A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

Mammalian genomes are pervasively transcribed outside mapped protein-coding genes. One class of extragenic transcription products is represented by long non-coding RNAs (lncRNAs), some of which result from Pol_II transcription of bona-fide RNA genes. Whether all lncRNAs described insofar are products of RNA genes, however, is still unclear. Here we have characterized transcription sites located outside protein-coding genes in a highly regulated response, macrophage activation by endotoxin. Using chromatin signatures, we could unambiguously classify extragenic Pol_II binding sites as belonging to either canonical RNA genes or transcribed enhancers. Unexpectedly, 70% of extragenic Pol_II peaks were associated…

• WT
  Wellcome Trust

  Award: 075491/Z/04
• MO
  Ministry of Education, Culture, Sports, Science and Technology
• AI
  Associazione Italiana per la Ricerca sul Cancro