RNA-mediated Chromatin Regulation and Transgenerational Epigenetic Inheritance in C. elegans

Project Summary/Abstract: Nuclear RNAi is an evolutionarily conserved epigenetic silencing pathway that targets transposons and other foreign DNA. The defining features of this pathway are small RNA-guided chromatin modifications and transcriptional repression at a target gene. In C. elegans, nuclear RNAi is essential for genome stability and

promotes germline immortality. Nuclear RNAi can be conveniently triggered by feeding worms with dsRNA, which leads to heritable silencing at the target gene for multiple generations. These features, together with powerful genetics and genomic tools and a three-day reproductive cycle, make C. elegans a highly tractable

system to study transgenerational epigenetic inheritance (TEI) in animals. Project 1. Investigating the biochemistry and cellular function of a novel histone modification H3K23me3. The broad and long-term objectives of this project are to comprehensively identify and characterize the histone post-translational

modifications and corresponding chromatin enzymes in the context of TEI. In the proposed funding cycle, this application will investigate the function and enzymology of a novel histone modification H3K23me3, which can be induced by nuclear RNAi. H3K23me3 is an understudied heterochromatin mark even though it is conserved

from plants to mammals. This application will take combined genetic, genomic, and biochemical approaches to (1) determine the functional relationship between three key heterochromatin marks: H3K9me3, H3K23me3, and H3K27me3, (2) understand why the nuclear RNAi pathway is required for C. elegans germline immortality

under heat stress, and (3) identify additional H3K23 histone methyltransferases in C. elegans. The results will advance the histone code theory and provide mechanistic insight into nuclear RNAi and TEI. Project 2. Investigating how C. elegans germline distinguishes self and nonself siRNAs. The broad and long-term

objectives of this project are to dissect the diverse functions of small RNAs in C. elegans and understand how cells distinguish self and foreign genetic material. As a short-term goal, this project will investigate a newly identified genetic activity termed “siRNA suppression”, which enables C. elegans to distinguish siRNAs that

target self-genes from ones that target nonself DNA such transposons. Both classes of siRNAs play important but different functions in animal development. This project will identify the protein factors, subcellular location, and molecular rules of siRNA suppression. As an overall significance, this application will identify new

components in chromatin and small RNA, both of which are fundamental to our understanding of transgenerational epigenetics and long-term environmental impacts on human health.