Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories. Issue 14 (20th April 2015)

• Record Type: Journal Article
• Authors: Caudron-Herger, Maïwen; Cook, Peter R.; Rippe, Karsten; Papantonis, Argyris
• Is Part Of: Nucleic acids research. Volume 43:Issue 14(2015)
• Page Start: e95
• Page End: e95
• Publication Date: 2015-04-20
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkv390
• Languages: English
• ISSNs: 0305-1048

Abstract

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 TNFα, 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.