title: Structural determinants of DNA recognition by plant MADS-domain transcription factors.
abstract: Plant MADS-domain transcription factors act as key regulators of many developmental processes. Despite the wealth of information that exists about these factors, the mechanisms by which they recognize their cognate DNA-binding site, called CArG-box (consensus CCW6GG), and how different MADS-domain proteins achieve DNA-binding specificity, are still largely unknown. We used information from in vivo ChIP-seq experiments, in vitro DNA-binding data and evolutionary conservation to address these important questions. We found that structural characteristics of the DNA play an important role in the DNA binding of plant MADS-domain proteins. The central region of the CArG-box largely resembles a structural motif called 'A-tract', which is characterized by a narrow minor groove and may assist bending of the DNA by MADS-domain proteins. Periodically spaced A-tracts outside the CArG-box suggest additional roles for this structure in the process of DNA binding of these transcription factors. Structural characteristics of the CArG-box not only play an important role in DNA-binding site recognition of MADS-domain proteins, but also partly explain differences in DNA-binding specificity of different members of this transcription factor family and their heteromeric complexes.
authors.affiliation: Bioscience, Plant Research International, Wageningen, PO Box 619, 6700 AP, The Netherlands, Laboratory of Bioinformatics, Wageningen University, PO Box 569, 6700 AN Wageningen, The Netherlands, Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany, Laboratory of Molecular Biology, Wageningen University, Wageningen, PO Box 633, 6700 AP, The Netherlands and Biometris, Wageningen University and Research Centre, Wageningen, PO Box 100, 6700 AC, The Netherlands.
authors.forename: Jose M
authors.initials: JM
authors.lastname: Muiño
authors.forename: Cezary
authors.initials: C
authors.lastname: Smaczniak
authors.forename: Gerco C
authors.initials: GC
authors.lastname: Angenent
authors.forename: Kerstin
authors.initials: K
authors.lastname: Kaufmann
authors.forename: Aalt D J
authors.initials: AD
authors.lastname: van Dijk
mesh_terms: D029681:Arabidopsis Proteins / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D016384:Consensus Sequence; D018744:DNA, Plant / Q000737:chemistry* / Q000378:metabolism; D018398:Homeodomain Proteins / Q000378:metabolism; D026161:MADS Domain Proteins / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D010940:Plant Proteins / Q000378:metabolism*; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D018398:Homeodomain Proteins; D026161:MADS Domain Proteins; D010940:Plant Proteins; C121158:SEP3 protein, Arabidopsis; D014157:Transcription Factors