Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development

Abstract

Summary In metazoan development, lineage specific gene expression is modulated by the delicate balance between transcription activation and repression. Despite much of our knowledge in the enhancer-centered transcription activation, silencers and their roles in normal development are poorly understood. Here, we performed chromatin interaction analyses of Polycomb repressive complex 2 (PRC2), a key regulator inducing transcriptional gene silencing, to uncover silencers, their molecular identity and associated chromatin connectivity. Systematic analysis of the cis -regulatory silencer elements reveals their chromatin features and gene targeting specificity. Deletion of these PRC2-bound silencers in mice results in transcriptional derepression of their interacting genes and pleiotropic developmental phenotypes, including embryonic lethality. While functioning as PRC2-bound silencers in pluripotent cells, they can transition into active tissue-specific enhancers during development, suggesting their regulatory versatility. Our study characterizes the molecular nature of silencers, their associated chromatin architectures, and offers the exciting possibility of targeted re-activation of epigenetically silenced genes.

Three-dimensional regulation ofHOXAcluster genes by acis-element in hematopoietic stem cell and leukemia

“…While the GLC is a polycomb target in CD34+ HSPCs, we observed that it can change epigenetic states across various tissues and cell lines. This is consistent with previous works that show how polycomb targets in early development can act as enhancers in Drosophila and mouse models [17][18][19][20] . We have previously shown that ablation of the silencing histone marks was sufficient to disrupt the interaction between GLC and HOXA and alters gene expression at the locus in cord blood CD34+ HSPC (Zhang et al Molecular Cell in press).…”

Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation

“…However, the relationship between PcG proteins, 3D chromatin landscape and silencing of gene expression remain unclear. Several studies have revealed that PRC1 and PRC2 establish long-range interactions in various cell types and organisms 4,7,10,[24][25][26][27][28] . Polycombassociated interactions occur in the larger context of genome architecture and chromatin modifications, including DNA methylation 8,29 and cohesin-dependent folding 9 , but there is emerging evidence that Polycomb can aggregate in a cohesin-independent manner 30 .…”

Annotation of Chromatin States in 66 Complete Mouse Epigenomes During Development

“…We used a set of 1800 silencers bound by Polycomb Group 2 proteins (PRC2), identified using ChIA-PET assays targeting PRC2 component proteins in mouse embryonic stem cells 28 The enrichment of the PRC2-bound silencers with chromatin states varied by silencer types. The silencers were clustered into four groups according to their H3K27ac signal profiles across the fetal mouse tissues 28 , a subset of the data we used to define chromatin states (H3K27ac is one of the ten marks used to train our ten-mark model).…”

“…We used a set of 1800 silencers bound by Polycomb Group 2 proteins (PRC2), identified using ChIA-PET assays targeting PRC2 component proteins in mouse embryonic stem cells 28 The enrichment of the PRC2-bound silencers with chromatin states varied by silencer types. The silencers were clustered into four groups according to their H3K27ac signal profiles across the fetal mouse tissues 28 , a subset of the data we used to define chromatin states (H3K27ac is one of the ten marks used to train our ten-mark model). Group 1 silencers (N = 371) had the highest H3K27ac signals in the fetal mouse tissues 28 , and the centers of these silencers were in the Tss and Enh states in some biosamples, especially in the brain, but not so much in the liver (Supplementary Fig.…”

“…The silencers were clustered into four groups according to their H3K27ac signal profiles across the fetal mouse tissues 28 , a subset of the data we used to define chromatin states (H3K27ac is one of the ten marks used to train our ten-mark model). Group 1 silencers (N = 371) had the highest H3K27ac signals in the fetal mouse tissues 28 , and the centers of these silencers were in the Tss and Enh states in some biosamples, especially in the brain, but not so much in the liver (Supplementary Fig. 11).…”