501
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March-Díaz R, Reyes JC. The beauty of being a variant: H2A.Z and the SWR1 complex in plants. MOLECULAR PLANT 2009; 2:565-577. [PMID: 19825639 DOI: 10.1093/mp/ssp019] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Numerous studies have shown that the nucleosome is a dynamic structure that strongly influences gene expression. Dynamism concerns different nucleosomal characteristics, including position, posttranslational modifications, and histone composition. Thus, within the nucleosome, canonical histones can be exchanged by histone variant proteins with specific functions-a process known as 'histone replacement'. The histone variant H2A.Z has an important function in transcription and, during the last few years, its role in plant development and immune response has become evident. Compiling genetic and biochemical studies from several laboratories has revealed that plants contain a multiprotein complex, similar to the SWR1/SRCAP complex from yeast and animals, involved in H2A.Z deposition. Despite intense research in different organisms, the mechanism by which H2A.Z influences transcription is still unknown. However, recent results from Arabidopsis have shown a strong inverse correlation between H2A.Z and DNA methylation, suggesting that H2A.Z might protect genes from silencing.
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Affiliation(s)
- Rosana March-Díaz
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), CSIC, Américo Vespucio s/n, E-41092 Sevilla, Spain
| | - Jose C Reyes
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), CSIC, Américo Vespucio s/n, E-41092 Sevilla, Spain.
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502
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Abstract
Complex transcriptional behaviours are encoded in the DNA sequences of gene regulatory regions. Advances in our understanding of these behaviours have been recently gained through quantitative models that describe how molecules such as transcription factors and nucleosomes interact with genomic sequences. An emerging view is that every regulatory sequence is associated with a unique binding affinity landscape for each molecule and, consequently, with a unique set of molecule-binding configurations and transcriptional outputs. We present a quantitative framework based on existing methods that unifies these ideas. This framework explains many experimental observations regarding the binding patterns of factors and nucleosomes and the dynamics of transcriptional activation. It can also be used to model more complex phenomena such as transcriptional noise and the evolution of transcriptional regulation.
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Affiliation(s)
- Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Jonathan Widom
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500 USA
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503
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Radman-Livaja M, Rando OJ. Nucleosome positioning: how is it established, and why does it matter? Dev Biol 2009; 339:258-66. [PMID: 19527704 DOI: 10.1016/j.ydbio.2009.06.012] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 06/05/2009] [Accepted: 06/08/2009] [Indexed: 11/18/2022]
Abstract
Packaging of eukaryotic genomes into chromatin affects every process that occurs on DNA. The positioning of nucleosomes on underlying DNA plays a key role in the regulation of these processes, as the nucleosome occludes underlying DNA sequences. Here, we review the literature on mapping nucleosome positions in various organisms, and discuss how nucleosome positions are established, what effect nucleosome positioning has on control of gene expression, and touch on the correlations between chromatin packaging, sequence evolution, and the evolution of gene expression programs.
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Affiliation(s)
- Marta Radman-Livaja
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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504
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Abstract
AbstractShort runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4–6 adenine base pairs (‘A-tracts’) are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.
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505
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Svotelis A, Gévry N, Gaudreau L. Regulation of gene expression and cellular proliferation by histone H2A.Z. Biochem Cell Biol 2009; 87:179-88. [PMID: 19234533 DOI: 10.1139/o08-138] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The mammalian genome is organized into a structure of DNA and proteins known as chromatin. In general, chromatin presents a barrier to gene expression that is regulated by several pathways, namely by the incorporation of histone variants into the nucleosome. In yeast, H2A.Z is an H2A histone variant that is incorporated into nucleosomes as an H2A.Z/H2B dimer by the Swr1 complex and by the SRCAP and p400/Tip60 complexes in mammalian cells. H2A.Z has been associated with the poising of genes for transcriptional activation in the yeast model system, and is essential for development in higher eukaryotes. Recent studies in our laboratory have demonstrated a p400-dependent deposition of H2A.Z at the promoter of p21WAF1/CIP1, a consequence that prevents the activation of the gene by p53, thereby inhibiting p53-dependent replicative senescence, a form of cell-cycle arrest crucial in the prevention of carcinogenic transformation of cells. Moreover, H2A.Z is overexpressed in several different types of cancers, and its overexpression has been associated functionally with the proliferation state of cells. Therefore, we suggest that H2A.Z is an important regulator of gene expression, and its deregulation may lead to the increased proliferation of mammalian cells.
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Affiliation(s)
- Amy Svotelis
- Departement de biologie, Faculte des Sciences, Universite de Sherbrooke, Sherbrooke, QCJ1K2R1, Canada
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506
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Chromatin structure is implicated in "late" elongation checkpoints on the U2 snRNA and beta-actin genes. Mol Cell Biol 2009; 29:4002-13. [PMID: 19451231 PMCID: PMC2704739 DOI: 10.1128/mcb.00189-09] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The negative elongation factor NELF is a key component of an early elongation checkpoint generally located within 100 bp of the transcription start site of protein-coding genes. Negotiation of this checkpoint and conversion to productive elongation require phosphorylation of the carboxy-terminal domain of RNA polymerase II (pol II), NELF, and DRB sensitivity-inducing factor (DSIF) by positive transcription elongation factor b (P-TEFb). P-TEFb is dispensable for transcription of the noncoding U2 snRNA genes, suggesting that a NELF-dependent checkpoint is absent. However, we find that NELF at the end of the 800-bp U2 gene transcription unit and RNA interference-mediated knockdown of NELF causes a termination defect. NELF is also associated 800 bp downstream of the transcription start site of the beta-actin gene, where a "late" P-TEFb-dependent checkpoint occurs. Interestingly, both genes have an extended nucleosome-depleted region up to the NELF-dependent control point. In both cases, transcription through this region is P-TEFb independent, implicating chromatin in the formation of the terminator/checkpoint. Furthermore, CTCF colocalizes with NELF on the U2 and beta-actin genes, raising the possibility that it helps the positioning and/or function of the NELF-dependent control point on these genes.
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507
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Fraser RM, Keszenman-Pereyra D, Simmen MW, Allan J. High-resolution mapping of sequence-directed nucleosome positioning on genomic DNA. J Mol Biol 2009; 390:292-305. [PMID: 19427325 DOI: 10.1016/j.jmb.2009.04.079] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Revised: 04/24/2009] [Accepted: 04/30/2009] [Indexed: 11/26/2022]
Abstract
We have mapped in vitro nucleosome positioning on the sheep beta-lactoglobulin gene using high-throughput sequencing to characterise the DNA sequences recovered from reconstituted nucleosomes. This methodology surpasses previous approaches for coverage, accuracy and resolution and, most importantly, offers a simple yet rapid and relatively inexpensive method to characterise genomic DNA sequences in terms of nucleosome positioning capacity. We demonstrate an unambiguous correspondence between in vitro and in vivo nucleosome positioning around the promoter of the gene; identify discrete, sequence-specific nucleosomal structures above the level of the canonical core particle-a feature that has implications for regulatory protein access and higher-order chromatin packing; and reveal new insights into the involvement of periodically organised dinucleotide sequence motifs of the type GG and CC and not AA and TT, as determinants of nucleosome positioning-an observation that supports the idea that the core histone octamer can exploit different patterns of sequence organisation, or structural potential, in the DNA to bring about nucleosome positioning.
