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

• Published in: Molecular biology and evolution 2016-01, Vol.33 (1), p.185-200
• Main Authors: Muiño, Jose M, de Bruijn, Suzanne, Pajoro, Alice, Geuten, Koen, Vingron, Martin, Angenent, Gerco C, Kaufmann, Kerstin
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Arabidopsis; Arabidopsis Proteins - chemistry; Arabidopsis Proteins - genetics; Arabidopsis thaliana; Binding Sites - genetics; BIOS Plant Development Systems; Chromatin; Chromatin Immunoprecipitation; Comparative analysis; Conserved Sequence; Deoxyribonucleic acid; Discoveries; DNA; Evolution, Molecular; Flowers & plants; Gene expression; Gene Expression Profiling; Genotype & phenotype; Homeodomain Proteins - chemistry; Homeodomain Proteins - genetics; Laboratorium voor Moleculaire biologie; Laboratory of Molecular Biology; Molecular Sequence Data; Mutation; Plant species; PRI BIOS Plant Development Systems; Sequence Alignment; Transcription Factors - chemistry; Transcription Factors - genetics
• ISSN: 0737-4038; 1537-1719
• DOI: 10.1093/molbev/msv210

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.