PRC1 collaborates with SMCHD1 to fold the X-chromosome and spread Xist RNA between chromosome compartments

Chen-Yu Wang,Danni Wang,Jeannie T Lee,David Colognori,Hongjae Sunwoo

doi:10.1038/s41467-019-10755-3

Abstract

X-chromosome inactivation triggers fusion of A/B compartments to inactive X (Xi)-specific structures known as S1 and S2 compartments. SMCHD1 then merges S1/S2s to form the Xi super-structure. Here, we ask how S1/S2 compartments form and reveal that Xist RNA drives their formation via recruitment of Polycomb repressive complex 1 (PRC1). Ablating Smchd1 in post-XCI cells unveils S1/S2 structures. Loss of SMCHD1 leads to trapping Xist in the S1 compartment, impairing RNA spreading into S2. On the other hand, depleting Xist, PRC1, or HNRNPK precludes re-emergence of S1/S2 structures, and loss of S1/S2 compartments paradoxically strengthens the partition between Xi megadomains. Finally, Xi-reactivation in post-XCI cells can be enhanced by depleting both SMCHD1 and DNA methylation. We conclude that Xist, PRC1, and SMCHD1 collaborate in an obligatory, sequential manner to partition, fuse, and direct self-association of Xi compartments required for proper spreading of Xist RNA.

Highlights

X-chromosome inactivation triggers fusion of A/B compartments to inactive X (Xi)-specific structures known as S1 and S2 compartments
Principal component 1 (PC1) showed that the Smchd1−/− Xa retained the ~63 A/B compartments that characterize the WT Xa (r = 0.94) (Supplementary Fig. 2b), but the Smchd1−/− Xi lost the compartment-less character of the WT Xi
Given that HNRNPK is required for targeting Polycomb repressive complex 1 (PRC1) to the Xi24,55,56, we examined the relationship of PRC1 to SMCHD1 localization

Summary

Introduction

X-chromosome inactivation triggers fusion of A/B compartments to inactive X (Xi)-specific structures known as S1 and S2 compartments. Many chromatin-associated factors phase separate[10,11,12,13] Evidence that these factors are required for forming large-scale chromosome compartments is currently lacking. By ablating an Xi-enriched protein, structural maintenance of chromosomes hinge domain containing 1 (SMCHD1)[25,26,27], in pre-XCI cells and observing effects during de novo XCI, we recently identified a hidden layer of Xi organization—S1/S2 compartments[28]. This Xi-specific structure marks a transition in the progression from A/B compartments to the “compartment-less” structure. It is clear that the merging of S1/S2 compartments relies on SMCHD1, the mechanism underlying their formation is presently unknown

Methods

Results

Conclusion