X-inactivation: quantitative predictions of protein interactions in the Xist network

Nucleic Acids Res. 2013 Jan 7;41(1):e31. doi: 10.1093/nar/gks968. Epub 2012 Oct 22.

Abstract

The transcriptional silencing of one of the female X-chromosomes is a finely regulated process that requires accumulation in cis of the long non-coding RNA X-inactive-specific transcript (Xist) followed by a series of epigenetic modifications. Little is known about the molecular machinery regulating initiation and maintenance of chromosomal silencing. Here, we introduce a new version of our algorithm catRAPID to investigate Xist associations with a number of proteins involved in epigenetic regulation, nuclear scaffolding, transcription and splicing processes. Our method correctly identifies binding regions and affinities of protein interactions, providing a powerful theoretical framework for the study of X-chromosome inactivation and other events mediated by ribonucleoprotein associations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Binding Sites
  • Enhancer of Zeste Homolog 2 Protein
  • Female
  • Heterogeneous-Nuclear Ribonucleoprotein U / metabolism
  • Matrix Attachment Region Binding Proteins / metabolism
  • Mice
  • Nuclear Proteins / metabolism
  • Polycomb Repressive Complex 2 / metabolism
  • RNA, Long Noncoding / chemistry
  • RNA, Long Noncoding / metabolism*
  • RNA-Binding Proteins / metabolism*
  • Repetitive Sequences, Nucleic Acid
  • Serine-Arginine Splicing Factors
  • X Chromosome Inactivation*
  • YY1 Transcription Factor / metabolism

Substances

  • Heterogeneous-Nuclear Ribonucleoprotein U
  • Matrix Attachment Region Binding Proteins
  • Nuclear Proteins
  • RNA, Long Noncoding
  • RNA-Binding Proteins
  • SAF-A protein, mouse
  • Satb1 protein, mouse
  • Suz12 protein, mouse
  • XIST non-coding RNA
  • YY1 Transcription Factor
  • Serine-Arginine Splicing Factors
  • Enhancer of Zeste Homolog 2 Protein
  • Ezh2 protein, mouse
  • Polycomb Repressive Complex 2