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MORC proteins regulate transcription factor binding through mediating chromatin compaction at active chromatin regions

ABSTRACT: MORC proteins regulate transcription factor binding through mediating chromatin compaction at active chromatin regions

PROVIDER: PRJNA877346 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21456808_1.fastq.gz	Fastqsanger.gz
	SRR21456808_2.fastq.gz	Fastqsanger.gz
	SRR21456809_1.fastq.gz	Fastqsanger.gz
	SRR21456809_2.fastq.gz	Fastqsanger.gz
	SRR21456810_1.fastq.gz	Fastqsanger.gz

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MORC proteins regulate transcription factor binding through mediating chromatin compaction at active chromatin regions

Project description:The Microrchidia (MORC) family proteins are evolutionarily conserved GHKL type ATPases involved in chromatin compaction and gene silencing. Arabidopsis MORC proteins act in the RNA-directed DNA methylation (RdDM) pathway where they act as molecular tethers to ensure the efficient establishment of RdDM and de novo gene silencing. However, they also have RdDM independent functions in which the underlying mechanism is unknown. In this study, we examined MORC binding regions that are devoid of RdDM to shed light on MORCs RdDM independent functions. We found that MORC proteins can compact chromatin, exclude the accessibility of DNA to transcription factors (TFs) and thereby repress gene expression. We also found that MORC-mediated repression is particularly important under stress conditions. In addition, we showed that MORC proteins may regulate TFs through direct or indirect interactions. These TFs in turn regulate their own transcription, indicating a feedforward loop. Our findings provide insights into the molecular mechanisms of MORC-mediated chromatin compaction and transcription regulation.

2023-03-27 | GSE212801 | GEO

MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions.

Project description:BackgroundThe microrchidia (MORC) proteins are a family of evolutionarily conserved GHKL-type ATPases involved in chromatin compaction and gene silencing. Arabidopsis MORC proteins act in the RNA-directed DNA methylation (RdDM) pathway, where they act as molecular tethers to ensure the efficient establishment of RdDM and de novo gene silencing. However, MORC proteins also have RdDM-independent functions although their underlying mechanisms are unknown.ResultsIn this study, we examine MORC binding regions where RdDM does not occur in order to shed light on the RdDM-independent functions of MORC proteins. We find that MORC proteins compact chromatin and reduce DNA accessibility to transcription factors, thereby repressing gene expression. We also find that MORC-mediated repression of gene expression is particularly important under conditions of stress. MORC-regulated transcription factors can in some cases regulate their own transcription, resulting in feedback loops.ConclusionsOur findings provide insights into the molecular mechanisms of MORC-mediated chromatin compaction and transcription regulation.

| S-EPMC10131428 | biostudies-literature

Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation

Project description:This SuperSeries is composed of the following subset Series: GSE38410: Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation (mRNA) GSE38442: Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation (ChIP-Seq) Refer to individual Series

2012-07-08 | E-GEOD-38448 | biostudies-arrayexpress

Polycomb-mediated chromatin compaction during cell differentiation

Project description:Polycomb-mediated chromatin compaction during cell differentiation

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Local states of chromatin compaction in HepG2 cells

Project description:We reported chromatin compaction states within several nucleosomes in HepG2 cells. To assess the local compaction, fromaldehyde-treated chromatin was appled to fractionation via a sedimentation velocity cetrifugation. While less-crosslinked nucleosomes remained in upper fractions as open chromatin, well-crosslinked nucleosomes were sedimented to lower fractions as compact chromatin.

2020-03-10 | GSE146632 | GEO

morc-1 regulates transgenerational heterochromatin maintenance at nuclear RNAi targets

