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 paralle...

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Bibliographic Details
Published in:Science (American Association for the Advancement of Science) 2008-12, Vol.322 (5909), p.1845-1848
Main Authors: Core, Leighton J, Waterfall, Joshua J, Lis, John T
Format: Article
Language:English
Subjects:
Biological and medical sciences
Cell Line
CpG Islands
DNA-Directed RNA Polymerases - metabolism
Electronic publishing
Fundamental and applied biological sciences. Psychology
Genes
Genome, Human
Genomes
Genomics
Histones
Humans
Messenger RNA
Molecular and cellular biology
Molecular biology
Molecular genetics
Molecules
Nucleosomes - metabolism
Promoter regions
Promoter Regions, Genetic
Research methodology
RNA
RNA polymerase
RNA Polymerase II - metabolism
RNA, Antisense - genetics
RNA, Antisense - metabolism
RNA, Messenger - genetics
RNA, Messenger - metabolism
Sequence Analysis, RNA
Sequencing
Transcription factors
Transcription Initiation Site
Transcription, Genetic
Transcription. Transcription factor. Splicing. Rna processing
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Summary: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 ~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.
ISSN:0036-8075
1095-9203
DOI:10.1126/science.1162228