Transcriptomics

Dataset Information

303

Nascent elongating transcript sequencing (NET-seq) for Escherichia coli and Bacillus subtilis reveals a consensus pause sequence enriched at translation start sites.


ABSTRACT: 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 identify a 16 nt consensus pause sequence in E. 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 B. subtilis. Our results thus implicate a conserved mechanism unifying known and newly identified pause events. Examination of nascent transcripts in E. coli and B. subtilis. 6 samples of E. coli NET-seq, 1 sample of E. coli mRNA-seq, and 1 sample of B. subtilis NET-seq.

SUBMITTER: J S Weissman   J M Peters  C A Gross  W J Greenleaf  R Landick  Matthew H Larson  S M Block  M H Larson  R A Mooney  D Nayak  T Windgassen 

PROVIDER: E-GEOD-56720 | ArrayExpress | 2014-05-05

SECONDARY ACCESSION(S): GSE56720SRP041112PRJNA244362

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

A pause sequence enriched at translation start sites drives transcription dynamics in vivo.

Larson Matthew H MH   Mooney Rachel A RA   Peters Jason M JM   Windgassen Tricia T   Nayak Dhananjaya D   Gross Carol A CA   Block Steven M SM   Greenleaf William J WJ   Landick Robert R   Weissman Jonathan S JS  

Science (New York, N.Y.) 20140501 6187


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 ensembl  ...[more]

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