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Effect of genomic distance on coexpression of coregulated genes in E. coli

Lucia Pannier, Enrique Merino, Kathleen Marchal UGent and Julio Collado-Vides (2017) PLOS ONE. 12(4).
abstract
In prokaryotes, genomic distance is a feature that in addition to coregulation affects coexpression. Several observations, such as genomic clustering of highly coexpressed small regulons, support the idea that coexpression behavior of coregulated genes is affected by the distance between the coregulated genes. However, the specific contribution of distance in addition to coregulation in determining the degree of coexpression has not yet been studied systematically. In this work, we exploit the rich information in RegulonDB to study how the genomic distance between coregulated genes affects their degree of coexpression, measured by pairwise similarity of expression profiles obtained under a large number of conditions. We observed that, in general, coregulated genes display higher degrees of coexpression as they are more closely located on the genome. This contribution of genomic distance in determining the degree of coexpression was relatively small compared to the degree of coexpression that was determined by the tightness of the coregulation (degree of overlap of regulatory programs) but was shown to be evolutionary constrained. In addition, the distance effect was sufficient to guarantee coexpression of coregulated genes that are located at very short distances, irrespective of their tightness of coregulation. This is partly but definitely not always because the close distance is also the cause of the coregulation. In cases where it is not, we hypothesize that the effect of the distance on coexpression could be caused by the fact that coregulated genes closely located to each other are also relatively more equidistantly located from their common TF and therefore subject to more similar levels of TF molecules. The absolute genomic distance of the coregulated genes to their common TF-coding gene tends to be less important in determining the degree of coexpression. Our results pinpoint the importance of taking into account the combined effect of distance and coregulation when studying prokaryotic coexpression and transcriptional regulation.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
TRANSCRIPTIONAL REGULATORY NETWORKS, NUCLEOID-ASSOCIATED PROTEINS, ESCHERICHIA-COLI, DIVERGENT PROMOTERS, EXPRESSION, OPERON, ORGANIZATION, EVOLUTION, DATABASE, CONTEXT
journal title
PLOS ONE
PLoS One
volume
12
issue
4
article number
e0174887
pages
20 pages
Web of Science type
Article
Web of Science id
000399875200005
ISSN
1932-6203
DOI
10.1371/journal.pone.0174887
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
8526797
handle
http://hdl.handle.net/1854/LU-8526797
date created
2017-07-12 07:45:00
date last changed
2017-08-10 11:03:14
@article{8526797,
  abstract     = {In prokaryotes, genomic distance is a feature that in addition to coregulation affects coexpression. Several observations, such as genomic clustering of highly coexpressed small regulons, support the idea that coexpression behavior of coregulated genes is affected by the distance between the coregulated genes. However, the specific contribution of distance in addition to coregulation in determining the degree of coexpression has not yet been studied systematically. In this work, we exploit the rich information in RegulonDB to study how the genomic distance between coregulated genes affects their degree of coexpression, measured by pairwise similarity of expression profiles obtained under a large number of conditions. We observed that, in general, coregulated genes display higher degrees of coexpression as they are more closely located on the genome. This contribution of genomic distance in determining the degree of coexpression was relatively small compared to the degree of coexpression that was determined by the tightness of the coregulation (degree of overlap of regulatory programs) but was shown to be evolutionary constrained. In addition, the distance effect was sufficient to guarantee coexpression of coregulated genes that are located at very short distances, irrespective of their tightness of coregulation. This is partly but definitely not always because the close distance is also the cause of the coregulation. In cases where it is not, we hypothesize that the effect of the distance on coexpression could be caused by the fact that coregulated genes closely located to each other are also relatively more equidistantly located from their common TF and therefore subject to more similar levels of TF molecules. The absolute genomic distance of the coregulated genes to their common TF-coding gene tends to be less important in determining the degree of coexpression. Our results pinpoint the importance of taking into account the combined effect of distance and coregulation when studying prokaryotic coexpression and transcriptional regulation.},
  articleno    = {e0174887},
  author       = {Pannier, Lucia and Merino, Enrique and Marchal, Kathleen and Collado-Vides, Julio},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  keyword      = {TRANSCRIPTIONAL REGULATORY NETWORKS,NUCLEOID-ASSOCIATED PROTEINS,ESCHERICHIA-COLI,DIVERGENT PROMOTERS,EXPRESSION,OPERON,ORGANIZATION,EVOLUTION,DATABASE,CONTEXT},
  language     = {eng},
  number       = {4},
  pages        = {20},
  title        = {Effect of genomic distance on coexpression of coregulated genes in E. coli},
  url          = {http://dx.doi.org/10.1371/journal.pone.0174887},
  volume       = {12},
  year         = {2017},
}

Chicago
Pannier, Lucia, Enrique Merino, Kathleen Marchal, and Julio Collado-Vides. 2017. “Effect of Genomic Distance on Coexpression of Coregulated Genes in E. Coli.” Plos One 12 (4).
APA
Pannier, L., Merino, E., Marchal, K., & Collado-Vides, J. (2017). Effect of genomic distance on coexpression of coregulated genes in E. coli. PLOS ONE, 12(4).
Vancouver
1.
Pannier L, Merino E, Marchal K, Collado-Vides J. Effect of genomic distance on coexpression of coregulated genes in E. coli. PLOS ONE. 2017;12(4).
MLA
Pannier, Lucia, Enrique Merino, Kathleen Marchal, et al. “Effect of Genomic Distance on Coexpression of Coregulated Genes in E. Coli.” PLOS ONE 12.4 (2017): n. pag. Print.