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Affiliation(s)
- Ross M Fraser
- Institute of Cell Biology, University of Edinburgh, UK
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508
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Cui F, Zhurkin VB. Distinctive sequence patterns in metazoan and yeast nucleosomes: implications for linker histone binding to AT-rich and methylated DNA. Nucleic Acids Res 2009; 37:2818-29. [PMID: 19282449 PMCID: PMC2685081 DOI: 10.1093/nar/gkp113] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 01/21/2009] [Accepted: 02/09/2009] [Indexed: 11/17/2022] Open
Abstract
Linker histones (LHs) bind to the DNA entry/exit points of nucleosomes and demonstrate preference for AT-rich DNA, although the recognized sequence patterns remain unknown. These patterns are expected to be more pronounced in metazoan nucleosomes with abundant LHs, compared to yeast nucleosomes with few LHs. To test this hypothesis, we compared the nucleosome core particle (NCP) sequences from chicken, Drosophila and yeast, extending them by the flanking sequences extracted from the genomes. We found that the known approximately 10-bp periodic oscillation of AT-rich elements goes beyond the ends of yeast nucleosomes, but is distorted in metazoan sequences where the 'out-of-phase' AT-peaks appear at the NCP ends. The observed difference is likely to be associated with sequence-specific LH binding. We therefore propose a new structural model for LH binding to metazoan nucleosomes, postulating that the highly conserved nonpolar 'wing' region of the LH globular domain (tetrapeptide GVGA) recognizes AT-rich fragments through hydrophobic interactions with the thymine methyl groups. These interactions lead to DNA bending at the NCP ends and formation of a 'stem-like' structure. The same mechanism accounts for the high affinity of LH to methylated DNA-a feature critical for stabilization of the higher-order structure of chromatin and for repression of transcription.
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Affiliation(s)
| | - Victor B. Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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509
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Layer JH, Weil PA. Ubiquitous antisense transcription in eukaryotes: novel regulatory mechanism or byproduct of opportunistic RNA polymerase? F1000 BIOLOGY REPORTS 2009; 1:33. [PMID: 20948652 PMCID: PMC2924692 DOI: 10.3410/b1-33] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
One of the more notable observations made in the last few years in gene regulation is that eukaryotic genomes appear to be pervasively transcribed. Recent transcriptome mapping studies have shown that much of the genome is transcribed, and in some instances transcripts from both strands of specific genomic loci are detectable. While some of these transcripts map to known RNA polymerase II transcription units [that is, protein encoding open reading frames (ORFs)], many are derived from regions of DNA thought to be non-genic. Parallel chromatin immunoprecipitation studies of template-bound RNA polymerase II have shown that it is indeed resident on those regions found to be transcribed, both ORF and non-ORF. However, the strandedness of these pervasive transcripts has never been measured on a genome-wide basis. Four recent reports have addressed this question and, in the process, have made the startling discovery that many loci of mRNA sense gene transcription are associated with very active antisense or divergent transcription that begins at mapped transcription start sites and proceeds in an upstream direction.
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Affiliation(s)
- Justin H Layer
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine Nashville, TN 37232-0615 USA
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510
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Lam E, Luo C, Watanabe N. Charting functional and physical properties of chromatin in living cells. Curr Opin Genet Dev 2009; 19:135-41. [PMID: 19327981 DOI: 10.1016/j.gde.2009.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 02/10/2009] [Accepted: 02/16/2009] [Indexed: 01/13/2023]
Abstract
With the vast transcriptome database now available, global patterns of gene expression have been mapped in various species to reveal higher order structures in the genome. Location-dependent control of gene expression has also been studied in human cell cultures and in Arabidopsis plants using well-characterized insertion and transposition cell line collections. With the added genome-wide mapping of chromatin features at a high resolution, via advanced microarray and sequencing technologies, comprehensive analysis of structure-function relationships deduced from chromatin organization and gene expression data is now feasible. This has begun to reveal micro-heterogeneity in the genome with respect to structural and functional segmentations.
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Affiliation(s)
- Eric Lam
- Biotechnology Center for Agriculture and the Environment, Rutgers University, New Brunswick, NJ 08901, USA.
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511
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Abstract
Epigenetics refers to mitotically and/or meiotically heritable variations in gene expression that are not caused by changes in DNA sequence. Epigenetic mechanisms regulate all biological processes from conception to death, including genome reprogramming during early embryogenesis and gametogenesis, cell differentiation and maintenance of a committed lineage. Key epigenetic players are DNA methylation and histone post-translational modifications, which interplay with each other, with regulatory proteins and with non-coding RNAs, to remodel chromatin into domains such as euchromatin, constitutive or facultative heterochromatin and to achieve nuclear compartmentalization. Besides epigenetic mechanisms such as imprinting, chromosome X inactivation or mitotic bookmarking which establish heritable states, other rapid and transient mechanisms, such as histone H3 phosphorylation, allow cells to respond and adapt to environmental stimuli. However, these epigenetic marks can also have long-term effects, for example in learning and memory formation or in cancer. Erroneous epigenetic marks are responsible for a whole gamut of diseases including diseases evident at birth or infancy or diseases becoming symptomatic later in life. Moreover, although epigenetic marks are deposited early in development, adaptations occurring through life can lead to diseases and cancer. With epigenetic marks being reversible, research has started to focus on epigenetic therapy which has had encouraging success. As we witness an explosion of knowledge in the field of epigenetics, we are forced to revisit our dogma. For example, recent studies challenge the idea that DNA methylation is irreversible. Further, research on Rett syndrome has revealed an unforeseen role for methyl-CpG-binding protein 2 (MeCP2) in neurons.
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Affiliation(s)
- Geneviève P Delcuve
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba, Canada
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512
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Vinayachandran V, Pusarla RH, Bhargava P. Multiple sequence-directed possibilities provide a pool of nucleosome position choices in different states of activity of a gene. Epigenetics Chromatin 2009; 2:4. [PMID: 19291282 PMCID: PMC2667510 DOI: 10.1186/1756-8935-2-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 03/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide mappings of nucleosome occupancy in different species have shown presence of well-positioned nucleosomes. While the DNA sequences may help decide their locations, the observed positions in vivo are end-results of chromatin remodeling, the state of gene activity and binding of the sequence-specific factors to the DNA, all of which influence nucleosome positions. Thus, the observed nucleosome locations in vivo do not reflect the true contribution of DNA sequence to the mapped position. Moreover, the naturally occurring nucleosome-positioning sequences are known to guide multiple translational positionings. RESULTS We show that yeast SNR6, a gene transcribed by RNA polymerase III, constitutes nucleosome-positioning sequence. In the absence of a chromatin remodeler or any factor binding, the gene sequence confers a unique rotational phase to nucleosomes in the gene region, and directs assembly of several translationally positioned nucleosomes on approximately 1.2 kb DNA from the gene locus, including the short approximately 250 bp gene region. Mapping of all these gene sequence-directed nucleosome positions revealed that the array of nucleosomes in the gene upstream region occupy the same positions as those observed in vivo but the nucleosomes on the gene region can be arranged in three distinct registers. Two of these arrangements differ from each other in the position of only one nucleosome, and match with the nucleosome positions on the gene in repressed and active states in vivo, where the gene-specific factor is known to occupy the gene in both the states. The two positions are interchanged by an ATP-dependent chromatin remodeler in vivo. The third register represents the positions which block the access of the factor to the gene promoter elements. CONCLUSION On a gene locus, multiple nucleosome positions are directed by a gene sequence to provide a pool of possibilities, out of which the preferred ones are selected by the chromatin remodeler and transcription factor of the gene under different states of activity of the gene.
