E-GEOD-56720 - Nascent elongating transcript sequencing (NET-seq) for Escherichia coli and Bacillus subtilis reveals a consensus pause sequence enriched at translation start sites

Released on 5 May 2014, last updated on 13 August 2014
Bacillus subtilis, Escherichia coli
Samples (8)
Protocols (9)
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.
Experiment types
other, RNA-seq of coding RNA 
Matthew H Larson <matthew.larson@ucsf.edu>, C A Gross, D Nayak, J M Peters, J S Weissman, M H Larson, R A Mooney, R Landick, S M Block, T Windgassen, W J Greenleaf
A pause sequence enriched at translation start sites drives transcription dynamics in vivo. Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D, Gross CA, Block SM, Greenleaf WJ, Landick R, Weissman JS. , Europe PMC 24789973
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-56720.idf.txt
Sample and data relationshipE-GEOD-56720.sdrf.txt
Processed data (1)E-GEOD-56720.processed.1.zip