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

Lookup NU author(s): Dr Katherine James, Dr Simon Cockell, Professor Nikolay Zenkin

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This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND).


Abstract

© 2017 Elsevier Inc. 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.


Publication metadata

Author(s): James K, Cockell SJ, Zenkin N

Publication type: Article

Publication status: Published

Journal: Methods

Year: 2017

Volume: 120

Pages: 76-84

Print publication date: 01/05/2017

Online publication date: 21/04/2017

Acceptance date: 18/04/2017

Date deposited: 03/07/2017

ISSN (print): 1046-2023

ISSN (electronic): 1095-9130

Publisher: Academic Press Inc.

URL: http://doi.org/10.1016/j.ymeth.2017.04.016

DOI: 10.1016/j.ymeth.2017.04.016


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