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

doi:10.1105/tpc.112.103010

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^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	3949-3965
Number of pages	17
Journal	The Plant Cell
Volume	24
Issue number	10
DOIs	https://doi.org/10.1105/tpc.112.103010
Publication status	Published - Oct 2012

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title = "Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants",

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.",

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AU - Baxter, Laura

AU - Jironkin, Aleksey

AU - Hickman, Richard

AU - Moore, Jay

AU - Barrington, Christopher

AU - Krusche, Peter

AU - Dyer, Nigel P.

AU - Buchanan-Wollaston, Vicky

AU - Tiskin, Alexander

AU - Beynon, Jim

AU - Denby, Katherine

AU - Ott, Sascha

PY - 2012/10

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AB - 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.

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Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants

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