Boundary Associated Long Noncoding RNA Mediates Long-Range Chromosomal Interactions

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Boundary Associated Long Noncoding RNA Mediates Long-Range Chromosomal Interactions

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Title: Boundary Associated Long Noncoding RNA Mediates Long-Range Chromosomal Interactions
Author(s):
Nwigwe, I. J.;
Kim, Yoon Jung (UT Dallas);
Wacker, D. A.;
Kim, Tae Hoon (UT Dallas);
Chadwick, B. P.
Item Type: Article
Keywords: Show Keywords
Description: Includes supporting data and figures.
Abstract: CCCTC binding factor (CTCF) is involved in organizing chromosomes into mega base-sized, topologically associated domains (TADs) along with other factors that define sub-TAD organization. CTCF-Cohesin interactions have been shown to be critical for transcription insulation activity as it stabilizes long-range interactions to promote proper gene expression. Previous studies suggest that heterochromatin boundary activity of CTCF may be independent of Cohesin, and there may be additional mechanisms for defining topological domains. Here, we show that a boundary site we previously identified known as CTCF binding site 5 (CBS5) from the homeotic gene cluster A (HOXA) locus exhibits robust promoter activity. This promoter activity from the CBS5 boundary element generates a long noncoding RNA that we designate as boundary associated long noncoding RNA-1 (blncRNA1). Functional characterization of this RNA suggests that the transcript stabilizes long-range interactions at the HOXA locus and promotes proper expression of HOXA genes. Additionally, our functional analysis also shows that this RNA is not needed in the stabilization of CTCF-Cohesin interactions however CTCF-Cohesin interactions are critical in the transcription of blncRNA1. Thus, the CTCF-associated boundary element, CBS5, employs both Cohesin and noncoding RNA to establish and maintain topologically associated domains at the HOXA locus.
Publisher: Public Library of Science
ISSN: 1932-6203
Persistent Link: http://hdl.handle.net/10735.1/4810
http://dx.doi.org/0.1371/journal. pone.0136104
Bibliographic Citation: Nwigwe, I. J., Y. J. Kim, D. A. Wacker, T. H. Kim, et al. 2015. "Boundary associated long noncoding RNA mediates long-range chromosomal interactions." PLOS One 10(8), doi: 10.1371/journal.pone.0136104
Terms of Use: CC-BY 4.0 (Attribution) License
©2015 The Authors
Sponsors: The National Institute of Allergy and Infection Disease (R21AI107067), and National Cancer Institute (R01CA140485) supported this work.

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