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Affiliation(s)
- Vinesh Vinayachandran
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Hyderabad-500007, India.
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513
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Leimgruber E, Seguín-Estévez Q, Dunand-Sauthier I, Rybtsova N, Schmid CD, Ambrosini G, Bucher P, Reith W. Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site. Nucleic Acids Res 2009; 37:2514-28. [PMID: 19264803 PMCID: PMC2677874 DOI: 10.1093/nar/gkp116] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleosome depletion at transcription start sites (TSS) has been documented genome-wide in multiple eukaryotic organisms. However, the mechanisms that mediate this nucleosome depletion and its functional impact on transcription remain largely unknown. We have studied these issues at human MHC class II (MHCII) genes. Activation-induced nucleosome free regions (NFR) encompassing the TSS were observed at all MHCII genes. Nucleosome depletion was exceptionally strong, attaining over 250-fold, at the promoter of the prototypical HLA-DRA gene. The NFR was induced primarily by the transcription factor complex that assembles on the conserved promoter-proximal enhancer situated upstream of the TSS. Functional analyses performed in the context of native chromatin demonstrated that displacing the NFR without altering the sequence of the core promoter induced a shift in the position of the TSS. The NFR thus appears to play a critical role in transcription initiation because it directs correct TSS positioning in vivo. Our results provide support for a novel mechanism in transcription initiation whereby the position of the TSS is controlled by nucleosome eviction rather than by promoter sequence.
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Affiliation(s)
- Elisa Leimgruber
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1 rue Michel-Servet, CH-1211, Geneva, Switzerland
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514
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Gervais AL, Gaudreau L. Discriminating nucleosomes containing histone H2A.Z or H2A based on genetic and epigenetic information. BMC Mol Biol 2009; 10:18. [PMID: 19261190 PMCID: PMC2660331 DOI: 10.1186/1471-2199-10-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 03/04/2009] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Nucleosomes are nucleoproteic complexes, formed of eight histone molecules and DNA, and they are responsible for the compaction of the eukaryotic genome. Their presence on DNA influences many cellular processes, such as transcription, DNA replication, and DNA repair. The evolutionarily conserved histone variant H2A.Z alters nucleosome stability and is highly enriched at gene promoters. Its localization to specific genomic loci in human cells is presumed to depend either on the underlying DNA sequence or on a certain epigenetic modification pattern. RESULTS We analyzed the differences in histone post-translational modifications and DNA sequences near nucleosomes that do or do not contain H2A.Z. We show that both the epigenetic context and underlying sequences can be used to classify nucleosomal regions, with highly significant accuracy, as likely to either contain H2A.Z or canonical histone H2A. Furthermore, our models accurately recapitulate the observed nucleosome occupancy near the transcriptional start sites of human promoters. CONCLUSION We conclude that both genetic and epigenetic features are likely to participate in targeting H2A.Z to distinct chromatin loci.
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Affiliation(s)
- Alain L Gervais
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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515
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Intrinsic variability of gene expression encoded in nucleosome positioning sequences. Nat Genet 2009; 41:498-503. [PMID: 19252489 DOI: 10.1038/ng.319] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 01/02/2009] [Indexed: 12/18/2022]
Abstract
Variation in gene expression is an essential material for biological diversity among single cells, individuals and populations or species. Here we show that expression variability is an intrinsic property that persists at those different levels. Each promoter seems to have a unique capacity to respond to external signals that can be environmental, genetic or even stochastic. Our investigation into nucleosome organization of variably responding promoters revealed a commonly positioned nucleosome at a critical regulatory region where most transcription start sites and TATA elements are located, a deviation from typical nucleosome-free status. The nucleotide sequences in this region of variable promoters showed a high propensity for DNA bending and a periodic distribution of particular dinucleotides, encoding preferences for DNA-nucleosome interaction. Variable expression is likely to occur during removal of this nucleosome for gene activation. This is a unique example of how promoter sequences intrinsically encode regulatory flexibility, which is vital for biological processes such as adaptation, development and evolution.
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516
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Abstract
Knowing the precise locations of nucleosomes in a genome is key to understanding how genes are regulated. Recent 'next generation' ChIP-chip and ChIP-Seq technologies have accelerated our understanding of the basic principles of chromatin organization. Here we discuss what high-resolution genome-wide maps of nucleosome positions have taught us about how nucleosome positioning demarcates promoter regions and transcriptional start sites, and how the composition and structure of promoter nucleosomes facilitate or inhibit transcription. A detailed picture is starting to emerge of how diverse factors, including underlying DNA sequences and chromatin remodelling complexes, influence nucleosome positioning.
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Affiliation(s)
- Cizhong Jiang
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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517
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Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ. Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res 2009; 19:967-77. [PMID: 19246569 DOI: 10.1101/gr.084830.108] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Eukaryotic DNA is wrapped around a histone protein core to constitute the fundamental repeating units of chromatin, the nucleosomes. The affinity of the histone core for DNA depends on the nucleotide sequence; however, it is unclear to what extent DNA sequence determines nucleosome positioning in vivo, and if the same rules of sequence-directed positioning apply to genomes of varying complexity. Using the data generated by high-throughput DNA sequencing combined with chromatin immunoprecipitation, we have identified positions of nucleosomes containing the H2A.Z histone variant and histone H3 trimethylated at lysine 4 in human CD4(+) T-cells. We find that the 10-bp periodicity observed in nucleosomal sequences in yeast and other organisms is not pronounced in human nucleosomal sequences. This result was confirmed for a broader set of mononucleosomal fragments that were not selected for any specific histone variant or modification. We also find that human H2A.Z nucleosomes protect only approximately 120 bp of DNA from MNase digestion and exhibit specific sequence preferences, suggesting a novel mechanism of nucleosome organization for the H2A.Z variant.
