YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses

Sci Rep. 2016 Nov 18;6:37324. doi: 10.1038/srep37324.


Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted in silico analyses of the sexes using human datasets to gain perspectives into such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study suggests a role for YY1 in transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Allelic Imbalance
  • Binding Sites / genetics
  • Cell Line
  • Computer Simulation
  • Female
  • Genes, X-Linked / genetics*
  • Humans
  • Male
  • Protein Binding
  • RNA, Long Noncoding / genetics*
  • Sex Factors
  • Transcription Initiation Site
  • Transcription, Genetic*
  • X Chromosome Inactivation / genetics*
  • YY1 Transcription Factor / genetics*
  • YY1 Transcription Factor / metabolism


  • RNA, Long Noncoding
  • XIST non-coding RNA
  • YY1 Transcription Factor