PortEco logo

PMID:23899370

From EcoliWiki
Jump to: navigation, search

Contents

Citation

Li, S, Dong, X and Su, Z (2013) Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics 14:520

Abstract

Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamically transcribed under different conditions, and a large portion of genes and intergenic regions have antisense RNA (asRNA) and non-coding RNA (ncRNA) transcripts, respectively. Ironically, similar studies have not been conducted in the model bacterium E coli K12, thus it is unknown whether or not the bacterium possesses similar complex transcriptomes. Furthermore, although RNA-seq becomes the major method for analyzing the complexity of prokaryotic transcriptome, it is still a challenging task to accurately assemble full length transcripts using short RNA-seq reads.

Links

PubMed PMC3734233 Online version:10.1186/1471-2164-14-520

Keywords

Algorithms; Escherichia coli/genetics; Genes, Bacterial; RNA, Messenger/genetics; Sequence Analysis, RNA; Transcriptome

Significance

You can help EcoliWiki by summarizing why this paper is useful

Useful Materials and Methods

You can help Ecoliwiki by describing the useful materials (strains, plasmids, antibodies, etc) described in this paper.

Data

Strain/Organism Assay Analyte Variable Conditions Notes Links

MG1655

RNA-seq

total RNA

Heat shock

MG1655

RNA-seq

total RNA

phosphorus starvation


Annotations

Gene product Qualifier GO ID GO term name Evidence Code with/from Aspect Notes Status

EcoliWiki Links

Add links to pages that link here (e.g. gene, product, method pages)

See also

References

See Help:References for how to manage references in EcoliWiki.