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MORC family ATPases required for heterochromatin condensation and gene silencing

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE37644 | GEO | 2012/05/03

SECONDARY ACCESSION(S): PRJNA162669

REPOSITORIES: GEO

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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

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

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.

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

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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

Plasmodium falciparum MORC protein modulates gene expression through interaction with heterochromatin

Project description:The MORC (microrchidia) family of proteins is highly conserved in all eukaryotic cells and have been shown to play diverse roles by forming protein-protein interactions with immune-responsive proteins, SWI chromatin remodeling complexes, histone deacetylases, and histone tail modifications across metazoans. To dissect the functional roles of MORC in the human malaria parasite, Plasmodium falciparum, we developed a glmS based ribozyme knockdown system to induce PfMORC knockdown upon glucosamine (GlcN) induction. We further conducted a transcriptomic analysis in PfMORC-HA-glmS knockdown parasites at the asexual stage to investigate alterations in global gene expression. Our results indicate an overrepresentation of downregulated genes belonging to the heterochromatin-associated hypervariable gene family proteins. Overall, we found that PfMORC controls the asexual gene expression of the P. falciparum and can be a potential target for malaria disease containment.

2023-11-15 | GSE241313 | GEO

Two components of the RNA-directed DNA methylation pathway associate with MORC6 and silence loci targeted by MORC6 in Arabidopsis

Project description:DNA methylation is a conserved epigenetic mark that is required for the silencing of transposons and introduced transgenes in eukaryotes. An RNA-directed DNA methylation pathway mediates de novo DNA methylation and thereby leads to transcriptional silencing in Arabidopsis. In this study, we find that two RNA-directed DNA methylation components interact with the microrchidia (MORC) protein MORC6 and lead to transcriptional silencing through a mechanism that is distinct from the RNA-directed DNA methylation pathway. MORC6 was previously thought to mediate transcriptional silencing through heterochromatin condensation. Our study suggests that the interaction of the RNA-directed DNA methylation components with MORC6 may mediate a link between DNA methylation and heterochromatin condensation.

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A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment

Project description:Purpose: T. gondii has a complex life cycle typified by an asexual development taking place in vertebrate and a sexual reproduction occurring exclusively in felids and thereby is less studied. The developmental transitions rely on changes in gene expression patterns, and recent studies have assigned roles for chromatin shapers, including histone modifications, in establishing specific programs for a given stage. Here, we identified T. gondii microrchidia (MORC) protein as an upstream transcriptional repressor of sexual commitment. MORC, in partnership with Apetala (AP2) transcription factors, was shown to recruit the histone deacetylase HDAC3, thereby impeding the chromatin accessibility of the genes predestined to be exclusively expressed in sexual stages. As such, MORC-depleted cells underwent marked transcriptional changes, resulting in the expression of a specific repertoire of genes, thus revealing a shift from asexual proliferation to sexual differentiation. MORC acts as a master regulator that directs the hierarchical expression of secondary AP2 factors, with these latter potentially contributing to the unidirectionality of the life cycle. Thus, MORC plays a cardinal role in the T. gondii life cycle, and its conditional depletion offers a way to study the parasite’s sexual development in vitro, and proposes an alternative to the requirement of cat infections.

2019-12-21 | GSE136123 | GEO

A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment

Project description:Toxoplasma gondii has a complex life cycle that is typified by asexual development that takes place in vertebrates, and sexual reproduction, which occurs exclusively in felids and is therefore less studied. The developmental transitions rely on changes in the patterns of gene expression, and recent studies have assigned roles for chromatin shapers, including histone modifications, in establishing specific epigenetic programs for each given stage. Here, we identified the T. gondii microrchidia (MORC) protein as an upstream transcriptional repressor of sexual commitment. MORC, in a complex with Apetala 2 (AP2) transcription factors, was shown to recruit the histone deacetylase HDAC3, thereby impeding the accessibility of chromatin at the genes that are exclusively expressed during sexual stages. We found that MORC-depleted cells underwent marked transcriptional changes, resulting in the expression of a specific repertoire of genes, and revealing a shift from asexual proliferation to sexual differentiation. MORC acts as a master regulator that directs the hierarchical expression of secondary AP2 transcription factors, and these transcription factors potentially contribute to the unidirectionality of the life cycle. Thus, MORC plays a cardinal role in the T. gondii life cycle, and its conditional depletion offers a method to study the sexual development of the parasite in vitro, and is proposed as an alternative to the requirement of T. gondii infections in cats.

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Project description:T. gondii has a complex life cycle typified by an asexual development taking place in vertebrate, and a sexual reproduction which occurs exclusively in felids and thereby is less studied. The developmental transitions rely on changes in gene expression patterns, and recent studies have assigned roles for chromatin shapers, including histone modifications, in establishing specific epigenetic programs for each given stage. Here, we identified T. gondii microrchidia (MORC) protein as an upstream transcriptional repressor of sexual commitment. We performed affinity purification coupled to tandem mass spectrometry analyses to identify its binding partners.

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