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Affiliation(s)
- Michael Y Tolstorukov
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
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518
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Lantermann A, Strålfors A, Fagerström-Billai F, Korber P, Ekwall K. Genome-wide mapping of nucleosome positions in Schizosaccharomyces pombe. Methods 2009; 48:218-25. [PMID: 19233281 DOI: 10.1016/j.ymeth.2009.02.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 02/03/2009] [Accepted: 02/06/2009] [Indexed: 11/27/2022] Open
Abstract
The majority of nuclear eukaryotic DNA is packaged into nucleosome cores where DNA is wrapped tightly around histone protein octamers. Such histone bound nucleosomal DNA is less accessible than the short linker DNA between nucleosome cores or the DNA in extended nucleosome free regions. Therefore, the positions of nucleosomes relative to a DNA sequence feature, like a transactivator binding site, a transcriptional start site or an origin of replication, can have profound effects on nuclear processes like transcription, replication, recombination and repair. Now that many DNA related processes are studied in a genome-wide manner, it is increasingly important to map the basic organization of their chromosomal DNA substrate, i.e., the positions of nucleosomes, on a genome-wide scale as well. To this end, the protection of nucleosomal DNA from digestion with micrococcal nuclease (MNase) is used as an assay for the presence of a nucleosome. The MNase protected DNA fragments, so called mononucleosomal DNA, can be mapped genome-wide by hybridization to microarrays. This method has been established for Saccharomyces cerevisiae, and we present here the adaptation of the method for Schizosaccharomyces pombe. As an independent method to validate genome-wide data for individual loci, we also include a protocol for the determination of locus specific nucleosome positioning by indirect end labeling.
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Affiliation(s)
- Alexandra Lantermann
- Adolf-Butenandt-Institut, University of Munich, Schillerstr. 44, 80336 Munich, Germany
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519
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Emberly E, Blattes R, Schuettengruber B, Hennion M, Jiang N, Hart CM, Käs E, Cuvier O. BEAF regulates cell-cycle genes through the controlled deposition of H3K9 methylation marks into its conserved dual-core binding sites. PLoS Biol 2009; 6:2896-910. [PMID: 19108610 PMCID: PMC2605929 DOI: 10.1371/journal.pbio.0060327] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 11/11/2008] [Indexed: 12/25/2022] Open
Abstract
Chromatin insulators/boundary elements share the ability to insulate a transgene from its chromosomal context by blocking promiscuous enhancer–promoter interactions and heterochromatin spreading. Several insulating factors target different DNA consensus sequences, defining distinct subfamilies of insulators. Whether each of these families and factors might possess unique cellular functions is of particular interest. Here, we combined chromatin immunoprecipitations and computational approaches to break down the binding signature of the Drosophila boundary element–associated factor (BEAF) subfamily. We identify a dual-core BEAF binding signature at 1,720 sites genome-wide, defined by five to six BEAF binding motifs bracketing 200 bp AT-rich nuclease-resistant spacers. Dual-cores are tightly linked to hundreds of genes highly enriched in cell-cycle and chromosome organization/segregation annotations. siRNA depletion of BEAF from cells leads to cell-cycle and chromosome segregation defects. Quantitative RT-PCR analyses in BEAF-depleted cells show that BEAF controls the expression of dual core–associated genes, including key cell-cycle and chromosome segregation regulators. beaf mutants that impair its insulating function by preventing proper interactions of BEAF complexes with the dual-cores produce similar effects in embryos. Chromatin immunoprecipitations show that BEAF regulates transcriptional activity by restricting the deposition of methylated histone H3K9 marks in dual-cores. Our results reveal a novel role for BEAF chromatin dual-cores in regulating a distinct set of genes involved in chromosome organization/segregation and the cell cycle. The genome of eukaryotes is packaged in chromatin, which consists of DNA, histones, and accessory proteins. This leads to a general repression of genes, particularly for those exposed to mostly condensed, heterochromatin regions. DNA sequences called chromatin insulators/boundary elements are able to insulate a gene from its chromosomal context by blocking promiscuous heterochromatin spreading. No common feature has been identified among the insulators/boundary elements known so far. Rather, distinct subfamilies of insulators harbor different DNA consensus sequences targeted by different DNA-binding factors, which confer their insulating activity. Determining whether distinct subfamilies possess distinct cellular functions is important for understanding genome regulation. Here, using Drosophila, we have combined computational and experimental approaches to address the function of the boundary element-associated factor (BEAF) subfamily of insulators. We identify hundreds of BEAF dual-cores that are defined by a particular arrangement of DNA sequence motifs bracketing nucleosome binding sequences, and that mark the genomic BEAF binding sites. BEAF dual-cores are close to hundreds of genes that regulate chromosome organization/segregation and the cell cycle. Since BEAF acts by restricting the deposition of repressing epigenetic histone marks, which affects the accessibility of chromatin, its depletion affects the expression of cell-cycle genes. Our data reveal a new role for BEAF in regulating the cell cycle through its binding to highly conserved chromatin dual-cores. Chromatin Dual-Cores define new potent nucleosome-associatedcis-regulatory elements that regulate the accessibility of promoters of genes controlling chromosome organization/segregation and the cell cycle.
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Affiliation(s)
- Eldon Emberly
- Physics Department, Simon Fraser University, Burnaby, British Columbia, Canada
- * To whom correspondence should be addressed. E-mail: (EE); (OC)
| | - Roxane Blattes
- CNRS, Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, UPS, France
| | - Bernd Schuettengruber
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana, United States of America
| | - Magali Hennion
- CNRS, Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, UPS, France
- Institut de Genetique Humaine, Department of Genome Dynamics, CNRS, Montpelier, France
| | - Nan Jiang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana, United States of America
| | - Craig M Hart
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana, United States of America
| | - Emmanuel Käs
- CNRS, Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, UPS, France
| | - Olivier Cuvier
- Institut de Genetique Humaine, Department of Genome Dynamics, CNRS, Montpelier, France
- * To whom correspondence should be addressed. E-mail: (EE); (OC)
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520
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Brickner JH. Transcriptional memory at the nuclear periphery. Curr Opin Cell Biol 2009; 21:127-33. [PMID: 19181512 DOI: 10.1016/j.ceb.2009.01.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 12/15/2008] [Accepted: 01/08/2009] [Indexed: 10/21/2022]
Abstract
A number of inducible yeast genes are targeted to the nuclear periphery upon transcriptional activation. However, when repressed again, the INO1 and GAL1 genes remain at the nuclear periphery for multiple generations. Retention at the nuclear periphery represents a novel type of transcriptional memory; the peripherally localized, recently repressed state of GAL1 is activated more rapidly than the nucleoplasmically localized long-term repressed state of GAL1. This rapid reactivation involves localization at the nuclear periphery, the SWI/SNF chromatin remodeling complex, the histone variant H2A.Z and the Gal1 protein itself. Here, I review what we have learned about this type of transcriptional memory in yeast, what remains to be resolved and the challenges associated with understanding such epigenetic phenomena.
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Affiliation(s)
- Jason H Brickner
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL, USA.
