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ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE234532 | GEO | 2023/09/14

REPOSITORIES: GEO

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ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements.

Project description:DNA methylation mediates silencing of transposable elements and genes in part via recruitment of the Arabidopsis MBD5/6 complex, which contains the methyl-CpG-binding domain (MBD) proteins MBD5 and MBD6, and the J-domain containing protein SILENZIO (SLN). Here we characterize two additional complex members: α-crystalline domain containing proteins ACD15 and ACD21. We show that they are necessary for gene silencing, bridge SLN to the complex, and promote higher order multimerization of MBD5/6 complexes within heterochromatin. These complexes are also highly dynamic, with the mobility of complex components regulated by the activity of SLN. Using a dCas9 system, we demonstrate that tethering the ACDs to an ectopic site outside of heterochromatin can drive massive accumulation of MBD5/6 complexes into large nuclear bodies. These results demonstrate that ACD15 and ACD21 are critical components of gene silencing complexes that act to drive the formation of higher order, dynamic assemblies.

| S-EPMC10473691 | biostudies-literature

ACD15, ACD21, and SLN regulate the accumulation and mobility of MBD6 to silence genes and transposable elements.

Project description:DNA methylation mediates silencing of transposable elements and genes in part via recruitment of the Arabidopsis MBD5/6 complex, which contains the methyl-CpG binding domain (MBD) proteins MBD5 and MBD6, and the J-domain containing protein SILENZIO (SLN). Here, we characterize two additional complex members: α-crystalline domain (ACD) containing proteins ACD15 and ACD21. We show that they are necessary for gene silencing, bridge SLN to the complex, and promote higher-order multimerization of MBD5/6 complexes within heterochromatin. These complexes are also highly dynamic, with the mobility of MBD5/6 complexes regulated by the activity of SLN. Using a dCas9 system, we demonstrate that tethering the ACDs to an ectopic site outside of heterochromatin can drive a massive accumulation of MBD5/6 complexes into large nuclear bodies. These results demonstrate that ACD15 and ACD21 are critical components of the gene-silencing MBD5/6 complex and act to drive the formation of higher-order, dynamic assemblies at CG methylation (meCG) sites.

| S-EPMC10651127 | biostudies-literature

ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements [RNA-seq]

2023-09-14 | GSE234530 | GEO

ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements [ChIP-seq]

2023-09-14 | GSE234531 | GEO

ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements

Project description:ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements

| PRJNA981636 | ENA

ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements [ChIP-seq]

Project description:ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements [ChIP-seq]

| PRJNA981638 | ENA

ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements [RNA-seq]

Project description:ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements [RNA-seq]

| PRJNA981637 | ENA

Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate

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

2018-11-28 | GSE122977 | GEO

Epigenetic control of genes and transposable elements

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

2018-12-11 | GSE108091 | GEO

Gene properties and chromatin state influence the accumulation of transposable elements in genes.

Project description:Transposable elements (TEs) are mobile DNA sequences found in the genomes of almost all species. By measuring the normalized coverage of TE sequences within genes, we identified sets of genes with conserved extremes of high/low TE density in the genomes of human, mouse and cow and denoted them as 'shared upper/lower outliers (SUOs/SLOs)'. By comparing these outlier genes to the genomic background, we show that a large proportion of SUOs are involved in metabolic pathways and tend to be mammal-specific, whereas many SLOs are related to developmental processes and have more ancient origins. Furthermore, the proportions of different types of TEs within human and mouse orthologous SUOs showed high similarity, even though most detectable TEs in these two genomes inserted after their divergence. Interestingly, our computational analysis of polymerase-II (Pol-II) occupancy at gene promoters in different mouse tissues showed that 60% of tissue-specific SUOs show strong Pol-II binding only in embryonic stem cells (ESCs), a proportion significantly higher than the genomic background (37%). In addition, our analysis of histone marks such as H3K4me3 and H3K27me3 in mouse ESCs also suggest a strong association between TE-rich genes and open-chromatin at promoters. Finally, two independent whole-transcriptome datasets show a positive association between TE density and gene expression level in ESCs. While this study focuses on genes with extreme TE densities, the above results clearly show that the probability of TE accumulation/fixation in mammalian genes is not random and is likely associated with different factors/gene properties and, most importantly, an association between the TE insertion/fixation rate and gene activity status in ES cells.

| S-EPMC3260225 | biostudies-literature

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