Picot, Emma, Krusche, Peter, Tiskin, Alexander, Carré, Isabelle A. and Ott, Sascha (2010) Evolutionary analysis of regulatory sequences (EARS) in plants. Plant Journal, Vol.64 (No.1). pp. 165-176. doi:10.1111/j.1365-313X.2010.04314.x

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Abstract

Identification of regulatory sequences within non-coding regions of DNA is an essential step towards elucidation of gene networks. This approach constitutes a major challenge, however, as only a very small fraction of non-coding DNA is thought to contribute to gene regulation. The mapping of regulatory regions traditionally involves the laborious construction of promoter deletion series which are then fused to reporter genes and assayed in transgenic organisms. Bioinformatic methods can be used to scan sequences for matches for known regulatory motifs, however these methods are currently hampered by the relatively small amount of such motifs and by a high false-discovery rate. Here, we demonstrate a robust and highly sensitive, in silico method to identify evolutionarily conserved regions within non-coding DNA. Sequence conservation within these regions is taken as evidence for evolutionary pressure against mutations, which is suggestive of functional importance. We test this method on a small set of well characterised promoters, and show that it successfully identifies known regulatory regions. We further show that these evolutionarily conserved sequences contain clusters of transcription binding sites, often described as regulatory modules. A version of the tool optimised for the analysis of plant promoters is available online at http://wsbc.warwick.ac.uk/ears/main.php.

Item Type:	Journal Article
Subjects:	S Agriculture > SB Plant culture
Divisions:	Faculty of Science > Computer Science Faculty of Science > Life Sciences (2010- ) Faculty of Science > Centre for Systems Biology
Journal or Publication Title:	Plant Journal
Publisher:	Blackwell
ISSN:	0960-7412
Official Date:	October 2010
Dates:	Date Event October 2010 Published
Volume:	Vol.64
Number:	No.1
Number of Pages:	12
Page Range:	pp. 165-176
DOI:	10.1111/j.1365-313X.2010.04314.x
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Funder:	Royal Society (Great Britain), Leverhulme Trust (LT), Engineering and Physical Sciences Research Council (EPSRC), Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Research Councils United Kingdom (RCUK), University of Warwick. Centre for Discrete Mathematics and its Applications
Grant number:	BB/F022832/1 (BBSRC)

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