Long-Distance Repression by Human Silencers: Chromatin Interactions and Phase Separation in Silencers

Abstract

Three-dimensional genome organization represents an additional layer in the epigenetic regulation of gene expression. Active transcription controlled by enhancers or super-enhancers has been extensively studied. Enhancers or super-enhancers can recruit activators or co-activators to activate target gene expression through long-range chromatin interactions. Chromatin interactions and phase separation play important roles in terms of enhancer or super-enhancer functioning. Silencers are another major type of cis-regulatory element that can mediate gene regulation by turning off or reducing gene expression. However, compared to active transcription, silencer studies are still in their infancy. This review covers the current knowledge of human silencers, especially the roles of chromatin interactions and phase separation in silencers. This review also proposes future directions for human silencer studies.

Keywords: chromatin interactions; phase separation; silencers.

Figure 1

Different identification methods of human silencers. (A) H3K27me3-DHS sites that were negatively correlated with expression of nearby genes in different cell lines were termed silencers. DHS—DNase I hypersensitive sites. (B) Identifying silencers using the subtractive approach. (C) Identifying human silencers by high-throughput functional screen via measuring the repressive ability of silencer elements (ReSE). (D) Identifying H3K27me3-rich regions (MRRs) as silencers.

Figure 2

Mechanisms for silencer repression. Silencers can repress gene expression in two ways: (A) One way is to compete with activators or general transcription factors (GTF) for binding sites. For example, BCL6 competes with STAT6 and CEBPB for binding at the IL4 promoter to prevent transcription [36]. (B) Another way is to generate a repressive chromatin environment, for example by methylating the histones at the gene promoter, thereby preventing the binding of activators and transcriptional machinery. For example, the REST complex binds at the promoter of STMN2 [37], recruiting the PRC2 complex and depositing H3K27me3. (C) Silencers can interact with linearly distant gene promoters through chromatin looping, to perform their repressive functions. The IGF2 promoter interacts with a distal H3K27me3-rich region (MRR) and forms a repressive chromatin structure [32]. CRISPR/Cas9 excision of the MRR increases IGF2 transcription.

Figure 3

Phase separation in silencing. Repressors bind to heterochromatin domains and form protein–protein interactions with each other, assembling into a phase-separated condensate that selectively incorporates repressive factors and excludes transcription activators.