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

Abstract

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.

Cultivar-specific gene modulation in Vitis vinifera: analysis of the promoters regulating the expression of WOX transcription factors

“…The relationship among these promoters is typical of a subdivision into evolutionary lineages previously reported for the WOX proteins in grapevine and other species: a modern clade (WUS, WOX1, 2, 3, 4, 5, 6, and 7) separated from an intermediate clade (WOX8, 9, 11, and 12) and an ancient clade (WOX10, 13, and 14)82034. These results showed that the evolutionary relations among different WOX proteins can also be conserved in promoter sequences, suggesting a parallel evolution between coding sequences and gene regulation35.…”

Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize

“…The previously defined binding site for DREB/CBF transcription factors, which are induced in response to drought and cold stress (Muiño et al, 2016), showed significant enrichment in the proximal promoters of gene pairs in the DE2 category, as well as significant purification in the proximal promoters of gene pairs in the DE0 category (Supplemental Figure 5). As transcription factors are often associated with larger quantities of conserved noncoding sequences (CNSs) (Freeling et al, 2007;Turco et al, 2013), we also investigated the number and quantity of conserved noncoding sequence associated with different classes of genes; however, no strong patterns were observed ( Figure 6D).…”

Floral Organogenesis: When Knowing Your ABCs Is Not Enough

“…These genes could provide the information necessary for establishing the basic blueprint for the different types of floral organs. While such studies have not yet been conducted systematically, the first steps in this direction have already been taken (Muiño et al, 2016) and will likely lead to much activity in this area in years to come.…”