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521
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Dynamic histone variant exchange accompanies gene induction in T cells. Mol Cell Biol 2009; 29:1972-86. [PMID: 19158270 DOI: 10.1128/mcb.01590-08] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Changes in chromatin composition are often a prerequisite for gene induction. Nonallelic histone variants have recently emerged as key players in transcriptional control and chromatin modulation. While the changes in chromatin accessibility and histone posttranslational modification (PTM) distribution that accompany gene induction are well documented, the dynamics of histone variant exchange that parallel these events are still poorly defined. In this study, we have examined the changes in histone variant distribution that accompany activation of the inducible CD69 and heparanase genes in T cells. We demonstrate that the chromatin accessibility increases that accompany the induction of both of these genes are not associated with nucleosome loss but instead are paralleled by changes in histone variant distribution. Specifically, induction of these genes was paralleled by depletion of the H2A.Z histone variant and concomitant deposition of H3.3. Furthermore, H3.3 deposition was accompanied by changes in PTM patterns consistent with H3.3 enriching or depleting different PTMs upon incorporation into chromatin. Nevertheless, we present evidence that these H3.3-borne PTMs can be negated by recruited enzymatic activities. From these observations, we propose that H3.3 deposition may both facilitate chromatin accessibility increases by destabilizing nucleosomes and compete with recruited histone modifiers to alter PTM patterns upon gene induction.
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522
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Vanti M, Gallastegui E, Respaldiza I, Rodríguez-Gil A, Gómez-Herreros F, Jimeno-González S, Jordan A, Chávez S. Yeast genetic analysis reveals the involvement of chromatin reassembly factors in repressing HIV-1 basal transcription. PLoS Genet 2009; 5:e1000339. [PMID: 19148280 PMCID: PMC2613532 DOI: 10.1371/journal.pgen.1000339] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 12/12/2008] [Indexed: 12/22/2022] Open
Abstract
Rebound of HIV viremia after interruption of anti-retroviral therapy is due to the small population of CD4+ T cells that remain latently infected. HIV-1 transcription is the main process controlling post-integration latency. Regulation of HIV-1 transcription takes place at both initiation and elongation levels. Pausing of RNA polymerase II at the 5' end of HIV-1 transcribed region (5'HIV-TR), which is immediately downstream of the transcription start site, plays an important role in the regulation of viral expression. The activation of HIV-1 transcription correlates with the rearrangement of a positioned nucleosome located at this region. These two facts suggest that the 5'HIV-TR contributes to inhibit basal transcription of those HIV-1 proviruses that remain latently inactive. However, little is known about the cell elements mediating the repressive role of the 5'HIV-TR. We performed a genetic analysis of this phenomenon in Saccharomyces cerevisiae after reconstructing a minimal HIV-1 transcriptional system in this yeast. Unexpectedly, we found that the critical role played by the 5'HIV-TR in maintaining low levels of basal transcription in yeast is mediated by FACT, Spt6, and Chd1, proteins so far associated with chromatin assembly and disassembly during ongoing transcription. We confirmed that this group of factors plays a role in HIV-1 postintegration latency in human cells by depleting the corresponding human orthologs with shRNAs, both in HIV latently infected cell populations and in particular single-integration clones, including a latent clone with a provirus integrated in a highly transcribed gene. Our results indicate that chromatin reassembly factors participate in the establishment of the equilibrium between activation and repression of HIV-1 when it integrates into the human genome, and they open the possibility of considering these factors as therapeutic targets of HIV-1 latency.
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Affiliation(s)
- Manuela Vanti
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Edurne Gallastegui
- Centre de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona, Spain
| | - Iñaki Respaldiza
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | | | | | | | - Albert Jordan
- Centre de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
- * E-mail:
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523
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Sasaki S, Mello CC, Shimada A, Nakatani Y, Hashimoto SI, Ogawa M, Matsushima K, Gu SG, Kasahara M, Ahsan B, Sasaki A, Saito T, Suzuki Y, Sugano S, Kohara Y, Takeda H, Fire A, Morishita S. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 2009; 323:401-4. [PMID: 19074313 PMCID: PMC2757552 DOI: 10.1126/science.1163183] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Might DNA sequence variation reflect germline genetic activity and underlying chromatin structure? We investigated this question using medaka (Japanese killifish, Oryzias latipes), by comparing the genomic sequences of two strains (Hd-rR and HNI) and by mapping approximately 37.3 million nucleosome cores from Hd-rR blastulae and 11,654 representative transcription start sites from six embryonic stages. We observed a distinctive approximately 200-base pair (bp) periodic pattern of genetic variation downstream of transcription start sites; the rate of insertions and deletions longer than 1 bp peaked at positions of approximately +200, +400, and +600 bp, whereas the point mutation rate showed corresponding valleys. This approximately 200-bp periodicity was correlated with the chromatin structure, with nucleosome occupancy minimized at positions 0, +200, +400, and +600 bp. These data exemplify the potential for genetic activity (transcription) and chromatin structure to contribute to molding the DNA sequence on an evolutionary time scale.
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Affiliation(s)
- Shin Sasaki
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, 277-0882, Japan
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524
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Travers A, Caserta M, Churcher M, Hiriart E, Di Mauro E. Nucleosome positioning—what do we really know? MOLECULAR BIOSYSTEMS 2009; 5:1582-92. [DOI: 10.1039/b907227f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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525
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Wong HM, Huppert JL. Stable G-quadruplexes are found outside nucleosome-bound regions. MOLECULAR BIOSYSTEMS 2009; 5:1713-9. [DOI: 10.1039/b905848f] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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526
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Abstract
It could be argued that the greatest transformative aspect of the Human Genome Project has been not the sequencing of the genome itself, but the resultant development of new technologies. A host of new approaches has fundamentally changed the way we approach problems in basic and translational research. Now, a new generation of high-throughput sequencing technologies promises to again transform the scientific enterprise, potentially supplanting array-based technologies and opening up many new possibilities. By allowing DNA/RNA to be assayed more rapidly than previously possible, these next-generation platforms promise a deeper understanding of genome regulation and biology. Significantly enhancing sequencing throughput will allow us to follow the evolution of viral and bacterial resistance in real time, to uncover the huge diversity of novel genes that are currently inaccessible, to understand nucleic acid therapeutics, to better integrate biological information for a complete picture of health and disease at a personalized level and to move to advances that we cannot yet imagine.
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527
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Wu WH, Wu CH, Ladurner A, Mizuguchi G, Wei D, Xiao H, Luk E, Ranjan A, Wu C. N terminus of Swr1 binds to histone H2AZ and provides a platform for subunit assembly in the chromatin remodeling complex. J Biol Chem 2008; 284:6200-7. [PMID: 19088068 DOI: 10.1074/jbc.m808830200] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Variant histone H2AZ-containing nucleosomes are involved in the regulation of gene expression. In Saccharomyces cerevisiae, chromatin deposition of histone H2AZ is mediated by the fourteen-subunit SWR1 complex, which catalyzes ATP-dependent exchange of nucleosomal histone H2A for H2AZ. Previous work defined the role of seven SWR1 subunits (Swr1 ATPase, Swc2, Swc3, Arp6, Swc5, Yaf9, and Swc6) in maintaining complex integrity and H2AZ histone replacement activity. Here we examined the function of three additional SWR1 subunits, bromodomain containing Bdf1, actin-related protein Arp4 and Swc7, by analyzing affinity-purified mutant SWR1 complexes. We observed that depletion of Arp4 (arp4-td) substantially impaired the association of Bdf1, Yaf9, and Swc4. In contrast, loss of either Bdf1 or Swc7 had minimal effects on overall complex integrity. Furthermore, the basic H2AZ histone replacement activity of SWR1 in vitro required Arp4, but not Bdf1 or Swc7. Thus, three out of fourteen SWR1 subunits, Bdf1, Swc7, and previously noted Swc3, appear to have roles auxiliary to the basic histone replacement activity. The N-terminal region of the Swr1 ATPase subunit is necessary and sufficient to direct association of Bdf1 and Swc7, as well as Arp4, Act1, Yaf9 and Swc4. This same region contains an additional H2AZ-H2B specific binding site, distinct from the previously identified Swc2 subunit. These findings suggest that one SWR1 enzyme might be capable of binding two H2AZ-H2B dimers, and provide further insight on the hierarchy and interdependency of molecular interactions within the SWR1 complex.
