Dri1 mediates heterochromatin assembly via RNAi and histone deacetylation

• Published in: Genetics (Austin) 2021-05, Vol.218 (1)
• Main Authors: Ban, Hyoju, Sun, Wenqi, Chen, Yu-hang, Chen, Yong, Li, Fei
• Format: Article
• Language: English
• Subjects: Acetylation; Assembly; C-Terminus; Cell Nucleus - metabolism; Chromatin; Chromatin - metabolism; Chromatin Assembly and Disassembly - genetics; Chromosomal Proteins, Non-Histone - genetics; Deacetylation; DNA methylation; DNA polymerase; DNA Polymerase II - metabolism; DNA-directed DNA polymerase; Epigenetics; Gene expression; Gene silencing; Genetics; Genomes; Heterochromatin; Heterochromatin - genetics; Heterochromatin - metabolism; Heterochromatin protein 1; Histone deacetylase; Histone-Lysine N-Methyltransferase - metabolism; Histones; Histones - genetics; Investigation; Lysine; Methylation; Proteins; Recruitment; Ribonucleic acid; RNA; RNA Interference; RNA, Small Interfering - genetics; RNA-binding protein; RNA-mediated interference; S phase; Schizosaccharomyces - genetics; Schizosaccharomyces pombe Proteins - genetics; Schizosaccharomyces pombe Proteins - metabolism; siRNA; Yeasts; Zinc finger proteins
• ISSN: 1943-2631; 0016-6731; 1943-2631
• DOI: 10.1093/genetics/iyab032

Abstract Heterochromatin, a transcriptionally silenced chromatin domain, is important for genome stability and gene expression. Histone 3 lysine 9 methylation (H3K9me) and histone hypoacetylation are conserved epigenetic hallmarks of heterochromatin. In fission yeast, RNA interference (RNAi) plays a key role in H3K9 methylation and heterochromatin silencing. However, how RNAi machinery and histone deacetylases (HDACs) are coordinated to ensure proper heterochromatin assembly is still unclear. Previously, we showed that Dpb4, a conserved DNA polymerase epsilon subunit, plays a key role in the recruitment of HDACs to heterochromatin during S phase. Here, we identified a novel RNA-binding protein Dri1 that interacts with Dpb4. GFP-tagged Dri1 forms distinct foci mostly in the nucleus, showing a high degree of colocalization with Swi6/Heterochromatin Protein 1. Deletion of dri1+ leads to defects in silencing, H3K9me, and heterochromatic siRNA generation. We also showed that Dri1 physically associates with heterochromatic transcripts, and is required for the recruitment of the RNA-induced transcriptional silencing (RITS) complex via interacting with the complex. Furthermore, loss of Dri1 decreases the association of the Sir2 HDAC with heterochromatin. We further demonstrated that the C-terminus of Dri1 that includes an intrinsically disordered (IDR) region and three zinc fingers is crucial for its role in silencing. Together, our evidences suggest that Dri1 facilitates heterochromatin assembly via the RNAi pathway and HDAC.