![]() Modularity of plant development is based on the ability of plants to maintain pools of undifferentiated stem cells throughout the life cycle of the plant. In contrast to animals, most developmental processes of plants occur postembryonically and integrate a variety of internal and environmental cues. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist.Ĭhromatin immunoprecipitation ChIP-CHIP,Ĭhromatin immunoprecipitation coupled with DNA microarray hybridization ChIP-SEQ,Ĭhromatin immunoprecipitation coupled with Solexa sequencing FDR, This project was cofinanced by the Centre for BioSystems Genomics (CBSG) and Netherlands Proteomics Centre (NPC), which are part of the Netherlands Genomics Initiative. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.įunding: KK, JMM, RJ, and CAA were supported by fellowships of the EU-Marie Curie Research Training program (Transistor-MRTN-CT-2004–512285). Received: OctoAccepted: MaPublished: April 21, 2009Ĭopyright: © 2009 Kaufmann et al. PLoS Biol 7(4):Īcademic Editor: Detlef Weigel, Max Planck Institute for Developmental Biology, Germany (2009) Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower. In addition to effects on genes involved in floral organ identity, our data suggest that SEP3 binds to, and modulates, the transcription of target genes involved in hormonal signaling pathways.Ĭitation: Kaufmann K, Muiño JM, Jauregui R, Airoldi CA, Smaczniak C, Krajewski P, et al. We provide insight into mechanisms of DNA recognition by SEP3, and suggest roles for other transcription factor families in SEP3 target gene regulation. We show that the MADS-domain protein SEPALLATA3 (SEP3) binds to the regulatory regions of thousands of potential target genes, many of which are also transcription factors. Here, we present the first genome-wide analysis of binding sites of a MADS-box transcription factor in plants. In different combinations, transcription factors of the MADS-box family control the identities of the different types of floral organs: sepals, petals, stamens, and carpels. One of the best-understood developmental processes in plants is flower development. In plants in particular, which genes are directly controlled by these transcription factors, and the molecular mechanisms of target gene recognition in vivo, are still largely unexplored. Most regulatory genes encode transcription factors, which modulate gene expression by binding to regulatory sequences of their target genes. Furthermore, the binding of the SEPALLATA3 protein to cis-regulatory elements of other MADS-box genes and expression analyses reveal that this protein is a key component in the regulatory transcriptional network underlying the formation of floral organs. Our gene expression analyses link the genomic binding site data with the phenotype of plants expressing a dominant repressor version of SEPALLATA3, suggesting that it modulates auxin response to facilitate floral organ outgrowth and morphogenesis. In particular, the results suggest multiple links between SEPALLATA3 and auxin signaling pathways. Characterization of the target genes shows that SEPALLATA3 integrates and modulates different growth-related and hormonal pathways in a combinatorial fashion with other MADS-box proteins and possibly with non-MADS transcription factors. Most potential target sites that were strongly bound in wild-type inflorescences are also bound in the floral homeotic agamous mutant, which displays only the perianth organs, sepals, and petals. The results demonstrate that SEPALLATA3 binds to thousands of sites in the genome. We used chromatin immunoprecipitation followed by ultrahigh-throughput sequencing or hybridization to whole-genome tiling arrays to obtain genome-wide DNA-binding patterns of SEPALLATA3. In order to characterize the roles of the SEPALLATA3 transcription factor complexes at the molecular level, we analyzed genome-wide the direct targets of SEPALLATA3. Major mediators of protein interactions are MADS-domain proteins of the SEPALLATA subfamily, which play a crucial role in the development of all types of floral organs. Floral homeotic genes encode transcription factors of the MADS-box family, which are supposed to assemble in a combinatorial fashion into organ-specific multimeric protein complexes. The molecular mechanisms by which floral homeotic genes act as major developmental switches to specify the identity of floral organs are still largely unknown. ![]()
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