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Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility [ChIP-Seq]

ABSTRACT: Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility [ChIP-Seq]

PROVIDER: PRJNA795478 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17487742_1.fastq.gz	Fastqsanger.gz
	SRR17487742_2.fastq.gz	Fastqsanger.gz
	SRR17487743_1.fastq.gz	Fastqsanger.gz
	SRR17487743_2.fastq.gz	Fastqsanger.gz
	SRR17487744_1.fastq.gz	Fastqsanger.gz

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Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility [ATAC-Seq]

Project description:We identify three classes of Arabidopsis SWI/SNF chromatin remodeling complexes and demonstrate that they regulate different developmental processes by affecting chromatin accessibility.

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Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility

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Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility [RNA-Seq]

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Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility [ATAC-Seq]

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PKA-dependent Phosphorylation of A Histone Demethylase Drives Higher Order Chromatin Structures by Association with SWI/SNF Chromatin Remodeler

Project description:The current studies show that JMJD1A is phosphorylated at S265 by protein kinase A (PKA), and this is pivotal to activate expression of the b1-adrenergic receptor gene (Adrb1) and downstream targets including Ucp1. Phosphorylation of JMJD1A increases its interaction with the SWI/SNF nucleosome remodeling complex and DNA-bound PPARg. This complex conferred b-adrenergic-induced JMJD1A recruitment to target sites throughout the genome. Phospho-JMJD1A also facilitated long-range chromatin looping to recruit PPARg-bound distal-enhancers, SWI/SNF, and RNA polymerase close to the Adrb1 locus to activate transcription. Mutation of the PKA-phosphorylation site on JMJD1A abolished interactions with SWI/SNF without affecting demethylase activity suggesting the two functions are independent of each other. Our results show that JMJD1A demethylase is also a signal-sensing scaffold that regulates cAMP-responsive transcription via interactions with SWI/SNF and hormone stimulated higher-order chromatin conformational changes. There are 3 samples analyzed. No duplication from each sample. Isoproterenol stimulation at 0hr is used as the relative to fold change in manuscript.

2015-04-15 | E-GEOD-58936 | biostudies-arrayexpress

Genome-wide profile of the SWI/SNF chromatin remodeling complex

Project description:A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes including gene expression, nuclear organization, centromere function and chromosomal stability, and mutations in SWI/SNF components have been linked to several types of cancer. To better understand the biological processes in which chromatin remodeling proteins participate we globally mapped binding regions for several components of the SWI/SNF complex throughout the human genome using ChIP-Seq. SWI/SNF components were found to lie near regulatory elements integral to transcription (e.g. 5M-bM-^@M-^Y ends, RNA Polymerases II and III and enhancers) as well as regions critical for chromosome organization (e.g. CTCF, lamins and DNA replication origins). To further elucidate the association of SWI/SNF subunits with each other as well as with other nuclear proteins we also analyzed SWI/SNF immunoprecipitated complexes by mass spectrometry. Individual SWI/SNF factors are associated with their own family members as well as with cellular constituents such as nuclear matrix proteins, key transcription factors and centromere components implying a ubiquitous role in gene regulation and nuclear function. We find an overrepresentation of both SWI/SNF-associated regions and proteins in cell cycle and chromosome organization. Taken together the results from our ChIP and immunoprecipitation experiments suggest that SWI/SNF facilitates gene regulation and genome function more broadly and through a greater diversity of interactions than previously appreciated. ChIP-Seq analysis of the SWI/SNF subunits Ini1, Brg1, BAF155 and BAF170 in HeLa S3 cells

2011-01-10 | E-GEOD-24397 | biostudies-arrayexpress

Organization, genomic targeting and assembly of three distinct SWI/SNF chromatin remodeling complexes in Arabidopsis [ChIP-seq]

Project description:Switch defective/sucrose non-fermentable (SWI/SNF) complexes are evolutionarily conserved multi-subunit machines that play vital roles in chromatin architecture regulation for modulating gene expression via sliding or ejection of nucleosomes in eukaryotes. In plants, perturbations of SWI/SNF subunits often result in severe developmental disorders. However, the subunit composition, pathways of assembly, and genomic targeting of the plant SWI/SNF complexes remain undefined. Here, we reveal that Arabidopsis SWI/SNF complexes exist in three distinct final form assemblies: BRM-associated SWI/SNF complexes (BAS), SYD-associated SWI/SNF complexes (SAS) and MINU-associated SWI/SNF complexes (MAS). We show that BAS complexes are equivalent to human ncBAF, whereas SAS and MAS complexes evolve in multiple subunits unique to plants, suggesting a plant-specific functional evolution of SWI/SNF complexes. We further demonstrate overlapping and specific genomic targeting of the three plant SWI/SNF complexes on chromatin and reveal that SAS complexes are necessary for the correct genomic localization of the BAS complexes. Finally, by focusing on the SAS and BAS complexes, we establish a requirement for both the core module subunit and the ATPase in the assembly of the plant SWI/SNF complexes. Together, our work highlights the divergence of SWI/SNF chromatin remodelers during the eukaryote evolution and provides a comprehensive landscape for understanding the plant SWI/SNF complexes organization, assembly, genomic targeting, and function.

2023-04-24 | GSE218841 | GEO

ANGUSTIFOLIA 3 binds SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development

Project description:The transcriptional coactivator ANGUSTIFOLIA 3 (AN3) stimulates cell proliferation during Arabidopsis leaf development, but the molecular mechanism is largely unknown. We show here that inducible nuclear localization of AN3 during initial leaf growth results in differential expression of important transcriptional regulators, including GROWTH REGULATING FACTORs (GRFs). Chromatin purification further revealed the presence of AN3 at the loci of GRF5, GRF6, CYTOKININ RESPONSE FACTOR 2 (CRF2), CONSTANS-LIKE 5 (COL5), HECATE 1 (HEC1), and ARABIDOPSIS RESPONSE REGULATOR 4 (ARR4). Tandem affinity purification of protein complexes using AN3 as bait identified plant SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complexes formed around the ATPases BRAHMA (BRM) or SPLAYED (SYD). Moreover, SWI/SNF ASSOCIATED PROTEIN 73B (SWP73B) is recruited by AN3 to the promoter of GRF5, GRF3, COL5, and ARR4, and both SWP73B and BRM occupy the HEC1 promoter. Furthermore, we show that AN3 and BRM genetically interact. The data indicate that AN3 associates with chromatin remodelers to regulate transcription. In addition, modification of SWI3C expression levels increases leaf size, underlining the importance of chromatin dynamics for growth regulation. Our results place the SWI/SNF-AN3 module as a major player at the transition from cell proliferation to cell differentiation in a developing leaf. AN3-GR and wild-type (Col-0) plants were grown in vitro for 8 days and subsequently transferred to dexamethasone-containing medium for 8 hours. Developing leaves 1&2 of AN3-GR and wild-type plants were micro-dissected, and RNA was extracted. RNA from three biological repeats of dexamethasone-treated AN3-GR and dexamethasone-treated wild-type leaves was hybridized to Affymetrix ATH1 microarrays.

2014-09-09 | E-GEOD-42875 | biostudies-arrayexpress

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