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Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor

Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understoo...

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Autores principales: Muiño, Jose M., de Bruijn, Suzanne, Pajoro, Alice, Geuten, Koen, Vingron, Martin, Angenent, Gerco C., Kaufmann, Kerstin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4693976/
https://www.ncbi.nlm.nih.gov/pubmed/26429922
http://dx.doi.org/10.1093/molbev/msv210
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author Muiño, Jose M.
de Bruijn, Suzanne
Pajoro, Alice
Geuten, Koen
Vingron, Martin
Angenent, Gerco C.
Kaufmann, Kerstin
author_facet Muiño, Jose M.
de Bruijn, Suzanne
Pajoro, Alice
Geuten, Koen
Vingron, Martin
Angenent, Gerco C.
Kaufmann, Kerstin
author_sort Muiño, Jose M.
collection PubMed
description Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon.
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spelling pubmed-46939762016-01-04 Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor Muiño, Jose M. de Bruijn, Suzanne Pajoro, Alice Geuten, Koen Vingron, Martin Angenent, Gerco C. Kaufmann, Kerstin Mol Biol Evol Discoveries Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon. Oxford University Press 2016-01 2015-10-01 /pmc/articles/PMC4693976/ /pubmed/26429922 http://dx.doi.org/10.1093/molbev/msv210 Text en © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Discoveries
Muiño, Jose M.
de Bruijn, Suzanne
Pajoro, Alice
Geuten, Koen
Vingron, Martin
Angenent, Gerco C.
Kaufmann, Kerstin
Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor
title Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor
title_full Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor
title_fullStr Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor
title_full_unstemmed Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor
title_short Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor
title_sort evolution of dna-binding sites of a floral master regulatory transcription factor
topic Discoveries
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4693976/
https://www.ncbi.nlm.nih.gov/pubmed/26429922
http://dx.doi.org/10.1093/molbev/msv210
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