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Affiliation(s)
- Wei-Hua Wu
- Laboratory of Biochemistry and Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA.
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528
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Henikoff S, Henikoff JG, Sakai A, Loeb GB, Ahmad K. Genome-wide profiling of salt fractions maps physical properties of chromatin. Genome Res 2008; 19:460-9. [PMID: 19088306 DOI: 10.1101/gr.087619.108] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes. Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and unbound intermediates in active processes, thus providing a simple, powerful strategy for mapping epigenome dynamics.
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Affiliation(s)
- Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA.
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529
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Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008; 322:1845-8. [PMID: 19056941 DOI: 10.1126/science.1162228] [Citation(s) in RCA: 1490] [Impact Index Per Article: 93.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA polymerases are highly regulated molecular machines. We present a method (global run-on sequencing, GRO-seq) that maps the position, amount, and orientation of transcriptionally engaged RNA polymerases genome-wide. In this method, nuclear run-on RNA molecules are subjected to large-scale parallel sequencing and mapped to the genome. We show that peaks of promoter-proximal polymerase reside on approximately 30% of human genes, transcription extends beyond pre-messenger RNA 3' cleavage, and antisense transcription is prevalent. Additionally, most promoters have an engaged polymerase upstream and in an orientation opposite to the annotated gene. This divergent polymerase is associated with active genes but does not elongate effectively beyond the promoter. These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription.
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Affiliation(s)
- Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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530
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Kotekar AS, Weissman JD, Gegonne A, Cohen H, Singer DS. Histone modifications, but not nucleosomal positioning, correlate with major histocompatibility complex class I promoter activity in different tissues in vivo. Mol Cell Biol 2008; 28:7323-36. [PMID: 18809568 PMCID: PMC2593446 DOI: 10.1128/mcb.00889-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Revised: 07/08/2008] [Accepted: 09/16/2008] [Indexed: 11/20/2022] Open
Abstract
To examine the role of chromatin in transcriptional regulation of the major histocompatibility complex (MHC) class I gene, we determined nucleosome occupancy and positioning, histone modifications, and H2A.Z occupancy across its regulatory region in murine tissues that have widely different expression levels. Surprisingly, nucleosome occupancy and positioning were indistinguishable between the spleen, kidney, and brain. In all three tissues, the 200 bp upstream of the transcription start site had low nucleosome occupancy. In contrast, nuclease hypersensitivity, histone modifications, and H2A.Z occupancy showed tissue-specific differences. Thus, tissue-specific differences in MHC class I transcription correlate with histone modifications and not nucleosomal organization. Further, activation of class I transcription by gamma interferon or its inhibition by alpha-amanitin did not alter nucleosome occupancy, positioning, nuclease hypersensitivity, histone modifications, or H2A.Z occupancy in any of the tissues examined. Thus, chromatin remodeling was not required to dynamically modulate transcriptional levels. These findings suggest that the MHC class I promoter remains poised and accessible to rapidly respond to infection and environmental cues.
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Affiliation(s)
- Aparna S Kotekar
- Molecular Regulation Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, NIH, Bethesda, MD 20892, USA
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531
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Salih F, Salih B, Trifonov EN. Sequence Structure of Hidden 10.4-base Repeat in the Nucleosomes ofC. elegans. J Biomol Struct Dyn 2008; 26:273-82. [DOI: 10.1080/07391102.2008.10531241] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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532
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Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 2008; 4:e1000216. [PMID: 18989395 PMCID: PMC2570626 DOI: 10.1371/journal.pcbi.1000216] [Citation(s) in RCA: 365] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 09/24/2008] [Indexed: 11/19/2022] Open
Abstract
The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence. However, less is known about the functional consequences of this encoding. Here, we address this question using a genome-wide map of ∼380,000 yeast nucleosomes that we sequenced in their entirety. Utilizing the high resolution of our map, we refine our understanding of how nucleosome organizations are encoded by the DNA sequence and demonstrate that the genomic sequence is highly predictive of the in vivo nucleosome organization, even across new nucleosome-bound sequences that we isolated from fly and human. We find that Poly(dA:dT) tracts are an important component of these nucleosome positioning signals and that their nucleosome-disfavoring action results in large nucleosome depletion over them and over their flanking regions and enhances the accessibility of transcription factors to their cognate sites. Our results suggest that the yeast genome may utilize these nucleosome positioning signals to regulate gene expression with different transcriptional noise and activation kinetics and DNA replication with different origin efficiency. These distinct functions may be achieved by encoding both relatively closed (nucleosome-covered) chromatin organizations over some factor binding sites, where factors must compete with nucleosomes for DNA access, and relatively open (nucleosome-depleted) organizations over other factor sites, where factors bind without competition. The detailed positions of nucleosomes along genomes have critical roles in transcriptional regulation. Consequently, it is important to understand the principles that govern the organization of nucleosomes in vivo and the functional consequences of this organization. Here we report on progress in identifying the functional consequences of nucleosome organization, in understanding the way in which nucleosome organization is encoded in the DNA, and in linking the two, by suggesting that distinct transcriptional behaviors are encoded through the genome's intrinsic nucleosome organization. Our results thus provide insight on the broader question of understanding how transcriptional programs are encoded in the DNA sequence. These new insights were enabled by individually sequencing ∼380,000 nucleosomes from yeast in their entirety. Using this map, we refine our previous model for predicting nucleosome positions and demonstrate that our new model predicts nucleosome organizations in yeast with high accuracy and that its nucleosome positioning signals are predictive across eukaryotes. We show that the yeast genome may utilize these nucleosome positioning signals to encode regions with both relatively open (nucleosome-depleted) chromatin organizations and relatively closed (nucleosome-covered) chromatin organizations and that this encoding can partly explain aspects of transcription factor binding, gene expression, transcriptional noise, and DNA replication.
