Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.
RNA polymerases are highly regulated molecular machines. We present a method (global run-on sequencing, GRO-seq) that maps the position, amount, and orientation of transcriptionally engaged RNA polymerases genome-wide. In this method, nuclear run-on RNA molecules are subjected to large-scale parallel sequencing and mapped to the genome. We show that peaks of promoter-proximal polymerase reside on approximately 30% of human genes, transcription extends beyond pre-messenger RNA 3' cleavage, and antisense transcription is prevalent. Additionally, most promoters have an engaged polymerase upstream and in an orientation opposite to the annotated gene. This divergent polymerase is associated with active genes but does not elongate effectively beyond the promoter. These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription.
Core
Leighton J
LJ
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
Waterfall
Joshua J
JJ
Lis
John T
JT
D002460:Cell Line; D018899:CpG Islands; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D015894:Genome, Human; D006801:Humans; D009707:Nucleosomes / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism*; D016372:RNA, Antisense / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
D009707:Nucleosomes; D016372:RNA, Antisense; D012333:RNA, Messenger; D012319:RNA Polymerase II; D012321:DNA-Directed RNA Polymerases