Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower.
Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower.
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DOI：
10.1371/journal.pbio.1000090
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发表时间：
2009-04-21
期刊：
影响因子：
9.8
通讯作者：
Angenent GC
中科院分区：
文献类型：
--
作者：
Kaufmann K;Muiño JM;Jauregui R;Airoldi CA;Smaczniak C;Krajewski P;Angenent GC
花的同源异型基因作为主要的发育开关来确定花器官的特性的分子机制在很大程度上仍不清楚。花的同源异型基因编码MADS-box家族的转录因子，这些转录因子被认为是以组合的方式组装成器官特异性的多聚体蛋白复合体。蛋白质相互作用的主要媒介是SEPALLATA亚家族的MADS结构域蛋白，它们在所有类型的花器官的发育中起着至关重要的作用。为了在分子水平上表征SEPALLATA3转录因子复合体的作用，我们对SEPALLATA3的直接靶标进行了全基因组分析。我们使用染色质免疫沉淀，然后超高通量测序或杂交到全基因组平铺阵列，获得了SEPALLATA3的全基因组DNA结合模式。结果表明，SEPALLATA3与基因组中的数千个位点结合。大多数在野生型花序中强烈结合的潜在靶点也都结合在花同源异型无性生殖突变体中，该突变体只显示花被器官、萼片和花瓣。对靶基因的分析表明，SEPALLATA3以一种与其他MADS-box蛋白以及可能与非MADS转录因子结合的方式整合并调控不同的生长相关和激素途径。特别是，结果表明SEPALLATA3和生长素信号通路之间存在多个联系。我们的基因表达分析将基因组结合位点数据与表达显性抑制型SEPALLATA3的植物的表型联系起来，表明它调节生长素的反应，以促进花器官的生长和形态发生。此外，SEPALLATA3蛋白与其他MADS-box基因的顺式调控元件的结合和表达分析表明，该蛋白是调控花器官形成的转录网络中的关键组成部分。大多数调控基因编码转录因子，转录因子通过与靶基因的调控序列结合来调节基因的表达。特别是在植物中，哪些基因直接受这些转录因子控制，以及体内靶基因识别的分子机制在很大程度上仍未被探索。植物中最被理解的发育过程之一是花的发育。在不同的组合中，MADS-box家族的转录因子控制着不同类型花器官的身份：萼片、花瓣、雄蕊和心皮。在这里，我们提出了第一个全基因组范围的分析MADS盒转录因子在植物中的结合部位。我们发现MADS结构域蛋白SEPALLATA3(SEP3)与数千个潜在靶基因的调节区结合，其中许多基因也是转录因子。我们深入了解了SEP3识别DNA的机制，并提出了其他转录因子家族在SEP3靶基因调控中的作用。除了对涉及花器官识别的基因的影响外，我们的数据表明SEP3结合并调节与激素信号通路有关的目标基因的转录。关键的花调节因子SEPALLATA3与大量潜在的直接靶基因的启动子结合，整合花发育中不同的生长相关和激素途径。
The molecular mechanisms by which floral homeotic genes act as major developmental switches to specify the identity of floral organs are still largely unknown. 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. 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. 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. 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. The results demonstrate that SEPALLATA3 binds to thousands of sites in the genome. 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. 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. In particular, the results suggest multiple links between SEPALLATA3 and auxin signaling pathways. 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. 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. Most regulatory genes encode transcription factors, which modulate gene expression by binding to regulatory sequences of their target genes. 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. One of the best-understood developmental processes in plants is flower development. 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. Here, we present the first genome-wide analysis of binding sites of a MADS-box transcription factor in plants. 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. We provide insight into mechanisms of DNA recognition by SEP3, and suggest roles for other transcription factor families in SEP3 target gene regulation. 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. The key floral regulator SEPALLATA3 binds to the promoters of a large number of potential direct target genes to integrate different growth-related and hormonal pathways in flower development.
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影响因子：
11.4
作者：
Cheng, Youfa;Zhao, Yunde
通讯作者：
Zhao, Yunde
影响因子：
4.6
作者：
Brewer, PB;Howles, PA;Smyth, DR
通讯作者：
Smyth, DR
影响因子：
10.5
作者：
Cheng, Youfa;Dai, Xinhua;Zhao, Yunde
通讯作者：
Zhao, Yunde
影响因子：
11.4
作者：
Egea-Cortines, M;Saedler, H;Sommer, H
通讯作者：
Sommer, H
DOI：
10.1093/bioinformatics/btn615
发表时间：
2009-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Carbon S;Ireland A;Mungall CJ;Shu S;Marshall B;Lewis S;AmiGO Hub;Web Presence Working Group
通讯作者：
Web Presence Working Group