Systematic discovery of Xist RNA binding proteins

By Ci Chu, Qiangfeng Cliff Zhang, S. Rocha, Ryan A. Flynn, Maheetha Bharadwaj, J. M. Calabrese, T. Magnuson, Edith Heard, Howard Y. Chang. 2015

989 citations recorded by the source corpus.

Summary Noncoding RNAs (ncRNAs) function with associated proteins to effect complex structural and regulatory outcomes. To reveal the composition and dynamics of specific noncoding RNA- protein complexes (RNPs) in vivo, we developed comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS). ChIRP-MS analysis of four ncRNAs captures key protein interactors, including a U1-specific link to the 3′ RNA processing machinery. Xist, an essential lncRNA for X-chromosome inactivation (XCI), interacts with 81 proteins from chromatin modification, nuclear matrix, and RNA remodeling pathways. The Xist RNA-protein particle assembles in two steps coupled with the transition from pluripotency to differentiation. Specific interactors include HnrnpK that participates in Xist-mediated gene silencing and histone modifications, but not Xist localization and Drosophila Split ends homolog Spen that interacts via the A-repeat domain of Xist and is required for gene silencing. Thus, Xist lncRNA engages with proteins in a modular and developmentally controlled manner to coordinate chromatin spreading and silencing.

Subfields: Cancer Research, Molecular Biology

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Citations in the corpus

Linking Long Noncoding RNA Localization and Function. (2016, methodology): “These methods have provided new mechanisms of X chromosome inactivation by identifying XIST-interacting genome architectures and proteins [84–86] and have also defined new genomic targets of NEAT1 [35] and MALAT1 [35,87].”
Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation (2018, background): “We went on to compare the effect of Spen deletion in iXist-ChrX cells with deletion of the Xist A-repeat, the critical silencing element linked to Spen recruitment 12,14 .”
Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading (2020, background): “The protein SPEN, which binds to the Arepeat region of Xist RNA through a triple RRM domain, plays a central role in Xistmediated gene silencing (8, 17, 22, 23).”
How do lncRNAs regulate transcription? (2017, methodology): “Another study used a similar approach but instead relied on formaldehyde cross-linking under nondenaturing conditions [chromatin isolation by RNA purification– mass spectrometry (ChIRP-MS)] (59).”