suggest how these data can be reconciled with previous findings.
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Affiliation(s)
- Taichi E Takasuka
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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11
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Takasuka TE, Cioffi A, Stein A. Sequence information encoded in DNA that may influence long-range chromatin structure correlates with human chromosome functions. PLoS One 2008; 3:e2643. [PMID: 18612465 PMCID: PMC2440353 DOI: 10.1371/journal.pone.0002643] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Accepted: 06/11/2008] [Indexed: 11/18/2022] Open
Abstract
Little is known about the possible function of the bulk of the human genome. We have recently shown that long-range regular oscillation in the motif non-T, A/T, G (VWG) existing at ten-nucleotide multiples influences large-scale nucleosome array formation. In this work, we have determined the locations of all 100 kb regions that are predicted to form distinctive chromatin structures throughout each human chromosome (except Y). Using these data, we found that a significantly greater fraction of 300 kb sequences lacked annotated transcripts in genomic DNA regions > or = 300 kb that contained nearly continuous chromatin organizing signals than in control regions. We also found a relationship between the meiotic recombination frequency and the presence of strong VWG chromatin organizing signals. Large (> or = 300 kb) genomic DNA regions having low average recombination frequency are enriched in chromatin organizing signals. As additional controls, we show using chromosome 1 that the VWG motif signals are not enriched in randomly selected DNA regions having the mean size of the recombination coldspots, and that non-VWG motif sets do not generate signals that are enriched in recombination coldspots. We also show that tandemly repeated alpha satellite DNA contains strong VWG signals for the formation of distinctive nucleosome arrays, consistent with the low recombination activity of centromeres. Our correlations cannot be explained simply by variations in the GC content. Our findings suggest that a specific set of periodic DNA motifs encoded in genomic DNA, which provide signals for chromatin organization, influence human chromosome function.
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Affiliation(s)
- Taichi E. Takasuka
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Alfred Cioffi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Arnold Stein
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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12
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Babbitt GA, Kim Y. Inferring natural selection on fine-scale chromatin organization in yeast. Mol Biol Evol 2008; 25:1714-27. [PMID: 18515262 DOI: 10.1093/molbev/msn127] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Despite its potential role in the evolution of complex phenotypes, the detection of negative (purifying) and positive selection on noncoding regulatory sequence has been elusive because of the inherent difficulty in predicting the functional consequences of mutations on noncoding sequence. Because the functioning of regulatory sequence depends upon both chromatin configuration and cis-regulatory factor binding, we investigate the idea that the functional conservation of regulatory regions should be associated with the conservation of sequence-dependent bending properties of DNA that determine its affinity for the nucleosome. Recent advances in the computational prediction of sequence-dependent affinity to nucleosomes provide an opportunity to distinguish between neutral and nonneutral evolution of fine-scale chromatin organization. Here, a statistical test is presented for detecting evolutionary conservation and/or adaptive evolution of nucleosome affinity from interspecies comparisons of DNA sequences. Local nucleosome affinities of homologous sequences were calculated using 2 recently published methods. A randomization test was applied to sites of mutation to evaluate the similarity of DNA-nucleosome affinity between several closely related species of Saccharomyces yeast. For most of the genes we analyzed, the conservation of local nucleosome affinity was detected at a few distinct locations in the upstream noncoding region. Our results also demonstrate that different patterns of chromatin evolution have shaped DNA-nucleosome interaction at the core promoters of TATA-containing and TATA-less genes and that elevated purifying selection has maintained low affinity for nucleosome in the core promoters of the latter group. Across the entire yeast genome, DNA-nucleosome interaction was also discovered to be significantly more conserved in TATA-less genes compared with TATA-containing genes.
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Affiliation(s)
- G A Babbitt
- Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, USA.
