期刊
NUCLEIC ACIDS RESEARCH
卷 43, 期 14, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkv390
关键词
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资金
- Biotechnology and Biological Sciences Research Council
- Federal Ministry for Education and Research (BMBF)
- DKFZ scholarship
- CMMC
- UoC Advanced Researcher Grant via the DFG Excellence Initiative
- Biotechnology and Biological Sciences Research Council [BB/I00467X/1] Funding Source: researchfish
- Medical Research Council [G0400628] Funding Source: researchfish
- BBSRC [BB/I00467X/1] Funding Source: UKRI
- MRC [G0400628] Funding Source: UKRI
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.
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