A pause sequence enriched at translation start sites drives transcription dynamics in vivo.
Transcription by RNA polymerase (RNAP) is interrupted by pauses that play diverse regulatory roles. Although individual pauses have been studied in vitro, the determinants of pauses in vivo and their distribution throughout the bacterial genome remain unknown. Using nascent transcript sequencing, we identified a 16-nucleotide consensus pause sequence in Escherichia coli that accounts for known regulatory pause sites as well as ~20,000 new in vivo pause sites. In vitro single-molecule and ensemble analyses demonstrate that these pauses result from RNAP-nucleic acid interactions that inhibit next-nucleotide addition. The consensus sequence also leads to pausing by RNAPs from diverse lineages and is enriched at translation start sites in both E. coli and Bacillus subtilis. Our results thus reveal a conserved mechanism unifying known and newly identified pause events.
Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
Matthew H
MH
Larson
Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
Rachel A
RA
Mooney
Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
Jason M
JM
Peters
Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
Tricia
T
Windgassen
Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
Dhananjaya
D
Nayak
Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
Carol A
CA
Gross
Department of Biological Sciences, Stanford University, Stanford, CA 94025, USA. Department of Applied Physics; Stanford University, Stanford, CA 94025, USA.
Steven M
SM
Block
Department of Genetics, Stanford University, Stanford, CA 94025, USA. wjg@stanford.edu landick@biochem.wisc.edu weissman@cmp.ucsf.edu.
William J
WJ
Greenleaf
Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA. Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA. wjg@stanford.edu landick@biochem.wisc.edu weissman@cmp.ucsf.edu.
Robert
R
Landick
Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA. wjg@stanford.edu landick@biochem.wisc.edu weissman@cmp.ucsf.edu.
Jonathan S
JS
Weissman
D001483:Base Sequence; D018387:Codon, Initiator / Q000235:genetics*; D016384:Consensus Sequence; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D010442:Peptide Chain Initiation, Translational / Q000235:genetics*; D050436:Regulatory Elements, Transcriptional; D014158:Transcription, Genetic
D018387:Codon, Initiator; D012321:DNA-Directed RNA Polymerases