» Articles » PMID: 19935729

Prokaryotic Transcriptomics: a New View on Regulation, Physiology and Pathogenicity

Overview
Journal Nat Rev Genet
Specialty Genetics
Date 2009 Nov 26
PMID 19935729
Citations 188
Authors
Affiliations
Soon will be listed here.
Abstract

Transcriptome-wide studies in eukaryotes have been instrumental in the characterization of fundamental regulatory mechanisms for more than a decade. By contrast, in prokaryotes (bacteria and archaea) whole-transcriptome studies have not been performed until recently owing to the general view that microbial gene structures are simple, as well as technical difficulties in enriching for mRNAs that lack poly(A) tails. Deep RNA sequencing and tiling array studies are now revolutionizing our understanding of the complexity, plasticity and regulation of microbial transcriptomes.

Citing Articles

The Effects of Milk and Posterior Intestinal Microorganisms on the Lactation Performance of Dual-Purpose Cattle () Revealed by 16S rRNA Sequencing.

Wang W, Ma S, Wang D, Xu L, Zhang M, Yan M Microorganisms. 2025; 13(2).

PMID: 40005814 PMC: 11857882. DOI: 10.3390/microorganisms13020448.


TSS-Captur: a user-friendly pipeline for characterizing unclassified RNA transcripts.

Witte Paz M, Vogel T, Nieselt K NAR Genom Bioinform. 2024; 6(4):lqae168.

PMID: 39703424 PMC: 11655288. DOI: 10.1093/nargab/lqae168.


Exploring the transcription start sites and other genomic features facilitates the accurate identification and annotation of small RNAs across multiple stress conditions in Mycobacterium tuberculosis.

Cheah H, Citartan M, Lee L, Ahmed S, Salleh M, Teh L Funct Integr Genomics. 2024; 24(5):160.

PMID: 39264475 DOI: 10.1007/s10142-024-01437-5.


Patterns of methylation and transcriptional plasticity during thermal acclimation in a reef-building coral.

Guerrero L, Bay R Evol Appl. 2024; 17(7):e13757.

PMID: 39027686 PMC: 11254580. DOI: 10.1111/eva.13757.


An improved bacterial mRNA enrichment strategy in dual RNA sequencing to unveil the dynamics of plant-bacterial interactions.

Shilpha J, Lee J, Kwon J, Lee H, Nam J, Jang H Plant Methods. 2024; 20(1):99.

PMID: 38951818 PMC: 11218159. DOI: 10.1186/s13007-024-01227-x.


References
1.
Koide T, Reiss D, Bare J, Pang W, Facciotti M, Schmid A . Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol. 2009; 5:285. PMC: 2710873. DOI: 10.1038/msb.2009.42. View

2.
Waters L, Storz G . Regulatory RNAs in bacteria. Cell. 2009; 136(4):615-28. PMC: 3132550. DOI: 10.1016/j.cell.2009.01.043. View

3.
Strausberg R, Riggins G . Navigating the human transcriptome. Proc Natl Acad Sci U S A. 2001; 98(21):11837-8. PMC: 59724. DOI: 10.1073/pnas.221463598. View

4.
Frias-Lopez J, Shi Y, Tyson G, Coleman M, Schuster S, Chisholm S . Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A. 2008; 105(10):3805-10. PMC: 2268829. DOI: 10.1073/pnas.0708897105. View

5.
Pace N . A molecular view of microbial diversity and the biosphere. Science. 1997; 276(5313):734-40. DOI: 10.1126/science.276.5313.734. View