Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq]
Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. However, until now, the evolutionary turnover and dynamics of TF binding sites among plant species has not yet experimentally determined. Here, we performed comparative ChIP-seq studies of the MADS-box TF SEPALLATA3 (SEP3) in inflorescences of two Arabidopsis species: A. thaliana and A. lyrata. Comparative RNA-seq analysis shows that the loss/gain of BSs is often followed by a change in gene expression. RNA-seq libraries were generated from 3 tissues: A. lyrata leaves, A. lyrata inflorescences, and A.thaliana inflorescences. 3 biological replicates were sequenced.
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Wageningen University & Research
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Subjects: | Arabidopsis lyrata, Arabidopsis thaliana, |
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dig-wur-nl-wurpubs-5204322024-09-23 Muiño, J.M. de Bruijn, S.A. Vingron, Martin Angenent, G.C. Kaufmann, Kerstin Dataset Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq] 2015 Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. However, until now, the evolutionary turnover and dynamics of TF binding sites among plant species has not yet experimentally determined. Here, we performed comparative ChIP-seq studies of the MADS-box TF SEPALLATA3 (SEP3) in inflorescences of two Arabidopsis species: A. thaliana and A. lyrata. Comparative RNA-seq analysis shows that the loss/gain of BSs is often followed by a change in gene expression. RNA-seq libraries were generated from 3 tissues: A. lyrata leaves, A. lyrata inflorescences, and A.thaliana inflorescences. 3 biological replicates were sequenced. Wageningen University & Research text/html https://research.wur.nl/en/datasets/evolutionary-dynamics-of-dna-binding-sites-and-direct-target-gene-3 https://edepot.wur.nl/415275 Arabidopsis lyrata Arabidopsis thaliana Wageningen University & Research |
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Arabidopsis lyrata Arabidopsis thaliana Arabidopsis lyrata Arabidopsis thaliana Muiño, J.M. de Bruijn, S.A. Vingron, Martin Angenent, G.C. Kaufmann, Kerstin Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq] |
description |
Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. However, until now, the evolutionary turnover and dynamics of TF binding sites among plant species has not yet experimentally determined. Here, we performed comparative ChIP-seq studies of the MADS-box TF SEPALLATA3 (SEP3) in inflorescences of two Arabidopsis species: A. thaliana and A. lyrata. Comparative RNA-seq analysis shows that the loss/gain of BSs is often followed by a change in gene expression. RNA-seq libraries were generated from 3 tissues: A. lyrata leaves, A. lyrata inflorescences, and A.thaliana inflorescences. 3 biological replicates were sequenced. |
format |
Dataset |
topic_facet |
Arabidopsis lyrata Arabidopsis thaliana |
author |
Muiño, J.M. de Bruijn, S.A. Vingron, Martin Angenent, G.C. Kaufmann, Kerstin |
author_facet |
Muiño, J.M. de Bruijn, S.A. Vingron, Martin Angenent, G.C. Kaufmann, Kerstin |
author_sort |
Muiño, J.M. |
title |
Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq] |
title_short |
Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq] |
title_full |
Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq] |
title_fullStr |
Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq] |
title_full_unstemmed |
Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq] |
title_sort |
evolutionary dynamics of dna-binding sites and direct target genes of a floral master regulatory transcription factor [rna-seq] |
publisher |
Wageningen University & Research |
url |
https://research.wur.nl/en/datasets/evolutionary-dynamics-of-dna-binding-sites-and-direct-target-gene-3 |
work_keys_str_mv |
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1813201175532535808 |