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DDT-RELATED PROTEIN4-IMITATION SWITCH alters nucleosome distribution to relieve transcriptional silencing in Arabidopsis [MNase-seq]

ABSTRACT: DNA methylation is a conserved epigenetic modification that usually functions to repress gene expression. However, not all DNA methylated loci are faithfully silenced, and genes bearing promoter DNA methylation often show varying levels of transcription. The flexibility in transcription allows for greater adaptability in response to environmental and developmental cues, the mechanisms of which are not fully understood. In this work, we demonstrate that a plant-specific ISWI complex, consisting of CHR11, CHR17, DDR4, and DDR5, functions to partially de-repress DNA methylated genes and TEs through chromatin relaxation. This action requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. We also show that the anti-silencing effects of enhanced chromatin accessibility can be genetically uncoupled from that of DNA demethylation, and is antagonized by the chromatin compactor, MORC proteins. Our work reveals a mechanism for balancing between the needs of transcriptional flexibility and faithful silencing of DNA methylated loci. As both ISWI and MORC family genes are distributed widely across plant and animal species, the findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic repression.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE227074 | GEO | 2023/05/08

REPOSITORIES: GEO

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Project description:DNA methylation is a conserved epigenetic modification that usually functions to repress gene expression. However, not all DNA methylated loci are faithfully silenced, and genes bearing promoter DNA methylation often show varying levels of transcription. The flexibility in transcription allows for greater adaptability in response to environmental and developmental cues, the mechanisms of which are not fully understood. In this work, we demonstrate that a plant-specific ISWI complex, consisting of CHR11, CHR17, DDR4, and DDR5, functions to partially de-repress DNA methylated genes and TEs through chromatin relaxation. This action requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. We also show that the anti-silencing effects of enhanced chromatin accessibility can be genetically uncoupled from that of DNA demethylation, and is antagonized by the chromatin compactor, MORC proteins. Our work reveals a mechanism for balancing between the needs of transcriptional flexibility and faithful silencing of DNA methylated loci. As both ISWI and MORC family genes are distributed widely across plant and animal species, the findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic repression.

2023-05-08 | GSE202270 | GEO

2023-05-08 | GSE202205 | GEO

2023-05-08 | GSE202204 | GEO

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-05-08 | GSE202271 | 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.

2021-07-02 | PXD026674 | Pride

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 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

Arabidopsis AtMORC4 and AtMORC7 form Nuclear Bodies and Repress a Large Number of Protein-Coding Genes

Project description:The MORC family of GHKL ATPases are an enigmatic class of proteins with diverse chromatin related functions. In Arabidopsis, AtMORC1, AtMORC2, and AtMORC6 act together in heterodimeric complexes to mediate transcriptional silencing of methylated DNA elements. Here, we studied Arabidopsis AtMORC4 and AtMORC7. We found that, in contrast to AtMORC1,2,6, they act to suppress a wide set of non-methylated protein-coding genes that are enriched for those involved in pathogen response. Furthermore, atmorc4 atmorc7 double mutants show a pathogen response phenotype. We found that AtMORC4 and AtMORC7 form homomeric complexes in vivo and are concentrated in discrete nuclear bodies adjacent to chromocenters. Analysis of an atmorc1,2,4,5,6,7 hextuple mutant demonstrates that transcriptional de-repression is largely uncoupled from changes in DNA methylation in plants devoid of MORC function. However, we also uncover a requirement for MORC in both DNA methylation and silencing at a small but distinct subset of RNA-directed DNA methylation target loci. These regions are characterized by poised transcriptional potential and a low density of sites for symmetric cytosine methylation. These results provide insights into the biological function of MORC proteins in higher eukaryotes.

2016-05-11 | GSE78836 | GEO

MORC family ATPases required for heterochromatin condensation and gene silencing

2012-05-03 | GSE37644 | GEO

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

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