Project description:The germline is an immortal cell lineage and therefore must accurately transmit genetic and epigenetic information over infinite cell divisions to ensure fertility and species survival. Endogenous siRNAs (endo-siRNAs), which are highly expressed in the parental germline and inherited in their progeny, represent one mechanism by which epigenetic information can be transmitted from one generation to the next. In C. elegans, this is accomplished by the nuclear RNAi pathway, which ensures robust inheritance of endo-siRNAs and of target gene silencing through deposition of H3K9me3 marks at target loci. How these marks are maintained in subsequent generations is unknown. Here, we show that the C. elegans micro-orchidia homolog, MORC-1, functions downstream of endo-siRNAs to mediate target silencing and maintenance of siRNA-dependent H3K9me3 marks. Like the established members of the nuclear RNAi pathway, morc-1 is essential for germline maintenance and thus morc-1(-) mutants exhibit a mortal germline phenotype. Furthermore, morc-1(-) mutants exhibit severe decondensation of germline chromatin. Through a forward genetic screen, we have identified mutations in the gene encoding MET-1, a H3K36 histone methyltransferase, that potently suppress morc-1(-) germline mortality. We show that morc-1(-) mutants exhibit progressive, met-1-dependent enrichment of H3K36me3 and that mutation of met-1 can restore germline chromatin organization in late generation morc-1(-) mutants. Our data suggest that MORC-1 is required to repress MET-1 activity at nuclear RNAi target genes and that in the absence of this repression, MET-1-mediated encroachment of euchromatin leads to detrimental decondensation of germline chromatin and germline mortality.

2017-05-22 | GSE89887 | GEO

Local states of chromatin compaction in HepG2 cells

Project description:Local states of chromatin compaction in HepG2 cells

| PRJNA611547 | ENA

MORC family ATPases required for heterochromatin condensation and gene silencing

Project description:Transposable elements (TEs) and DNA repeats are commonly targeted by DNA and histone methylation to achieve epigenetic gene silencing. We isolated mutations in two Arabidopsis genes, CRT1 and CRH6, which cause de-repression of DNA-methylated genes and TEs, but no losses of DNA or histone methylation. CRT1 and CRH6 are members of the conserved Microrchidia (MORC) ATPase family, predicted to catalyze alterations in chromosome superstructure. The crt1 and crh6 mutants show decondensation of pericentromeric heterochromatin, increased interaction of pericentromeric regions with the rest of the genome, and transcriptional defects that are largely restricted to loci residing in pericentromeric regions. Knockdown of the single MORC homolog in Caenorhabditis elegans also impairs transgene silencing. We propose that the MORC ATPases are conserved regulators of gene silencing in eukaryotes. For Col wild type control and each of two T-DNA mutants, a single sample each of small RNA (sRNA), mRNA-Seq, 5'-methylcytosine DNA methylation (BS-Seq), ChIP H3K9me2 histone methylation, and ChIP H3 histone control. For each of two EMS mutants, and as controls, their respective backgrounds, two batches of single mRNA samples, with the first batch also having a single mRNA sample for a double EMS mutant.

2012-05-02 | E-GEOD-37644 | biostudies-arrayexpress

Mitotic post-translational modifications of histones promote chromatin compaction in vitro

Project description:As histones undergo major changes in their post-translational modifications during mitotic entry, we speculated that the spectrum of cell cycle-specific histone modifications might contribute to chromosome compaction during mitosis. To test this hypothesis, we isolated core histones from interphase and mitotic cells and reconstituted chromatin with them. We used mass spectrometry to show that key post-translational modifications remained intact during our isolation procedure.

2018-10-24 | PXD007116 | Pride

Arabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation

Project description:The Microrchidia (MORC) family of ATPases are required for transposable element (TE) silencing and heterochromatin condensation in plants and animals, and C. elegans MORC-1 has been shown to topologically entrap and condense DNA. In Arabidopsis thaliana, mutation of MORCs has been shown to reactivate silent methylated genes and transposons and to decondense heterochromatic chromocenters, despite only minor changes in the maintenance of DNA methylation. Here we provide the first evidence localizing Arabidopsis MORC proteins to specific regions of chromatin and find that MORC4 and MORC7 are closely co-localized with sites of RNA directed DNA methylation (RdDM). We further show that MORC7, when tethered to DNA by an artificial zinc finger, can facilitate the establishment of RdDM. Finally, we show that MORCs are required for the efficient RdDM mediated establishment of DNA methylation and silencing of a newly integrated FWA transgene, even though morc mutations have no effect on the maintenance of preexisting methylation at the endogenous FWA gene. We propose that MORCs function as a molecular tether in RdDM complexes to reinforce RdDM activity for methylation establishment. These findings have implications for MORC protein function in a variety of other eukaryotic organisms.

2021-07-02 | PXD026674 | Pride

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