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

Science. 2010 Jan 15;327(5963):335-8. doi: 10.1126/science.1181421. Epub 2009 Dec 10.


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 polymerase elongation. Nucleotide composition of the initially transcribed sequence played an important role in promoting transcriptional stalling by rendering polymerase elongation complexes highly susceptible to backtracking and arrest. These results indicate that the intrinsic efficiency of early elongation can greatly affect gene expression.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Animals
  • Base Composition
  • Cell Line
  • Drosophila melanogaster
  • Gene Expression Regulation*
  • Genes, Insect*
  • Genome, Insect
  • Oligonucleotide Array Sequence Analysis
  • Promoter Regions, Genetic*
  • RNA / genetics
  • RNA / metabolism*
  • RNA Caps / genetics
  • RNA Caps / metabolism
  • RNA Polymerase II / metabolism*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Transcription Initiation Site
  • Transcription, Genetic*


  • RNA Caps
  • RNA, Messenger
  • RNA
  • RNA Polymerase II

Associated data

  • GEO/GSE18643