English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Long ncRNA expression associates with tissue-specific enhancers

Vucicevic, D., Corradin, O., Ntini, E., Scacheri, P. C., & Ørom, U. A. (2015). Long ncRNA expression associates with tissue-specific enhancers. Cell Cycle, 14(2), 253-260. doi:10.4161/15384101.2014.977641.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-5888-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-5889-6
Genre: Journal Article

Files

show Files
hide Files
:
Vucicevic.pdf (Publisher version), 2MB
Name:
Vucicevic.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
© 2015 The Author(s). Published with license by Taylor & Francis Group, LLC

Locators

show
hide
Description:
-

Creators

show
hide
 Creators:
Vucicevic, Dubravka1, Author              
Corradin, Olivia, Author
Ntini, Evgenia, Author
Scacheri, Peter C., Author
Ørom, Ulf Andersson1, Author              
Affiliations:
1Long non-coding RNA (Ulf Andersson Ørom), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479659              

Content

show
hide
Free keywords: Cell Line Enhancer Elements, Genetic Gene Expression HeLa Cells Hep G2 Cells Histones/metabolism Human Umbilical Vein Endothelial Cells Humans K562 Cells MCF-7 Cells RNA, Long Noncoding/*metabolism Sequence Analysis, RNA Enhancer activating long non-coding RNA enhancer prediction long non-coding RNA tissue-specific enhancer
 Abstract: Long non-coding RNAs (ncRNA) have recently been demonstrated to be expressed from a subset of enhancers and to be required for the distant regulation of gene expression. Several approaches to predict enhancers have been developed based on various chromatin marks and occupancy of enhancer-binding proteins. Despite the rapid advances in the field, no consensus how to define tissue specific enhancers yet exists. Here, we identify 2,695 long ncRNAs annotated by ENCODE (corresponding to 28% of all ENCODE annotated long ncRNAs) that overlap tissue-specific enhancers. We use a recently developed algorithm to predict tissue-specific enhancers, PreSTIGE, that is based on the H3K4me1 mark and tissue specific expression of mRNAs. The expression of the long ncRNAs overlapping enhancers is significantly higher when the enhancer is predicted as active in a specific cell line, suggesting a general interdependency of active enhancers and expression of long ncRNAs. This dependency is not identified using previous enhancer prediction algorithms that do not account for expression of their downstream targets. The predicted enhancers that overlap annotated long ncRNAs generally have a lower ratio of H3K4me1 to H3K4me3, suggesting that enhancers expressing long ncRNAs might be associated with specific epigenetic marks. In conclusion, we demonstrate the tissue-specific predictive power of PreSTIGE and provide evidence for thousands of long ncRNAs that are expressed from active tissue-specific enhancers, suggesting a particularly important functional relationship between long ncRNAs and enhancer activity in determining tissue-specific gene expression.

Details

show
hide
Language(s): eng - English
 Dates: 2014-10-132015-01-212015
 Publication Status: Published in print
 Pages: 8
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.4161/15384101.2014.977641
ISSN: 1551-4005 (Electronic)
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Cell Cycle
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: Georgetown, TX : Landes Bioscience
Pages: - Volume / Issue: 14 (2) Sequence Number: - Start / End Page: 253 - 260 Identifier: ISSN: 1538-4101
CoNE: https://pure.mpg.de/cone/journals/resource/111088196488836