Literature DB >> 21460078

Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli.

Rahul Raghavan1, Alan Sage, Howard Ochman.   

Abstract

Intergenic regions often contain regulatory elements that control the expression of flanking genes. Using a deep-sequencing approach, we identified numerous new transcription start sites in Escherichia coli, yielding a new thermosensing regulatory RNA and seven genes previously unknown to be under the control of the global regulator CRP.

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Year:  2011        PMID： 21460078      PMCID： PMC3133129          DOI： 10.1128/JB.00398-11

Source DB:  PubMed          Journal:  J Bacteriol        ISSN： 0021-9193            Impact factor:   3.490


  21 in total

1.  EcoGene: a genome sequence database for Escherichia coli K-12.

Authors:  K E Rudd
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.

Authors:  X Liu; D L Brutlag; J S Liu
Journal:  Pac Symp Biocomput       Date:  2001

3.  Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals.

Authors:  Araceli M Huerta; Julio Collado-Vides
Journal:  J Mol Biol       Date:  2003-10-17       Impact factor: 5.469

4.  Mfold web server for nucleic acid folding and hybridization prediction.

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Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

5.  The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA.

Authors:  Anna Maria Giuliodori; Fabio Di Pietro; Stefano Marzi; Benoit Masquida; Rolf Wagner; Pascale Romby; Claudio O Gualerzi; Cynthia L Pon
Journal:  Mol Cell       Date:  2010-01-15       Impact factor: 17.970

6.  Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity.

Authors:  M E Mulligan; D K Hawley; R Entriken; W R McClure
Journal:  Nucleic Acids Res       Date:  1984-01-11       Impact factor: 16.971

7.  RNA switches out in the cold.

Authors:  Ronald R Breaker
Journal:  Mol Cell       Date:  2010-01-15       Impact factor: 17.970

8.  Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site.

Authors:  R H Ebright; Y W Ebright; A Gunasekera
Journal:  Nucleic Acids Res       Date:  1989-12-25       Impact factor: 16.971

9.  Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays.

Authors:  Brian Tjaden; Rini Mukherjee Saxena; Sergey Stolyar; David R Haynor; Eugene Kolker; Carsten Rosenow
Journal:  Nucleic Acids Res       Date:  2002-09-01       Impact factor: 16.971

10.  Changes in Escherichia coli transcriptome during acclimatization at low temperature.

Authors:  Alessandra Polissi; Walter De Laurentis; Sandro Zangrossi; Federica Briani; Vera Longhi; Graziano Pesole; Gianni Dehò
Journal:  Res Microbiol       Date:  2003-10       Impact factor: 3.992
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  15 in total

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Authors:  Rahul Raghavan; Yogeshwar D Kelkar; Howard Ochman
Journal:  Proc Natl Acad Sci U S A       Date:  2012-08-20       Impact factor: 11.205

Review 2.  Recent molecular insights into rickettsial pathogenesis and immunity.

Authors:  Sanjeev K Sahni; Hema P Narra; Abha Sahni; David H Walker
Journal:  Future Microbiol       Date:  2013-10       Impact factor: 3.165

3.  Adenylate cyclase and the cyclic AMP receptor protein modulate stress resistance and virulence capacity of uropathogenic Escherichia coli.

Authors:  Grant T Donovan; J Paul Norton; Jean M Bower; Matthew A Mulvey
Journal:  Infect Immun       Date:  2012-10-31       Impact factor: 3.441

4.  Intracellular concentrations of 65 species of transcription factors with known regulatory functions in Escherichia coli.

Authors:  Akira Ishihama; Ayako Kori; Etsuko Koshio; Kayoko Yamada; Hiroto Maeda; Tomohiro Shimada; Hideki Makinoshima; Akira Iwata; Nobuyuki Fujita
Journal:  J Bacteriol       Date:  2014-05-16       Impact factor: 3.490

5.  Antisense transcription is pervasive but rarely conserved in enteric bacteria.

Authors:  Rahul Raghavan; Daniel B Sloan; Howard Ochman
Journal:  MBio       Date:  2012-08-07       Impact factor: 7.867

6.  How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

Authors:  Brian J Haas; Melissa Chin; Chad Nusbaum; Bruce W Birren; Jonathan Livny
Journal:  BMC Genomics       Date:  2012-12-27       Impact factor: 3.969

7.  Genome rearrangements can make and break small RNA genes.

Authors:  Rahul Raghavan; Fenil R Kacharia; Jess A Millar; Christine D Sislak; Howard Ochman
Journal:  Genome Biol Evol       Date:  2015-01-18       Impact factor: 3.416

8.  Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12.

Authors:  Brian P Anton; Emmanuel F Mongodin; Sonia Agrawal; Alexey Fomenkov; Devon R Byrd; Richard J Roberts; Elisabeth A Raleigh
Journal:  PLoS One       Date:  2015-05-26       Impact factor: 3.240

9.  Novel Functions and Regulation of Cryptic Cellobiose Operons in Escherichia coli.

Authors:  Vinuselvi Parisutham; Sung Kuk Lee
Journal:  PLoS One       Date:  2015-06-29       Impact factor: 3.240

10.  Evidence classification of high-throughput protocols and confidence integration in RegulonDB.

Authors:  Verena Weiss; Alejandra Medina-Rivera; Araceli M Huerta; Alberto Santos-Zavaleta; Heladia Salgado; Enrique Morett; Julio Collado-Vides
Journal:  Database (Oxford)       Date:  2013-01-17       Impact factor: 3.451
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