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Affiliation(s)
- Yair Field
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Kaplan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Yvonne Fondufe-Mittendorf
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Irene K. Moore
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Eilon Sharon
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Yaniv Lubling
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Jonathan Widom
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America
- * E-mail: (JW); (ES)
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (JW); (ES)
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533
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Creyghton MP, Markoulaki S, Levine SS, Hanna J, Lodato MA, Sha K, Young RA, Jaenisch R, Boyer LA. H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment. Cell 2008; 135:649-61. [PMID: 18992931 DOI: 10.1016/j.cell.2008.09.056] [Citation(s) in RCA: 264] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 07/29/2008] [Accepted: 09/19/2008] [Indexed: 12/20/2022]
Abstract
Elucidating how chromatin influences gene expression patterns and ultimately cell fate is fundamental to understanding development and disease. The histone variant H2AZ has emerged as a key regulator of chromatin function and plays an essential but unknown role during mammalian development. Here, genome-wide analysis reveals that H2AZ occupies the promoters of developmentally important genes in a manner that is remarkably similar to that of the Polycomb group (PcG) protein Suz12. By using RNAi, we demonstrate a role for H2AZ in regulating target gene expression, find that H2AZ and PcG protein occupancy is interdependent at promoters, and further show that H2AZ is necessary for ES cell differentiation. Notably, H2AZ occupies a different subset of genes in lineage-committed cells, suggesting that its dynamic redistribution is necessary for cell fate transitions. Thus, H2AZ, together with PcG proteins, may establish specialized chromatin states in ES cells necessary for the proper execution of developmental gene expression programs.
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Affiliation(s)
- Menno P Creyghton
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
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534
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Gatta R, Mantovani R. NF-Y substitutes H2A-H2B on active cell-cycle promoters: recruitment of CoREST-KDM1 and fine-tuning of H3 methylations. Nucleic Acids Res 2008; 36:6592-607. [PMID: 18940868 PMCID: PMC2582630 DOI: 10.1093/nar/gkn699] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The CCAAT box is a frequent promoter element, as illustrated by bioinformatic analysis, and it is bound by NF-Y, a trimer with H2A-H2B-like subunits. We developed a MNase I-based ChIP protocol on homogeneous cell populations to study cell-cycle promoters at the single nucleosome level. We analyzed histone methylations and the association of enzymatic activities. Two novel results emerged: (i) H3-H4 are present on core promoters under active conditions, with the expected cohort of ‘positive’ modifications; H2A-H2B are removed and substituted by NF-Y. Through the use of a dominant negative mutant we show that NF-Y is important for H3K36me3 deposition and for elongation, not recruitment of Pol II; (ii) H3K4 methylations are highly dynamic and H3K4me1 is a crucial positive mark. Functional siRNA inactivation and treatment with Tranylcypromine determined that KDM1 (LSD1) plays a positive role in transcription, specifically of G2/M genes. It requires CoREST, which is recruited on active promoters through direct interactions with NF-Y. These data are the first in vivo indication of a crucial interplay between core histones and ‘deviant’ histone-fold such as NF-Y, leading to fine-tuning of histone methylations.
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Affiliation(s)
- Raffaella Gatta
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Via Celoria 26, 20133 Milano, Italy
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535
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de Wit E, van Steensel B. Chromatin domains in higher eukaryotes: insights from genome-wide mapping studies. Chromosoma 2008; 118:25-36. [PMID: 18853173 DOI: 10.1007/s00412-008-0186-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 09/22/2008] [Accepted: 09/23/2008] [Indexed: 01/22/2023]
Abstract
In genomes of higher eukaryotes, adjacent genes often show coordinated regulation of their expression. Compartmentalization of multiple neighboring genes into a shared chromatin environment can facilitate this coordinated expression. New mapping techniques have begun to reveal that such multigene chromatin domains are a common feature of fly and mammalian genomes. Many different types of chromatin domains have been identified based on the genomic binding patterns of various proteins and histone modifications. In addition, maps of genome-nuclear lamina associations and of looping interactions between loci provide the first systematic views of the three-dimensional folding of interphase chromosomes. These genome-wide datasets uncover new architectural principles of eukaryotic genomes and indicate that multigene chromatin domains are prevalent and important regulatory units.
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Affiliation(s)
- Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
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536
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Loss of the histone variant H2A.Z restores capping to checkpoint-defective telomeres in Drosophila. Genetics 2008; 180:1869-75. [PMID: 18845840 DOI: 10.1534/genetics.108.095547] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The conserved histone variant H2A.Z fulfills many functions by being an integral part of the nucleosomes placed at specific regions of the genome. Telomeres cap natural ends of chromosomes to prevent their recognition as double-strand breaks. At yeast telomeres, H2A.Z prevents the spreading of silent chromatin into proximal euchromatin. A role for H2A.Z in capping, however, has not been reported in any organism. Here, I uncover such a role for Drosophila H2A.Z. Loss of H2A.Z, through mutations in either its gene or the domino gene for the Swr1 chromatin-remodeling protein, suppressed the fusion of telomeres that lacked the protection of checkpoint proteins: ATM, ATR, and the Mre11-Rad50-NBS complex. Loss of H2A.Z partially restores the loading of the HOAP capping protein, possibly accounting for the partial restoration in capping. I propose that, in the absence of H2A.Z, checkpoint-defective telomeres adopt alternative structures, which are permissive for the loading of the capping machinery at Drosophila telomeres.
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537
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Ahsan B, Saito TL, Hashimoto SI, Muramatsu K, Tsuda M, Sasaki A, Matsushima K, Aigaki T, Morishita S. MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. Nucleic Acids Res 2008; 37:D49-53. [PMID: 18842623 PMCID: PMC2686457 DOI: 10.1093/nar/gkn694] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MachiBase (http://machibase.gi.k.u-tokyo.ac.jp/) provides a comprehensive and freely accessible resource regarding Drosophila melanogaster 5′-end mRNA transcription at different developmental states, supporting studies on the variabilities of promoter transcriptional activities and gene-expression profiles in the fruitfly. The data were generated in conjunction with the recently developed high-throughput genome sequencer Illumina/Solexa using a newly developed 5′-end mRNA collection method.
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Affiliation(s)
- Budrul Ahsan
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
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538
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Gilmour DS. Promoter proximal pausing on genes in metazoans. Chromosoma 2008; 118:1-10. [PMID: 18830703 DOI: 10.1007/s00412-008-0182-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 09/14/2008] [Accepted: 09/14/2008] [Indexed: 10/21/2022]
Abstract
The past two decades of research into transcriptional control of protein-encoding genes in eukaryotes have focused on regulatory mechanisms that act by controlling the recruitment of Pol II to a gene's promoter. Recent genome-wide analyses of the distribution of Pol II indicates that Pol II is concentrated in the promoter regions of thousands of genes in human and Drosophila cells. In many cases, Pol II may have initiated transcription but paused in the promoter proximal region. Hence, release of Pol II from the promoter region into the body of a gene is now recognized as a common rate-limiting step in the control of gene expression. Notably, most genes with paused Pol II are expressed indicating that the pause can be transient. What causes Pol II to concentrate in the promoter region and how it is released to transcribe a gene are the focus of this review.
