2. Academic Validation
  3. Systematic discovery of Xist RNA binding proteins

Systematic discovery of Xist RNA binding proteins

  • Cell. 2015 Apr 9;161(2):404-16. doi: 10.1016/j.cell.2015.03.025.
Ci Chu 1,  Qiangfeng Cliff Zhang 2,  Simão Teixeira da Rocha 3,  Ryan A Flynn 2,  Maheetha Bharadwaj 2,  J Mauro Calabrese 4,  Terry Magnuson 5,  Edith Heard 3,  Howard Y Chang 6
Affiliations

Affiliations

  • 1 Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.
  • 2 Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • 3 Institut Curie, CNRS UMR3215, INSERM U934, 26 rue d'Ulm, Paris 75248, France.
  • 4 Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
  • 5 Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
  • 6 Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: howchang@stanford.edu.
PMID: 25843628 DOI: 10.1016/j.cell.2015.03.025
Abstract

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, which participates in Xist-mediated gene silencing and histone modifications but not Xist localization, and Drosophila Split ends homolog Spen, which 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.

Figures