The Xist lncRNA directly interacts with SHARP to silence transcription through HDAC3

By C. A. McHugh, Chun-Kan Chen, A. Chow, Christine Surka, Christina Tran, P. McDonel, Amy Pandya-Jones, M. Blanco, Christina P. Burghard, A. Moradian and 7 more. 2015

714 citations recorded by the source corpus.

Many long non-coding RNAs (lncRNAs) affect gene expression, but the mechanisms by which they act are still largely unknown. One of the best-studied lncRNAs is Xist, which is required for transcriptional silencing of one X chromosome during development in female mammals. Despite extensive efforts to define the mechanism of Xist-mediated transcriptional silencing, we still do not know any proteins required for this role. The main challenge is that there are currently no methods to comprehensively define the proteins that directly interact with a lncRNA in the cell. Here we develop a method to purify a lncRNA from cells and identify proteins interacting with it directly using quantitative mass spectrometry. We identify ten proteins that specifically associate with Xist, three of these proteins—SHARP, SAF-A and LBR—are required for Xist-mediated transcriptional silencing. We show that SHARP, which interacts with the SMRT co-repressor that activates HDAC3, is not only essential for silencing, but is also required for the exclusion of RNA polymerase II (Pol II) from the inactive X. Both SMRT and HDAC3 are also required for silencing and Pol II exclusion. In addition to silencing transcription, SHARP and HDAC3 are required for Xist-mediated recruitment of the polycomb repressive complex 2 (PRC2) across the X chromosome. Our results suggest that Xist silences transcription by directly interacting with SHARP, recruiting SMRT, activating HDAC3, and deacetylating histones to exclude Pol II across the X chromosome.

Subfields: Cancer Research, Genetics, Molecular Biology

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Christina S. Leslie

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Citations in the corpus

Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing (2015, background): “Recently SPEN and RBM15 have been shown to be essential for Xist-mediated X 68 chromosome inactivation (Chu et al., 2015; McHugh et al., 2015; Minajigi et al., 2015; Moindrot et al., 69 2015; Monfort et al., 2015).”
Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation (2018, background): “Discrepancies with prior studies 15,23 may again be linked to the use of different silencing and loss of function assays, as well as allelic vs non-allelic analysis.”
Non-coding RNAs in disease: from mechanisms to therapeutics (2023, neutral): “…proteins, lncRNAs can also bind to the DNA and regulate chromatin by recruiting chromatin modifiers to the promoter region of their target genes 60–62 . of sequence-specific mRNAs, causing mRNA degradation or translational repression, as illustrated for miR-34a targeting PDL1 transcripts. b ,…”