Universität zu Köln

Caudron-Herger, Maiwen ORCID: 0000-0002-7030-8153, Cook, Peter R., Rippe, Karsten ORCID: 0000-0001-9951-9395 and Papantonis, Argyris ORCID: 0000-0001-7551-1073 (2015). Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories. Nucleic Acids Res., 43 (14). OXFORD: OXFORD UNIV PRESS. ISSN 1362-4962

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Abstract

While mapping total and poly-adenylated human transcriptomes has now become routine, characterizing nascent transcripts remains challenging, largely because nascent RNAs have such short half-lives. Here, we describe a simple, fast and cost-effective method to isolate RNA associated with transcription factories, the sites responsible for the majority of nuclear transcription. Following stimulation of human endothelial cells with the pro-inflammatory cytokine TNF alpha, we isolate and analyse the RNA content of factories by sequencing. Comparison with total, poly(A)(+) and chromatin RNA fractions reveals that sequencing of purified factory RNA maps the complete nascent transcriptome; it is rich in intronic unprocessed transcript, as well as long intergenic non-coding (lincRNAs) and enhancer-associated RNAs (eRNAs), micro-RNA precursors and repeat-derived RNAs. Hence, we verify that transcription factories produce most nascent RNA and confer a regulatory role via their association with a set of specifically-retained non-coding transcripts.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Caudron-Herger, Maiwen UNSPECIFIED orcid.org/0000-0002-7030-8153 UNSPECIFIED Cook, Peter R. UNSPECIFIED UNSPECIFIED UNSPECIFIED Rippe, Karsten UNSPECIFIED orcid.org/0000-0001-9951-9395 UNSPECIFIED Papantonis, Argyris UNSPECIFIED orcid.org/0000-0001-7551-1073 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-396360
DOI:	10.1093/nar/gkv390
Journal or Publication Title:	Nucleic Acids Res.
Volume:	43
Number:	14
Date:	2015
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1362-4962
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language HUMAN CELL; REVEALS; NUCLEAR; GENOME; DYNAMICS; GENES; ENHANCERS; ORDER Multiple languages Biochemistry & Molecular Biology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/39636