Where to begin? Mapping transcription start sites genome-wide in Escherichia coli.

Journal of bacteriology ·Vol. 197 ·No. 1 ·2015-01-01 ·Pages 4-6

Wade JT

Abstract

Recent genome-wide studies of bacterial transcription have revealed large numbers of promoters located inside genes. In this issue of the Journal of Bacteriology, Thomason and colleagues (J. Bacteriol. 197:18-28, 2015, doi:10.1128/JB.02096-14) map transcription start sites in Escherichia coli on an unprecedented scale. This work provides important insights into the regulation of transcripts that initiate inside genes and sources of variability between studies aimed at identifying these RNAs.

MeSH Terms

Escherichia coli/metabolism Gene Expression Regulation, Bacterial/physiology RNA, Antisense/metabolism RNA, Bacterial/metabolism Transcription Initiation Site/physiology

Chemicals

RNA, Antisense RNA, Bacterial

Authors & Affiliations

1 authors, click to expand affiliations / ORCID

Wade Joseph T

Wadsworth Center, New York State Department of Health, Albany, New York, USA Department of Biomedical Sciences, University at Albany, Albany, New York, USA joseph.wade@health.ny.gov.

References (19)

19 references, click to expand

Pervasive transcription: detecting functional RNAs in bacteria.
Transcription. 2014;5(4):e944039 PMID: 25483405
Regulatory RNAs in bacteria.
Cell. 2009 Feb 20;136(4):615-28 PMID: 19239884
Pervasive transcription: illuminating the dark matter of bacterial transcriptomes.
Nat Rev Microbiol. 2014 Sep;12(9):647-53 PMID: 25069631
Widespread antisense transcription in Escherichia coli.
mBio. 2010 May 18;1(1): PMID: 20689751
The double-stranded transcriptome of Escherichia coli.
Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3134-9 PMID: 24453212
Bacterial antisense RNAs: how many are there, and what are they doing?
Annu Rev Genet. 2010;44:167-88 PMID: 20707673
Antisense transcription is pervasive but rarely conserved in enteric bacteria.
mBio. 2012 Aug 07;3(4): PMID: 22872780
Conservation of transcription start sites within genes across a bacterial genus.
mBio. 2014 Jul 01;5(4):e01398-14 PMID: 24987095
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli.
BMC Genomics. 2011 Aug 24;12:428 PMID: 21864382
Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation.
RNA Biol. 2014;11(5):641-54 PMID: 24922322
The primary transcriptome of the major human pathogen Helicobacter pylori.
Nature. 2010 Mar 11;464(7286):250-5 PMID: 20164839
RNA expression analysis using a 30 base pair resolution Escherichia coli genome array.
Nat Biotechnol. 2000 Dec;18(12):1262-8 PMID: 11101804
cis-antisense RNA, another level of gene regulation in bacteria.
Microbiol Mol Biol Rev. 2011 Jun;75(2):286-300 PMID: 21646430
Dark Matter RNA: Existence, Function, and Controversy.
Front Genet. 2012 Apr 23;3:60 PMID: 22536205
Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli.
J Bacteriol. 2015 Jan 1;197(1):18-28 PMID: 25266388
MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein.
Genes Dev. 2014 Jul 15;28(14):1620-34 PMID: 25030700
Rho and NusG suppress pervasive antisense transcription in Escherichia coli.
Genes Dev. 2012 Dec 1;26(23):2621-33 PMID: 23207917
Genome-wide antisense transcription drives mRNA processing in bacteria.
Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20172-7 PMID: 22123973
Widespread suppression of intragenic transcription initiation by H-NS.
Genes Dev. 2014 Feb 1;28(3):214-9 PMID: 24449106

Article Info

Journal

Journal of bacteriology

Abbr.

J Bacteriol

ISSN

1098-5530

DOI

10.1128/JB.02410-14

joseph.wade@health.ny.gov

Published

2015-01-01

Epub

2014-00-20

Pages

4-6

Language

English

Region

United States

NLM ID

2985120R

PMCID

PMC4288686

Subset

Corrections

CommentOn

PMID: 25266388

External Links

PubMed source DOI: 10.1128/JB.02410-14 PMC Full Text View journal details

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Where to begin? Mapping transcription start sites genome-wide in Escherichia coli.

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