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Originally published in Science Express on 4 December 2008
Science 19 December 2008:
Vol. 322. no. 5909, pp. 1845 - 1848
DOI: 10.1126/science.1162228
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Reports

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

Leighton J. Core,* Joshua J. Waterfall,* John T. Lis{dagger}

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.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: jtl10{at}cornell.edu

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