PT  - JOURNAL ARTICLE
AU  - Yichao Cai
AU  - Ying Zhang
AU  - Yan Ping Loh
AU  - Jia Qi Tng
AU  - Mei Chee Lim
AU  - Zhendong Cao
AU  - Anandhkumar Raju
AU  - Shang Li
AU  - Lakshmanan Manikandan
AU  - Vinay Tergaonkar
AU  - Greg Tucker-Kellogg
AU  - Melissa Jane Fullwood
TI  - H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions
AID  - 10.1101/684712
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 684712
4099  - http://biorxiv.org/content/early/2019/07/09/684712.short
4100  - http://biorxiv.org/content/early/2019/07/09/684712.full
AB  - Gene repression and silencers are poorly understood. H3K27me3 is a repressive histone modification; we reason that H3K27me3-rich regions (MRRs) of the genome defined from clusters of H3K27me3 peaks may be used to identify silencers that can regulate gene expression via proximity or looping. We found that MRRs are associated with chromatin interactions and tend to interact preferentially with each other. EZH2 inhibition or knockout showed that H3K27me3 was not required for maintenance of chromatin interactions, but genes at or looping to MRRs were upregulated upon loss of H3K27me3. To understand the function of MRRs, we used CRISPR to excise components of MRRs at interaction anchors and functionally characterized the knockouts in cellular assays and xenograft models. MRR removal can lead to upregulation of interacting target genes, altered chromatin interactions, changes in phenotype associated with cell identity, and altered xenograft tumor growth. Our results characterize silencers and their mechanisms of functioning.