University of North Carolina at Chapel Hill Graduate School
Doi
Abstract
Cis-repressive long non-coding RNAs (lncRNAs) spread Polycomb Repressive Complexes (PRCs) within specific genomic regions to achieve chromatin compaction and stable gene silencing. Xist is the best characterized lncRNA; it is required to spread PRCs and silence genes across the entire 165 Mb X chromosome. Despite decades of research using the Xist lncRNA as a model, the relationship between lncRNAs and PRCs remains unclear. Airn and Kcnq1ot1 lncRNAs function similarly to Xist, but in smaller genomic regions. In this dissertation, we gained novel insights into lncRNA and PRC mechanism by comparing and contrasting lncRNA features and the genomic environments of Xist, Airn, and Kcnq1ot1. First, we found that Airn and Kcnq1ot1 spread PRCs and silence genes across multi megabase domains in mouse trophoblast stem cells (TSCs). Similar to the X chromosome, Airn and Kcnq1ot1 targeted regions contained non-uniform patterns of PRCs. We showed that PRC density in the 13 Mb Airn target region correlated with Airn abundance and was dependent on multiple aspects of genome architecture: linear distance to the Airn locus, pre-existing structure, TAD boundaries, and high-affinity chromatin sites of Airn. In Airn overexpression TSCs, eight PRC-bound CpG islands (CGIs) appeared to nucleate the spread of Polycomb. Deletion of one 2kb CGI caused loss of Polycomb across 4.5 Mb. Xist and Kcnq1ot1 targeted regions showed similar patterns of Polycomb at PRC-bound CGIs. This suggests a common mechanism where lncRNAs depend on pre-bound CGIs to specifically target and spread Polycomb in cis.Doctor of Philosoph
