a large fraction of extragenic rna pol ii transcription sites overlap enhancers大部分基因外转录rna聚合酶ii网站重叠增强剂.pdfVIP

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers 1. 1. 1. 1 1 Francesca De Santa , Iros Barozzi , Flore Mietton , Serena Ghisletti , Sara Polletti , Betsabeh 1 1 2 3 1 Khoramian Tusi , Heiko Muller , Jiannis Ragoussis , Chia-Lin Wei , Gioacchino Natoli * 1 Department of Experimental Oncology, European Institute of Oncology (IEO) Campus IFOM-IEO, Milan, Italy, 2 Genomics Laboratory, Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, Oxford, United Kingdom, 3 Genome Technology and Biology Group, Genome Institute of Singapore, Singapore Abstract 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 with genomic regions with a canonical chromatin signature of enhancers. Enhancer-associated extragenic transcription was frequently adjacent to inducible inflammatory genes, was regulated in response to endotox