Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories

Nucleic Acids Res. 2015 Aug 18;43(14):e95. doi: 10.1093/nar/gkv390. Epub 2015 Apr 20.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cells, Cultured
  • Chromatin / metabolism
  • Gene Expression Profiling / methods*
  • Humans
  • Introns
  • RNA / isolation & purification
  • RNA Processing, Post-Transcriptional
  • RNA, Long Noncoding / biosynthesis
  • RNA, Small Untranslated / biosynthesis
  • RNA, Untranslated / biosynthesis*
  • Sequence Analysis, RNA / methods*
  • Transcriptome*


  • Chromatin
  • RNA, Long Noncoding
  • RNA, Small Untranslated
  • RNA, Untranslated
  • RNA