Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics

James, Katherine, Cockell, Simon J. and Zenkin, Nikolay (2018) Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics. Methods, 120. pp. 76-84. ISSN 1046-2023

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Official URL: https://doi.org/10.1016/j.ymeth.2017.04.016

Abstract

The identification of the protein-coding regions of a genome is straightforward due to the universality of start and stop codons. However, the boundaries of the transcribed regions, conditional operon structures, non-coding RNAs and the dynamics of transcription, such as pausing of elongation, are non-trivial to identify, even in the comparatively simple genomes of prokaryotes. Traditional methods for the study of these areas, such as tiling arrays, are noisy, labour-intensive and lack the resolution required for densely-packed bacterial genomes. Recently, deep sequencing has become increasingly popular for the study of the transcriptome due to its lower costs, higher accuracy and single nucleotide resolution. These methods have revolutionised our understanding of prokaryotic transcriptional dynamics. Here, we review the deep sequencing and data analysis techniques that are available for the study of transcription in prokaryotes, and discuss the bioinformatic considerations of these analyses.

Item Type: Article
Additional Information: This work was supported by Grants from UK Biotechnology and Biological Sciences Research Council, Wellcome Trust and Leverhulme Trust to N.Z.
Uncontrolled Keywords: deep-sequencing, prokaryotic transcription, transcription start sites, transcription termination sites, transcriptional dynamics, bioinformatics
Subjects: C400 Genetics
C500 Microbiology
C700 Molecular Biology, Biophysics and Biochemistry
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: John Coen
Date Deposited: 09 Mar 2020 14:31
Last Modified: 09 Mar 2020 14:31
URI: http://nrl.northumbria.ac.uk/id/eprint/42421

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