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Research ArticleLARGE-SCALE BIOLOGY ARTICLES
Open Access

Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants

Laura Baxter, Aleksey Jironkin, Richard Hickman, Jay Moore, Christopher Barrington, Peter Krusche, Nigel P. Dyer, Vicky Buchanan-Wollaston, Alexander Tiskin, Jim Beynon, Katherine Denby, Sascha Ott
Laura Baxter
aWarwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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Aleksey Jironkin
aWarwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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Richard Hickman
aWarwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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Jay Moore
aWarwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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Christopher Barrington
aWarwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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Peter Krusche
aWarwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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Nigel P. Dyer
bMolecular Organisation and Assembly in Cells Doctoral Training Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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Vicky Buchanan-Wollaston
aWarwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
cSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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Alexander Tiskin
dDepartment of Computer Science, University of Warwick, Coventry CV4 7AL, United Kingdom
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Jim Beynon
aWarwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
cSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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Katherine Denby
aWarwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
cSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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Sascha Ott
aWarwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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  • For correspondence: s.ott@warwick.ac.uk

Published October 2012. DOI: https://doi.org/10.1105/tpc.112.103010

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  • © 2012 American Society of Plant Biologists. All rights reserved.

Abstract

Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research.

  • Glossary

    TF
    transcription factor
    PSSM
    plant-specific position-specific scoring matrix
    TFBS
    transcription factor binding site
    CNS
    conserved noncoding sequence
    TSS
    transcription start site
    Mya
    million years ago
    GO
    Gene Ontology
    UTR
    untranslated region
    • Received July 18, 2012.
    • Revised September 10, 2012.
    • Accepted October 9, 2012.
    • Published October 30, 2012.

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    Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants
    Laura Baxter, Aleksey Jironkin, Richard Hickman, Jay Moore, Christopher Barrington, Peter Krusche, Nigel P. Dyer, Vicky Buchanan-Wollaston, Alexander Tiskin, Jim Beynon, Katherine Denby, Sascha Ott
    The Plant Cell Oct 2012, 24 (10) 3949-3965; DOI: 10.1105/tpc.112.103010

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    Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants
    Laura Baxter, Aleksey Jironkin, Richard Hickman, Jay Moore, Christopher Barrington, Peter Krusche, Nigel P. Dyer, Vicky Buchanan-Wollaston, Alexander Tiskin, Jim Beynon, Katherine Denby, Sascha Ott
    The Plant Cell Oct 2012, 24 (10) 3949-3965; DOI: 10.1105/tpc.112.103010
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    The Plant Cell Online: 24 (10)
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    Vol. 24, Issue 10
    Oct 2012
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