A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

Abstract

The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform “identification of direct RNA interacting proteins” (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of interactors, including cohesins, condensins, topoisomerases, RNA helicases, chromatin remodelers and modifiers, which synergistically repress Xi transcription. Inhibiting two or three interactors destabilizes silencing. While Xist attracts some interactors, it repels architectural factors. Xist evicts cohesins from the Xi and directs an Xi-specific chromosome conformation. Upon deleting Xist, the Xi acquires the cohesin-binding and chromosomal architecture of the active X. Our study unveils many layers of Xi repression and demonstrates a central role for RNA in the topological organization of mammalian chromosomes.

Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture

“…Notably, despite extensive rearrangement of the murine X chromosome relative to its human counterpart, the boundary between the superdomains again occurred at Dxz4 [chrX: 75.7-75.8 megabases (Mb), mm10] (18). [While this manuscript was in preparation, this point was reported by multiple groups (19,20).] As in human, we also observed superloops between Dxz4 and Firre, between Dxz4 and Xist, and between Dxz4 and x75 ( Fig.…”

“…Compartment structure was almost entirely absent in the murine Xi chromosome: The Hi-C map of the Xi chromosome did not have a plaid appearance, and square domains were rarely seen along its diagonal. To check whether the absence of compartment structure is a feature of mice in general or of the Patski cell line in particular, we reanalyzed data from the two recent Hi-C studies of murine X chromosome inactivation mentioned above (19,20). A map of the Patski cell line from ref.…”

Sexual dimorphism in cancer

“…To counteract differences in X chromosome gene dosage, mammals utilize the X inactivation (Xi) process, involving transcriptional silencing and chromatin compaction promoted by the long non coding RNA (lncRNA) Xist 102,103 . Female tissues are mosaic for most X-linked genes, resulting from Xi in every cell.…”

LncRNAs: Bridging environmental sensing and gene expression

“…Aberrant expression of lncRNAs is associated with various diseases such as prostate cancer, 89 breast cancer, 90 HIV, 91 Type-2 diabetes, 92,93 and obesity, 93,94 underscoring a need for understanding the precise roles of lncRNAs. It should be emphasized that, although pioneering discoveries regarding lncRNA scaffolding of chromatin remodeling factors 21 and remodeling of the 3D genome 95 have relied on mammalian systems, transcriptional interference 28 and lncRNA R-loops were initially discovered in budding yeast. 53 As we continue to define biological roles for individual lncRNAs, it is essential to complement our studies of multicellular eukaryotes with simple model organisms, which have provided and continue to provide mechanistic paradigms for gene regulation.…”