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RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [Oxford Nanopore Technology Direct RNA Sequencing]

ABSTRACT: The centromere is a pivotal chromatin domain that ensures accurate chromosome segregation during cell division. However, the epigenome regulation of the centromere and its impact on centromere function remain largely elusive. Here in the model plant Arabidopsis, we show that CCR4, the catalytic subunit of the RNA deadenylation complex CCR4-NOT, is essential for maintenance of the centromere epigenome and chromosome integrity. We demonstrate that CCR4 is involved in shortening of the poly(A) tails of transcripts originated from centromeric transposons and repeats, thereby promoting the production of small interfering RNAs (siRNAs). The CCR4-dependent siRNAs guide non-CG DNA methylation at centromere repeats, and CCR4 cooperates with canonical DNA methylation pathways to enhance centromeric H3K9 methylation and ensure mitotic chromosome stability. Our study illustrates the crucial role of RNA quality control in RNA interference and reveals the elaborate mechanism that safeguards plant centromeres through epigenomic regulation.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE274200 | GEO | 2024/08/24

REPOSITORIES: GEO

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RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [RNA-seq]

Project description:The centromere is a pivotal chromatin domain that ensures accurate chromosome segregation during cell division. However, the epigenome regulation of the centromere and its impact on centromere function remain largely elusive. Here in the model plant Arabidopsis, we show that CCR4, the catalytic subunit of the RNA deadenylation complex CCR4-NOT, is essential for maintenance of the centromere epigenome and chromosome integrity. We demonstrate that CCR4 is involved in shortening of the poly(A) tails of transcripts originated from centromeric transposons and repeats, thereby promoting the production of small interfering RNAs (siRNAs). The CCR4-dependent siRNAs guide non-CG DNA methylation at centromere repeats, and CCR4 cooperates with canonical DNA methylation pathways to enhance centromeric H3K9 methylation and ensure mitotic chromosome stability. Our study illustrates the crucial role of RNA quality control in RNA interference and reveals the elaborate mechanism that safeguards plant centromeres through epigenomic regulation.

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The Chromatin-Remodeling Factor FACT Contributes to Centromeric Heterochromatin Independently of RNAi

Project description:Centromeres exert vital cellular functions in mitosis and meiosis. A specialized histone and other chromatin-bound factors nucleate a dynamic protein assembly that is required for the proper segregation of sister chromatids. In several organisms including the fission yeast S. pombe, a RNAi-related pathway further strengthens the epigenetic maintenance of centromere location, primarily through repressing transcription near centromeres. Little is known how accessory factors such as histone chaperones and chromatin remodelling factors might be required to establish a functioning centromere. Here we show that the chaperone and remodelling complex FACT is required for transcriptional gene silencing at centromeres and for accurate chromosome segregation during mitosis. We show that Spt16 and Pob3 are two subunits of the S. pombe FACT complex. Surprisingly, yeast strains deleted for Pob3 are viable and show a marked loss of gene silencing at centromeric repeats and at the mating locus. Importantly, Pob3-null strains fail to undergo mitosis at high accuracy and phenocopy histone methylation and RNAi mutants. Processing of centromeric RNA transcripts into siRNAs is maintained in Pob3 mutants, but Swi6-association at the centromere is affected. Our studies provide the first experimental evidence for a role of the RNA polymerase II cofactor FACT in centromere function. Keywords: Expression profiling of pob3 vs wt

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