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13
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Furuyama S, Biggins S. Centromere identity is specified by a single centromeric nucleosome in budding yeast. Proc Natl Acad Sci U S A 2007; 104:14706-11. [PMID: 17804787 PMCID: PMC1976213 DOI: 10.1073/pnas.0706985104] [Citation(s) in RCA: 201] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2007] [Indexed: 11/18/2022] Open
Abstract
Chromosome segregation ensures that DNA is equally divided between daughter cells during each round of cell division. The centromere (CEN) is the specific locus on each chromosome that directs formation of the kinetochore, the multiprotein complex that interacts with the spindle microtubules to promote proper chromosomal alignment and segregation during mitosis. CENs are organized into a specialized chromatin structure due to the incorporation of an essential CEN-specific histone H3 variant (CenH3) in the centromeric nucleosomes of all eukaryotes. Consistent with its essential role at the CEN, the loss or up-regulation of CenH3 results in mitotic defects. Despite the requirement for CenH3 in CEN function, it is unclear how CenH3 nucleosomes structurally organize centromeric DNA to promote formation of the kinetochore. To address this issue, we developed a modified chromatin immunoprecipitation approach to analyze the number and position of CenH3 nucleosomes at the budding yeast CEN. Using this technique, we show that yeast CENs have a single CenH3 nucleosome positioned over the CEN-determining elements. Therefore, a single CenH3 nucleosome forms the minimal unit of centromeric chromatin necessary for kinetochore assembly and proper chromosome segregation.
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Affiliation(s)
- Suzanne Furuyama
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, P.O. Box 19024, Seattle, WA 98109
| | - Sue Biggins
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, P.O. Box 19024, Seattle, WA 98109
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Cioffi A, Fleury TJ, Stein A. Aspects of large-scale chromatin structures in mouse liver nuclei can be predicted from the DNA sequence. Nucleic Acids Res 2006; 34:1974-81. [PMID: 16614447 PMCID: PMC1435979 DOI: 10.1093/nar/gkl078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The large amount of non-coding DNA present in mammalian genomes suggests that some of it may play a structural or functional role. We provide evidence that it is possible to predict computationally, from the DNA sequence, loci in mouse liver nuclei that possess distinctive nucleosome arrays. We tested the hypothesis that a 100 kb region of DNA possessing a strong, in-phase, dinucleosome period oscillation in the motif period-10 non-T, A/T, G, should generate a nucleosome array with a nucleosome repeat that is one-half of the dinucleosome oscillation period value, as computed by Fourier analysis of the sequence. Ten loci with short repeats, that would be readily distinguishable from the pervasive bulk repeat, were predicted computationally and then tested experimentally. We estimated experimentally that less than 20% of the chromatin in mouse liver nuclei has a nucleosome repeat length that is 15 bp, or more, shorter than the bulk repeat value of 195 +/- bp. All 10 computational predictions were confirmed experimentally with high statistical significance. Nucleosome repeats as short as 172 +/- 5 bp were observed for the first time in mouse liver chromatin. These findings may be useful for identifying distinctive chromatin structures computationally from the DNA sequence.
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Affiliation(s)
| | | | - Arnold Stein
- To whom correspondence should be addressed. Tel: +1 765 494 6546; Fax: +1 765 494 0876;
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15
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Giresi PG, Gupta M, Lieb JD. Regulation of nucleosome stability as a mediator of chromatin function. Curr Opin Genet Dev 2006; 16:171-6. [PMID: 16503136 DOI: 10.1016/j.gde.2006.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Accepted: 02/10/2006] [Indexed: 11/17/2022]
Abstract
Interactions among regulatory proteins, enzymes and DNA are required to use the information encoded in genomes. In eukaryotes, the location and timing of interactions between these proteins and DNA is determined in large part by whether DNA at a given locus is packaged into a nucleosome. Given the central role of nucleosome formation in regulating genome function, many mechanisms have evolved to control nucleosome stability at loci across the genome. New conclusions about the role of the DNA sequence itself in the regulation of nucleosome stability have come from two new types of experiment: high-resolution mapping of in vivo nucleosome occupancy on a genomic scale; and in vivo versus in vitro comparisons of nucleosome stability on natural DNA templates. These new types of data raise intriguing questions about the evolutionary constraints on DNA sequence with regard to nucleosome formation, and at long last might enable the derivation of DNA sequence-based rules that produce reliable predictions of nucleosome behavior.
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Affiliation(s)
- Paul G Giresi
- Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
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