In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control

Motivation:Cold acclimation involves a number of different cellular processes that together increase the freezing tolerance of an organism. The DREB1/CBFs are transcription factors (TFs) that are prominent in the regulation of cold responses in Arabidopsis thaliana, rice and many other crops. We inv...

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Autores principales: Lindlöf, Angelica, Bräutigam, Marcus, Chawade, Aakash, Olsson, Olof, Olsson, Björn
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Discovery Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682518/
https://www.ncbi.nlm.nih.gov/pubmed/19321735
http://dx.doi.org/10.1093/bioinformatics/btp172
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author Lindlöf, Angelica
Bräutigam, Marcus
Chawade, Aakash
Olsson, Olof
Olsson, Björn
author_facet Lindlöf, Angelica
Bräutigam, Marcus
Chawade, Aakash
Olsson, Olof
Olsson, Björn
author_sort Lindlöf, Angelica
collection PubMed
description Motivation:Cold acclimation involves a number of different cellular processes that together increase the freezing tolerance of an organism. The DREB1/CBFs are transcription factors (TFs) that are prominent in the regulation of cold responses in Arabidopsis thaliana, rice and many other crops. We investigated if the expression of DREB1/CBFs and co-expressed genes relies on combinatorial control by several TFs. Our results support this notion and indicate that methods for studying the regulation of complex cellular processes should include identification of combinations of motifs, in addition to searching for individual overrepresented binding sites. Contact:angelica.lindlof@his.se Supplementary information:Supplementary data are available at Bioinformatics online.
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spelling pubmed-26825182009-05-15 In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control Lindlöf, Angelica Bräutigam, Marcus Chawade, Aakash Olsson, Olof Olsson, Björn Bioinformatics Discovery Note Motivation:Cold acclimation involves a number of different cellular processes that together increase the freezing tolerance of an organism. The DREB1/CBFs are transcription factors (TFs) that are prominent in the regulation of cold responses in Arabidopsis thaliana, rice and many other crops. We investigated if the expression of DREB1/CBFs and co-expressed genes relies on combinatorial control by several TFs. Our results support this notion and indicate that methods for studying the regulation of complex cellular processes should include identification of combinations of motifs, in addition to searching for individual overrepresented binding sites. Contact:angelica.lindlof@his.se Supplementary information:Supplementary data are available at Bioinformatics online. Oxford University Press 2009-06-01 2009-03-25 /pmc/articles/PMC2682518/ /pubmed/19321735 http://dx.doi.org/10.1093/bioinformatics/btp172 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Discovery Note
Lindlöf, Angelica
Bräutigam, Marcus
Chawade, Aakash
Olsson, Olof
Olsson, Björn
In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control
title In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control
title_full In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control
title_fullStr In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control
title_full_unstemmed In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control
title_short In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control
title_sort in silico analysis of promoter regions from cold-induced genes in rice (oryza sativa l.) and arabidopsis thaliana reveals the importance of combinatorial control
topic Discovery Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682518/
https://www.ncbi.nlm.nih.gov/pubmed/19321735
http://dx.doi.org/10.1093/bioinformatics/btp172
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