Open Access
Nucleic Acids Research, volume 42, issue 21, pages 13254-13268
Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium
Mazin Pavel
1
,
Fisunov Gleb Yu.
2
,
Gorbachev Alexey
2
,
Kapitskaya Kristina Y
3
,
Altukhov Ilya
3
,
Semashko Tatiana
2
,
Alexeev Dmitry
,
Govorun Vadim M.
Publication type: Journal Article
Publication date: 2014-10-31
Journal:
Nucleic Acids Research
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 14.9
ISSN: 03051048, 13624962
PubMed ID:
25361977
Genetics
Abstract
The avian bacterial pathogen Mycoplasma gallisepticum is a good model for systems studies due to small genome and simplicity of regulatory pathways. In this study, we used RNA-Seq and MS-based proteomics to accurately map coding sequences, transcription start sites (TSSs) and transcript 3′-ends (T3Es). We used obtained data to investigate roles of TSSs and T3Es in stress-induced transcriptional responses. We identified 1061 TSSs at a false discovery rate of 10% and showed that almost all transcription in M. gallisepticum is initiated from classic TATAAT promoters surrounded by A/T-rich sequences. Our analysis revealed the pronounced operon structure complexity: on average, each coding operon has one internal TSS and T3Es in addition to the primary ones. Our transcriptomic approach based on the intervals between the two nearest transcript ends allowed us to identify two classes of T3Es: strong, unregulated, hairpin-containing T3Es and weak, heat shock-regulated, hairpinless T3Es. Comparing gene expression levels under different conditions revealed widespread and divergent transcription regulation in M. gallisepticum. Modeling suggested that the core promoter structure plays an important role in gene expression regulation. We have shown that the heat stress activation of cryptic promoters combined with the hairpinless T3Es suppression leads to widespread, seemingly non-functional transcription.
Citations by journals
Citations by publishers
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10
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Elsevier
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10 publications, 26.32%
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Springer Nature
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7 publications, 18.42%
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Frontiers Media S.A.
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6 publications, 15.79%
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American Society for Microbiology
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3 publications, 7.89%
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Multidisciplinary Digital Publishing Institute (MDPI)
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2 publications, 5.26%
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Public Library of Science (PLoS)
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2 publications, 5.26%
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Wiley
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Wiley
2 publications, 5.26%
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Microbiology Society
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1 publication, 2.63%
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Pleiades Publishing
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Pleiades Publishing
1 publication, 2.63%
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Oxford University Press
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Oxford University Press
1 publication, 2.63%
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Cold Spring Harbor Laboratory
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Cold Spring Harbor Laboratory
1 publication, 2.63%
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Research Square Platform LLC
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Research Square Platform LLC, 1, 2.63%
Research Square Platform LLC
1 publication, 2.63%
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2
4
6
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10
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Mazin P. et al. Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium // Nucleic Acids Research. 2014. Vol. 42. No. 21. pp. 13254-13268.
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Mazin P., Fisunov G. Y., Gorbachev A., Kapitskaya K. Y., Altukhov I., Semashko T., Alexeev D., Govorun V. M. Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium // Nucleic Acids Research. 2014. Vol. 42. No. 21. pp. 13254-13268.
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TY - JOUR
DO - 10.1093/nar/gku976
UR - https://doi.org/10.1093%2Fnar%2Fgku976
TI - Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium
T2 - Nucleic Acids Research
AU - Mazin, Pavel
AU - Fisunov, Gleb Yu.
AU - Gorbachev, Alexey
AU - Kapitskaya, Kristina Y
AU - Altukhov, Ilya
AU - Semashko, Tatiana
AU - Alexeev, Dmitry
AU - Govorun, Vadim M.
PY - 2014
DA - 2014/10/31 00:00:00
PB - Oxford University Press
SP - 13254-13268
IS - 21
VL - 42
PMID - 25361977
SN - 0305-1048
SN - 1362-4962
ER -
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@article{2014_Mazin,
author = {Pavel Mazin and Gleb Yu. Fisunov and Alexey Gorbachev and Kristina Y Kapitskaya and Ilya Altukhov and Tatiana Semashko and Dmitry Alexeev and Vadim M. Govorun},
title = {Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium},
journal = {Nucleic Acids Research},
year = {2014},
volume = {42},
publisher = {Oxford University Press},
month = {oct},
url = {https://doi.org/10.1093%2Fnar%2Fgku976},
number = {21},
pages = {13254--13268},
doi = {10.1093/nar/gku976}
}
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MLA
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Mazin, Pavel, et al. “Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium.” Nucleic Acids Research, vol. 42, no. 21, Oct. 2014, pp. 13254-13268. https://doi.org/10.1093%2Fnar%2Fgku976.
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