Abstract
BackgroundCorrect flower formation requires highly specific temporal and spatial regulation of gene expression. In Arabidopsis thaliana the majority of the master regulators that determine flower organ identity belong to the MADS-domain transcription factor family. The canonical DNA binding motif for this transcription factor family is the CArG-box, which has the consensus CC(A/T)6GG. However, so far, a comprehensive analysis of MADS-domain binding patterns has not yet been performed.ResultsEight publicly available ChIP-seq datasets of MADS-domain proteins that regulate the floral transition and flower formation were analyzed. Surprisingly, the preferred DNA binding motif of each protein was a CArG-box with an NAA extension. Furthermore, motifs of other transcription factors were found in the vicinity of binding sites of MADS-domain transcription factors, suggesting that interaction of MADS-domain proteins with other transcription factors is important for target gene regulation. Finally, conservation of CArG-boxes between Arabidopsis ecotypes was assessed to obtain information about their evolutionary importance. CArG-boxes that fully matched the consensus were more conserved than other CArG-boxes, suggesting that the perfect CArG-box is evolutionary more important than other CArG-box variants.ConclusionOur analysis provides detailed insight into MADS-domain protein binding patterns. The results underline the importance of an extended version of the CArG-box and provide a first view on evolutionary conservation of MADS-domain protein binding sites in Arabidopsis ecotypes.
Highlights
Correct flower formation requires highly specific temporal and spatial regulation of gene expression
A CArG-box like motif is enriched in all datasets Raw data from ChIP-seq experiments for AG [13], AP1 [15], AP3 [16], FLOWERING LOCUS C (FLC) [10], PI [16], SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) [9], SHORT VEGETATIVE PHASE (SVP) [10] and SEP3 [15] were re-analyzed
In this paper, several aspects of DNA binding by eight different MADS-domain proteins were analyzed by re-analyzing ChIP-seq data
Summary
Correct flower formation requires highly specific temporal and spatial regulation of gene expression. In Arabidopsis thaliana the majority of the master regulators that determine flower organ identity belong to the MADS-domain transcription factor family. A major part of this programming is regulated by a class of transcription factors called MADS-domain transcription factors Members of this transcription factor family play key roles in different aspects of development and have homologs in numerous other organisms in the plant, fungus and animal kingdom [1]. The much better characterized type II MADS-domain proteins have four domains in common; the MADS domain is involved in DNA binding, the intervening domain has a role in dimerization, the keratin-like domain, known as K-box, has a role in dimerization as well as in other protein-protein interactions, and the C-terminal domain has diverse functions, such as stabilizing protein complexes and activating transcription [2]
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