Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Nat Struct Mol Biol. 2014 Feb;21(2):198-206. doi: 10.1038/nsmb.2764. Epub 2014 Jan 26.


RNA, including long noncoding RNA (lncRNA), is known to be an abundant and important structural component of the nuclear matrix. However, the molecular identities, functional roles and localization dynamics of lncRNAs that influence nuclear architecture remain poorly understood. Here, we describe one lncRNA, Firre, that interacts with the nuclear-matrix factor hnRNPU through a 156-bp repeating sequence and localizes across an ~5-Mb domain on the X chromosome. We further observed Firre localization across five distinct trans-chromosomal loci, which reside in spatial proximity to the Firre genomic locus on the X chromosome. Both genetic deletion of the Firre locus and knockdown of hnRNPU resulted in loss of colocalization of these trans-chromosomal interacting loci. Thus, our data suggest a model in which lncRNAs such as Firre can interface with and modulate nuclear architecture across chromosomes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Chromatin / metabolism
  • Chromosomes / metabolism*
  • Chromosomes / ultrastructure
  • Embryonic Stem Cells
  • Female
  • Humans
  • Male
  • Mice
  • Models, Genetic*
  • Molecular Sequence Data
  • RNA, Long Noncoding / analysis
  • RNA, Long Noncoding / chemistry
  • RNA, Long Noncoding / physiology*
  • Sequence Analysis, RNA
  • X Chromosome Inactivation


  • Chromatin
  • RNA, Long Noncoding
  • long noncoding RNA Firre, human

Associated data

  • GEO/GSE45157