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Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II

ABSTRACT: We developed a novel approach to isolate and characterize, at nucleotide-level resolution, the RNAs derived from RNA polymerase II (Pol II) in early elongation complexes. We find that high numbers of these short RNAs are not correlated with gene expression but instead are indicative of promoter-proximally stalled polymerase. High amounts of these short RNAs are generated from more than one third of all genes, indicating that Pol II stalls in the promoter-proximal region on global scale. We also find that the nucleotide composition of the initially transcribed sequence plays an important role in promoting transcriptional stalling and that early elongation complexes are highly susceptible to backtracking and arrest. Global analysis of RNAs produced by promoter-proximal Pol II.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Sergei Nechaev

PROVIDER: E-GEOD-18643 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila.

Nechaev Sergei S Fargo David C DC dos Santos Gilberto G Liu Liwen L Gao Yuan Y Adelman Karen K

Science (New York, N.Y.) 20091210 5963

Emerging evidence indicates that gene expression in higher organisms is regulated by RNA polymerase II stalling during early transcription elongation. To probe the mechanisms responsible for this regulation, we developed methods to isolate and characterize short RNAs derived from stalled RNA polymerase II in Drosophila cells. Significant levels of these short RNAs were generated from more than one-third of all genes, indicating that promoter-proximal stalling is a general feature of early polyme ...[more]

PMID: 20007866

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