Literature DB >> 21839669

Progress in prokaryotic transcriptomics.

Melanie J Filiatrault1.   

Abstract

Genome-wide expression studies transformed the field of transcriptomics and made it feasible to study global gene expression in extraordinary detail. These new methods have revealed an enhanced view of the transcriptional landscape and have yielded many biological insights. It is increasingly clear that the prokaryotic transcriptome is much more complex than once thought. Recent advances in microbial transcriptome analyses are highlighted in this review. Areas of progress include the development of optimized techniques that minimize the abundance of ribosomal RNAs in RNA samples as well as the development of novel methods to create transcriptome libraries. Advances such as these have led to a new emphasis in areas such as metatranscriptomics and single cell gene expression studies. Published by Elsevier Ltd.

Mesh:

Year:  2011        PMID: 21839669     DOI: 10.1016/j.mib.2011.07.023

Source DB:  PubMed          Journal:  Curr Opin Microbiol        ISSN: 1369-5274            Impact factor:   7.934


  16 in total

Review 1.  Dual RNA-seq of pathogen and host.

Authors:  Alexander J Westermann; Stanislaw A Gorski; Jörg Vogel
Journal:  Nat Rev Microbiol       Date:  2012-09       Impact factor: 60.633

2.  Comparative transcriptomic analysis reveals novel genes and regulatory mechanisms of Tetragenococcus halophilus in response to salt stress.

Authors:  Licui Liu; Lifang Si; Xin Meng; Lixin Luo
Journal:  J Ind Microbiol Biotechnol       Date:  2015-01-08       Impact factor: 3.346

3.  Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems.

Authors:  Noémie Pascault; Valentin Loux; Sandra Derozier; Véronique Martin; Didier Debroas; Selma Maloufi; Jean-François Humbert; Julie Leloup
Journal:  Genetica       Date:  2014-09-13       Impact factor: 1.082

Review 4.  Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation.

Authors:  Ondrej Uhlik; Mary-Cathrine Leewis; Michal Strejcek; Lucie Musilova; Martina Mackova; Mary Beth Leigh; Tomas Macek
Journal:  Biotechnol Adv       Date:  2012-09-26       Impact factor: 14.227

5.  Rapid and accurate identification of ribosomal RNA sequences via deep learning.

Authors:  Zhi-Luo Deng; Philipp C Münch; René Mreches; Alice C McHardy
Journal:  Nucleic Acids Res       Date:  2022-06-10       Impact factor: 19.160

6.  Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes.

Authors:  Yongliang Fan; J Will Thompson; Laura G Dubois; M Arthur Moseley; Jennifer J Wernegreen
Journal:  J Proteome Res       Date:  2012-12-27       Impact factor: 4.466

7.  Interactions between closely related bacterial strains are revealed by deep transcriptome sequencing.

Authors:  Pedro González-Torres; Leszek P Pryszcz; Fernando Santos; Manuel Martínez-García; Toni Gabaldón; Josefa Antón
Journal:  Appl Environ Microbiol       Date:  2015-10-02       Impact factor: 4.792

8.  Dual 3'Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells.

Authors:  Fabian Afonso-Grunz; Klaus Hoffmeier; Sören Müller; Alexander J Westermann; Björn Rotter; Jörg Vogel; Peter Winter; Günter Kahl
Journal:  BMC Genomics       Date:  2015-04-19       Impact factor: 3.969

9.  Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans.

Authors:  Lin Zeng; Sang Chul Choi; Charles G Danko; Adam Siepel; Michael J Stanhope; Robert A Burne
Journal:  PLoS One       Date:  2013-03-28       Impact factor: 3.240

10.  Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling.

Authors:  Shan Li; Xia Dong; Zhengchang Su
Journal:  BMC Genomics       Date:  2013-07-30       Impact factor: 3.969

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