RNAi and Epigenetic Control of Higher-Order Chromatin Assembly

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Research in our laboratory is focused on the epigenetic control of higher-order chromatin assembly. The dynamic regulation of higher-order chromosome structure governs diverse cellular processes ranging from stable inheritance of gene expression patterns to other aspects of global chromosome structure essential for preserving genomic integrity. Our earlier studies revealed sequence of molecular events leading to the assembly of heterochromatic structures in the fission yeast Schizosaccharomyces pombe. We found that covalent modifications of histone tails by deacetylase and methyltransferase activities act in concert to establish the histone code essential for the assembly of heterochromatic structures. Moreover, we showed that distinct site-specific histone H3 methylation patterns dictate the organization of chromosomes into discrete structural and functional domains. Histone H3 methylated at lysine 9 is strictly localized to silent heterochromatic regions whereas H3 methylated at lysine 4, only a few amino acids away, is specific to the surrounding active euchromatic regions. We have continued to focus on the role of histone modifications and the factors that recognize specific histone modifications patterns (such as a chromodomain protein Swi6 that specifically binds histone H3 methylated at lysine 9) in the assembly of higher-order chromatin structures and have made significant progress in understanding the mechanism of higher-order chromatin assembly. More importantly, we provided evidence showing that RNA interference (RNAi), whereby double-stranded RNAs silence cognate genes, plays a critical role in targeting of heterochromatin complexes to specific locations in the genome. Our recent work has led to discovery of a self-enforcing loop mechanism though which RNAi machinery operates as a stable component of the heterochromatic domains (via tethering of RNAi complexes to heterochromatin marks) to destroy repeat transcripts that escape heterochromatin-mediated transcriptional silencing. In this loop mechanism, the processing of transcripts by RNAi machinery generate small interfering RNAs (siRNAs) that are utilized for further targeting of heterochromatin complexes, so the mechanism continues. In a comprehensive study, we have also developed a high-resolution map of the heterochromatin and euchromatin distribution across the entire fission yeast genome. These analyses together with mapping of RNAi components and large scale sequencing of siRNAs assocaited with an RNAi effector complex involved in heterochromatic silencing have yielded novel insights into the epigenetic profile of this model eukaryotic genome. Our work led to realization the heterochromatin serves as a dynamic platform of the genome involved in recruitment of diverse regulatory proteins (effectors) implicated in different chromosomal processes. Among other factors, these effectors include factors involved in deacetylation of histones and nucleosome remodeling proteins (such as SHREC complex described recently by our lab), which facilitate assembly of higher-order chromatin structures. The link between RNAi, heterochromatin, and chromatin-modifying factors is conserved in higher eukaryotes including mammals and has broad implications for human biology and disease including cancer. We have also uncovered a novel genome surveillance mechanism for retrotransposons by a family of transposase-derived CENP-B homologs. Retrotransposons are capable of exerting diverse effects on their hosts, profoundly influencing the organization, integrity and evolution of the host genome, and the host transcriptome. We discovered that CENP-Bs localize at and recruit histone deacetylases to silence retrotransposons. CENP-Bs also repress retrotransposon relics scattered throughout the fission yeast genome and often located near gene promoters to exert influence on expression of genes. Surprisingly, retroelements dispersed throughout the genome are clustered into specialized bodies, the organization of which depends on CENP-Bs. CENP-B-mediated surveillance is proactive, capable of preventing an extinct retrotransposon from reentering the host genome. These results reveal a likely ancient retrotransposon surveillance pathway important for host genome organization and maintenance of genomic integrity.