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The Functional Topography of the Arabidopsis Genome is Defined by Nine Chromatin States that Associate in a Small Number of Motifs

ABSTRACT: Chromatin is of major relevance for gene expression, cell division and differentiation, among other processes. Here we have used 16 chromatin features, including DNA sequence, CG methylation, histone modifications and variants, to obtain a high-resolution landscape of the Arabidopsis chromatin states. The combinatorial complexity of chromatin features can be reduced to 9 states defined by their distinct signatures. These chromatin states preferentially associate with certain genomic elements, gene expression levels, and DNase I accessibility. Each chromatin state has strong propensity to associate with only a subset of other states defining a small number of chromatin motifs. These topographical relationships revealed that Polycomb chromatin physically separates the two heterochromatin states from active chromatin domains. Two paths that mainly differ in their GC content and gene density join active and Polycomb chromatin. The remaining states are associated with active genes: four of them spanning gene bodies and two located upstream of transcription start sites. Our data provide a ground for better understanding the Arabidopsis genome topography and for obtaining new insights into establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE54489 | GEO | 2014/06/01

SECONDARY ACCESSION(S): PRJNA236623

REPOSITORIES: GEO

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The Functional Topography of the Arabidopsis Genome is Defined by Nine Chromatin States that Associate in a Small Number of Motifs

Project description:Chromatin is of major relevance for gene expression, cell division and differentiation, among other processes. Here we have used 16 chromatin features, including DNA sequence, CG methylation, histone modifications and variants, to obtain a high-resolution landscape of the Arabidopsis chromatin states. The combinatorial complexity of chromatin features can be reduced to 9 states defined by their distinct signatures. These chromatin states preferentially associate with certain genomic elements, gene expression levels, and DNase I accessibility. Each chromatin state has strong propensity to associate with only a subset of other states defining a small number of chromatin motifs. These topographical relationships revealed that Polycomb chromatin physically separates the two heterochromatin states from active chromatin domains. Two paths that mainly differ in their GC content and gene density join active and Polycomb chromatin. The remaining states are associated with active genes: four of them spanning gene bodies and two located upstream of transcription start sites. Our data provide a ground for better understanding the Arabidopsis genome topography and for obtaining new insights into establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains. In total 9 samples; 3 H3K9ac ChIP-chip, 3 H3K14ac ChIP-chip, 3 H3 ChIP-chip

2014-06-01 | E-GEOD-54489 | biostudies-arrayexpress

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Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

Project description:Interphase chromatin is organized into topologically associating domains (TADs). Within TADs, chromatin looping interactions are formed between DNA regulatory elements, but their functional importance for the establishment of the 3D genome organization and gene regulation during development is unclear. Using high-resolution Hi-C experiments, we analyze higher order 3D chromatin organization during Drosophila embryogenesis and identify active and repressive chromatin loops that are established with different kinetics and depend on distinct factors: Zelda-dependent active loops are formed before the midblastula transition between transcribed genes over long distances. Repressive loops within polycomb domains are formed after the midblastula transition between polycomb response elements by the action of GAGA factor and polycomb proteins. Perturbation of PRE function by CRISPR/Cas9 genome engineering affects polycomb domain formation and destabilizes polycomb-mediated silencing. Preventing loop formation without removal of polycomb components also decreases silencing efficiency, suggesting that chromatin architecture can play instructive roles in gene regulation during development.

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H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

Project description:The histone variant H2A.Z has been implicated in nucleosome exchange, transcriptional activation and Polycomb repression. However, the relationships among these seemingly disparate functions remain obscure. We mapped H2A.Z genome-wide in mammalian ES cells and neural progenitors. H2A.Z is deposited promiscuously at promoters and enhancers, and correlates strongly with H3K4 methylation. Accordingly, H2A.Z is present at poised promoters with bivalent chromatin and at active promoters with H3K4 methylation, but is absent from stably repressed promoters that are specifically enriched for H3K27 trimethylation. We also characterized post-translational modification states of H2A.Z, including a novel species dually-modified by ubiquitination and acetylation that is enriched at bivalent chromatin. Our findings associate H2A.Z with functionally distinct genomic elements, and suggest that post-translational modifications may reconcile its contrasting locations and roles. Examination of histone variant, histone modifications and transcription machinery in 3 cell types

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Mapping polycomb complexes in human and mouse embryonic stem cells

Project description:In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2000 genes. To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation followed by ultra high-throughput sequencing. We find that bivalent domains can be segregated into two classes: the first occupied by both PRC2 and PRC1 (PRC1-positive) and the second specifically bound by PRC2 (PRC2-only). PRC1-positive bivalent domains appear functionally distinct as they more efficiently retain lysine 27 tri-methylation upon differentiation, show stringent conservation of chromatin state, and associate with an overwhelming number of developmental regulator gene promoters. We also used computational genomics to search for sequence determinants of Polycomb binding. This analysis revealed that the genomewide locations of PRC2 and PRC1 can be largely predicted from the locations, sizes and underlying motif contents of CpG islands. We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes. Keywords: cell type comparison Suz12, Ezh2, Ring1b ChIP-Seq in singlicate from mouse embryonic stem (mES) cells. H3K4me3, H3K27me3, H3K36me3, Ezh2 and Ring1b ChIP-Seq in singlicate from human embyonic stem cells (hES; H9).

2008-11-01 | E-GEOD-13084 | biostudies-arrayexpress

3D Landscape of Regulatory Elements and Transcription Factors for Transcription in Arabidopsis

Project description:Whereas spatial genome organization at large scale of compartments and topologically associating domains (TADs) is relatively well studied, the spatial organization of regulatory elements at finer scales is poorly understood in plants. Here, using high-resolution chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) approach, we mapped histone modification-marked DNA elements-associated and RNA polymerase II (RNAPII)-tethered chromatin interactions involving in transcriptionally active, inactive and Polycomb-repressed states in Arabidopsis. Analysis of the regulatory repertoire showed that both active proximal and distal cis-regulatory elements (CREs) promote the transcription of their nearest and long-range connecting genes; poised CREs act as transcriptional repressors to repress their interacting genes’ expression, indicating that the linear juxtaposition is not the only guiding principle modulating gene transcription. Chromatin connectivity networks revealed that genes implicating in flowering-time control are functionally compartmentalized into separate subnuclear domains, linking active mark- and H3K27me3-associated chromatin conformation to coordinated gene expression. Our study uncovers fine-scale Arabidopsis genome organization and their roles in orchestrating transcription and development.

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Core components of the nuclear pore bind distinct states of chromatin and contribute to Polycomb repression I

Project description:Interactions between the genome and the nuclear pore complex (NPC) have been implicated in multiple gene regulatory processes, but the underlying logic of these interactions remains poorly defined. Here, we report high-resolution chromatin binding maps of two core components of the NPC, Nup107 and Nup93, which reveal differential binding of these NPC subunits to active genes and Polycomb-covered silent regions, respectively. Comparison to Lamin-associated domains (LADs) revealed that NPC binding sites are often found within LADs, demonstrating a linear binding of the genome along the nuclear envelope. Significantly, we identified a functional role of Nup93 in silencing of Polycomb target genes and in spatial folding of Polycomb domains. Our findings lend to a model where nuclear pores bind different types of chromatin via interactions with specific core sub-complexes of the NPC, and the Nup93 sub-complex functions as a stabilizing scaffold for Polycomb domains.

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