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

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. Two biological replicates of small RNA-seq samples using 5-week-old adult plant leaves in WT, ccr4a ccr4b, ddm1rdr2, ddm1 rdr2 ccr4a ccr4b, ddm1 rdr2 rdr6, rdr6.

着丝粒是确保细胞分裂过程中染色体精准分离的关键染色质结构域。然而，目前学界对着丝粒的表观基因组调控机制及其对着丝粒功能的影响仍知之甚少。本研究以模式植物拟南芥为材料，证实RNA脱腺苷化复合物CCR4-NOT的催化亚基CCR4对于维持着丝粒表观基因组及染色体完整性至关重要。研究表明，CCR4可介导着丝粒来源转座子及重复序列转录本的poly(A)尾缩短，进而促进小干扰RNA（small interfering RNAs，siRNAs）的生成。CCR4依赖型siRNAs可介导着丝粒重复序列区域的非CG DNA甲基化，并与经典DNA甲基化通路协同作用，增强着丝粒区域的组蛋白H3K9甲基化，维持有丝分裂过程中的染色体稳定性。本研究阐明了RNA质量控制在RNA干扰中的关键作用，并揭示了通过表观基因组调控维持植物着丝粒稳定性的精细机制。本研究的小RNA测序（small RNA-seq）样本取材于生长5周的成熟植株叶片，共设置6组基因型：野生型（wild type，WT）、ccr4a ccr4b双突变体、ddm1 rdr2双突变体、ddm1 rdr2 ccr4a ccr4b四突变体、ddm1 rdr2 rdr6三突变体及rdr6单突变体，每组均包含2次生物学重复。