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Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species

Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effec...

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Autores principales: Mateos, Julieta L., Tilmes, Vicky, Madrigal, Pedro, Severing, Edouard, Richter, René, Rijkenberg, Colin W. M., Krajewski, Paweł, Coupland, George
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5754749/
https://www.ncbi.nlm.nih.gov/pubmed/29203652
http://dx.doi.org/10.1073/pnas.1618075114
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author Mateos, Julieta L.
Tilmes, Vicky
Madrigal, Pedro
Severing, Edouard
Richter, René
Rijkenberg, Colin W. M.
Krajewski, Paweł
Coupland, George
author_facet Mateos, Julieta L.
Tilmes, Vicky
Madrigal, Pedro
Severing, Edouard
Richter, René
Rijkenberg, Colin W. M.
Krajewski, Paweł
Coupland, George
author_sort Mateos, Julieta L.
collection PubMed
description Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 14% of their BSs were conserved in both species and that these contained a CArG-box that is recognized by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared with the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets, and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated (COR) genes were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were usually different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared with WT, and this correlated with reduced growth in pep1-1. Therefore, FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.
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spelling pubmed-57547492018-01-08 Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species Mateos, Julieta L. Tilmes, Vicky Madrigal, Pedro Severing, Edouard Richter, René Rijkenberg, Colin W. M. Krajewski, Paweł Coupland, George Proc Natl Acad Sci U S A PNAS Plus Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 14% of their BSs were conserved in both species and that these contained a CArG-box that is recognized by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared with the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets, and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated (COR) genes were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were usually different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared with WT, and this correlated with reduced growth in pep1-1. Therefore, FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution. National Academy of Sciences 2017-12-19 2017-12-04 /pmc/articles/PMC5754749/ /pubmed/29203652 http://dx.doi.org/10.1073/pnas.1618075114 Text en Copyright © 2017 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/ This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle PNAS Plus
Mateos, Julieta L.
Tilmes, Vicky
Madrigal, Pedro
Severing, Edouard
Richter, René
Rijkenberg, Colin W. M.
Krajewski, Paweł
Coupland, George
Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species
title Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species
title_full Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species
title_fullStr Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species
title_full_unstemmed Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species
title_short Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species
title_sort divergence of regulatory networks governed by the orthologous transcription factors flc and pep1 in brassicaceae species
topic PNAS Plus
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5754749/
https://www.ncbi.nlm.nih.gov/pubmed/29203652
http://dx.doi.org/10.1073/pnas.1618075114
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