Welcome to the new version of CaltechAUTHORS. Login is currently restricted to library staff. If you notice any issues, please email coda@library.caltech.edu
Published February 2014 | Supplemental Material + Accepted Version
Journal Article Open

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


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.

Additional Information

© 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. Received 17 December 2013; accepted 30 December 2013; published online 26 January 2014. We thank Biosearch, especially M. Beal, H. Johansson, A. Orjalo, S. Coassin and R. Cook, for materials, advice and help with FISH experiments. We are grateful to the entire Rinn and Raj laboratories for generous help with experiments, bioinformatics and preparation of the manuscript. This work was supported by US National Institutes of Health grants 1DP2OD00667 (J.L.R.), P01GM099117 (J.L.R.), 1DP20D008514 (A.R.) and P50HG006193-01 (J.L.R.) and by the Howard Hughes Medical Institute (R.F.). Author Contributions: E.H. designed and performed experiments. L.A.G. performed computational analysis. J.L.R. directed research. E.H., L.A.G. and J.L.R. wrote the manuscript. C.T. and D.R.K. helped with computational analysis. M.S., D.G.H., P.M., J.E., M.G., A.R., M.M. and E.S.L. contributed experiments. A.W., J.H.-M. and R.F. generated knockout mESCs. L.S. and H.F.L. helped with experimental techniques.

Attached Files

Accepted Version - nihms552629.pdf

Supplemental Material - nsmb.2764-S1.pdf

Supplemental Material - nsmb.2764-S2.txt

Supplemental Material - nsmb.2764-S3.xlsx

Supplemental Material - nsmb.2764-S4.xlsx

Supplemental Material - nsmb.2764-S5.xlsx


Files (12.8 MB)
Name Size Download all
28.7 kB Preview Download
4.2 MB Preview Download
60.1 kB Download
30.1 kB Download
14.0 kB Download
8.4 MB Preview Download

Additional details

August 19, 2023
October 25, 2023