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

Ezgi Hacisuleyman, Loyal 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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)198-206
Number of pages9
JournalNature structural & molecular biology
Volume21
Issue number2
DOIs
StatePublished - Feb 2014
Externally publishedYes

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Long Noncoding RNA
Intergenic DNA
Nuclear Matrix
X Chromosome
Chromosomes
RNA

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. / Hacisuleyman, Ezgi; Goff, Loyal; Trapnell, Cole; Williams, Adam; Henao-Mejia, Jorge; Sun, Lei; McClanahan, Patrick; Hendrickson, David G.; Sauvageau, Martin; Kelley, David R.; Morse, Michael; Engreitz, Jesse; Lander, Eric S.; Guttman, Mitch; Lodish, Harvey F.; Flavell, Richard; Raj, Arjun; Rinn, John L.

In: Nature structural & molecular biology, Vol. 21, No. 2, 02.2014, p. 198-206.

Research output: Contribution to journalArticle

Hacisuleyman, E, Goff, L, Trapnell, C, Williams, A, Henao-Mejia, J, Sun, L, McClanahan, P, Hendrickson, DG, Sauvageau, M, Kelley, DR, Morse, M, Engreitz, J, Lander, ES, Guttman, M, Lodish, HF, Flavell, R, Raj, A & Rinn, JL 2014, 'Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre', Nature structural & molecular biology, vol. 21, no. 2, pp. 198-206. https://doi.org/10.1038/nsmb.2764
Hacisuleyman, Ezgi ; Goff, Loyal ; Trapnell, Cole ; Williams, Adam ; Henao-Mejia, Jorge ; Sun, Lei ; McClanahan, Patrick ; Hendrickson, David G. ; Sauvageau, Martin ; Kelley, David R. ; Morse, Michael ; Engreitz, Jesse ; Lander, Eric S. ; Guttman, Mitch ; Lodish, Harvey F. ; Flavell, Richard ; Raj, Arjun ; Rinn, John L. / Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. In: Nature structural & molecular biology. 2014 ; Vol. 21, No. 2. pp. 198-206.
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