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

Ezgi Hacisuleyman; Loyal A Goff; Cole Trapnell; Adam Williams; Jorge Henao-Mejia; Lei Sun; Patrick McClanahan; David G Hendrickson; Martin Sauvageau; David R Kelley; Michael Morse; Jesse Engreitz; Eric S Lander; Mitch Guttman; Harvey F Lodish; Richard Flavell; Arjun Raj; John L Rinn

doi:10.1038/nsmb.2764

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.

Authors

Ezgi Hacisuleyman¹, Loyal A Goff², Cole Trapnell³, Adam Williams⁴, Jorge Henao-Mejia⁴, Lei Sun⁵, Patrick McClanahan⁶, David G Hendrickson³, Martin Sauvageau³, David R Kelley³, Michael Morse⁷, Jesse Engreitz⁷, Eric S Lander⁷, Mitch Guttman⁸, Harvey F Lodish⁹, Richard Flavell¹⁰, Arjun Raj⁶, John L Rinn¹¹

Affiliations

¹ 1] Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA. [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA. [3] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. [4].
² 1] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA. [2] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. [3] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [4].
³ 1] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA. [2] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.
⁴ Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA.
⁵ Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.
⁶ Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
⁷ Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.
⁸ Department of Biology, California Institute of Technology, Pasadena, California, USA.
⁹ 1] Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA. [2] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
¹⁰ 1] Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA. [2] Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA.
¹¹ 1] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA. [2] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. [3] Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.

Abstract

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

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

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