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Affiliation(s)
- David S Gilmour
- Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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539
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Whittle CM, McClinic KN, Ercan S, Zhang X, Green RD, Kelly WG, Lieb JD. The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis. PLoS Genet 2008; 4:e1000187. [PMID: 18787694 PMCID: PMC2522285 DOI: 10.1371/journal.pgen.1000187] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 08/04/2008] [Indexed: 12/29/2022] Open
Abstract
In all eukaryotes, histone variants are incorporated into a subset of nucleosomes to create functionally specialized regions of chromatin. One such variant, H2A.Z, replaces histone H2A and is required for development and viability in all animals tested to date. However, the function of H2A.Z in development remains unclear. Here, we use ChIP-chip, genetic mutation, RNAi, and immunofluorescence microscopy to interrogate the function of H2A.Z (HTZ-1) during embryogenesis in Caenorhabditis elegans, a key model of metazoan development. We find that HTZ-1 is expressed in every cell of the developing embryo and is essential for normal development. The sites of HTZ-1 incorporation during embryogenesis reveal a genome wrought by developmental processes. HTZ-1 is incorporated upstream of 23% of C. elegans genes. While these genes tend to be required for development and occupied by RNA polymerase II, HTZ-1 incorporation does not specify a stereotypic transcription program. The data also provide evidence for unexpectedly widespread independent regulation of genes within operons during development; in 37% of operons, HTZ-1 is incorporated upstream of internally encoded genes. Fewer sites of HTZ-1 incorporation occur on the X chromosome relative to autosomes, which our data suggest is due to a paucity of developmentally important genes on X, rather than a direct function for HTZ-1 in dosage compensation. Our experiments indicate that HTZ-1 functions in establishing or maintaining an essential chromatin state at promoters regulated dynamically during C. elegans embryogenesis. To fit within a cell's nucleus, DNA is wrapped around protein spools composed of the histones H3, H4, H2A, and H2B. One spool and the DNA wrapped around it are called a nucleosome, and all of the packaged DNA in a cell's nucleus is collectively called “chromatin.” Chromatin is important because it modulates access to information encoded in the underlying DNA. Spools with specialized functions can be created by replacing a typical histone component with a variant version of the histone protein. Here, we examine the distribution and function of the C. elegans histone H2A variant H2A.Z (called HTZ-1) during development. We demonstrate that HTZ-1 is required for proper development, and that embryos are dependent on a contribution of HTZ-1 from their mothers for survival. We mapped the location of HTZ-1 incorporation genome-wide and found that HTZ-1 binds upstream of 23% of genes, which tend to be genes that are essential for development and occupied by RNA polymerase. Fewer sites of HTZ-1 incorporation were found on the X chromosome, probably due to an under-representation of essential genes on X rather than a direct role for HTZ-1 in X-chromosome dosage compensation. Our study reveals how the genome is remodeled by HTZ-1 to allow the proper regulation of genes critical for development.
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Affiliation(s)
- Christina M. Whittle
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Karissa N. McClinic
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- Genetics and Molecular Biology Program, Emory University, Atlanta, Georgia, United States of America
| | - Sevinc Ercan
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Xinmin Zhang
- Nimblegen Systems, Inc., Madison, Wisconsin, United States of America
| | - Roland D. Green
- Nimblegen Systems, Inc., Madison, Wisconsin, United States of America
| | - William G. Kelly
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- Genetics and Molecular Biology Program, Emory University, Atlanta, Georgia, United States of America
| | - Jason D. Lieb
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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540
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Gilchrist DA, Nechaev S, Lee C, Ghosh SKB, Collins JB, Li L, Gilmour DS, Adelman K. NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev 2008; 22:1921-33. [PMID: 18628398 DOI: 10.1101/gad.1643208] [Citation(s) in RCA: 232] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Negative Elongation Factor (NELF) is a transcription regulatory complex that induces stalling of RNA polymerase II (Pol II) during early transcription elongation and represses expression of several genes studied to date, including Drosophila Hsp70, mammalian proto-oncogene junB, and HIV RNA. To determine the full spectrum of NELF target genes in Drosophila, we performed a microarray analysis of S2 cells depleted of NELF and discovered that NELF RNAi affects many rapidly inducible genes involved in cellular responses to stimuli. Surprisingly, only one-third of NELF target genes were, like Hsp70, up-regulated by NELF-depletion, whereas the majority of target genes showed decreased expression levels upon NELF RNAi. Our data reveal that the presence of stalled Pol II at this latter group of genes enhances gene expression by maintaining a permissive chromatin architecture around the promoter-proximal region, and that loss of Pol II stalling at these promoters is accompanied by a significant increase in nucleosome occupancy and a decrease in histone H3 Lys 4 trimethylation. These findings identify a novel, positive role for stalled Pol II in regulating gene expression and suggest that there is a dynamic interplay between stalled Pol II and chromatin structure.
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Affiliation(s)
- Daniel A Gilchrist
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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541
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Pflumm M. Unraveling the nucleosome. Nat Methods 2008. [DOI: 10.1038/nmeth0808-666] [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]
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542
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Petesch SJ, Lis JT. Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci. Cell 2008; 134:74-84. [PMID: 18614012 DOI: 10.1016/j.cell.2008.05.029] [Citation(s) in RCA: 260] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 04/13/2008] [Accepted: 05/19/2008] [Indexed: 11/26/2022]
Abstract
To efficiently transcribe genes, RNA Polymerase II (Pol II) must overcome barriers imposed by nucleosomes and higher-order chromatin structure. Many genes, including Drosophila melanogaster Hsp70, undergo changes in chromatin structure upon activation. To characterize these changes, we mapped the nucleosome landscape of Hsp70 after an instantaneous heat shock at high spatial and temporal resolution. Surprisingly, we find an initial disruption of nucleosomes across the entire gene within 30 s after activation, faster than the rate of Pol II transcription, followed by a second further disruption within 2 min. This initial change occurs independently of Pol II transcription. Furthermore, the rapid loss of nucleosomes extends beyond Hsp70 and halts at the scs and scs' insulating elements. An RNAi screen of 28 transcription and chromatin-related factors reveals that depletion of heat shock factor, GAGA Factor, or Poly(ADP)-Ribose Polymerase or its activity abolishes the loss of nucleosomes upon Hsp70 activation.
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Affiliation(s)
- Steven J Petesch
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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543
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Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 2008; 18:1073-83. [PMID: 18550805 DOI: 10.1101/gr.078261.108] [Citation(s) in RCA: 503] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Most nucleosomes are well-organized at the 5' ends of S. cerevisiae genes where "-1" and "+1" nucleosomes bracket a nucleosome-free promoter region (NFR). How nucleosomal organization is specified by the genome is less clear. Here we establish and inter-relate rules governing genomic nucleosome organization by sequencing DNA from more than one million immunopurified S. cerevisiae nucleosomes (displayed at http://atlas.bx.psu.edu/). Evidence is presented that the organization of nucleosomes throughout genes is largely a consequence of statistical packing principles. The genomic sequence specifies the location of the -1 and +1 nucleosomes. The +1 nucleosome forms a barrier against which nucleosomes are packed, resulting in uniform positioning, which decays at farther distances from the barrier. We present evidence for a novel 3' NFR that is present at >95% of all genes. 3' NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3' NFRs in gene looping.
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Affiliation(s)
- Travis N Mavrich
- Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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544
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Opening promoters to flexible expression. Nat Rev Genet 2008. [DOI: 10.1038/nrg2390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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