Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture

9.575
Zefu Lu, Hong Yu, Guosheng Xiong, Jing Wang, Yongqing Jiao, Guifu Liu, Yanhui Jing, Xiangbing Meng, Xingming Hu, Qian Qian, Xiangdong Fu, Yonghong Wang, Jiayang Li
The Plant Cell, 2013, 25(10): 3743-3759  DOI: 10.1105/tpc.113.113639     追溯原文......本站官方QQ群:62473826

IDEAL PLANT ARCHITECTURE1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. The SQUAMOSA PROMOTER BINDING PROTEIN-box direct binding core motif GTAC was highly enriched in IPA1 binding peaks; interestingly, a previously uncharacterized indirect binding motif TGGGCC/T was found to be significantly enriched through the interaction of IPA1 with proliferating cell nuclear antigen PROMOTER BINDING FACTOR1 or PROMOTER BINDING FACTOR2. Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. Moreover, our results demonstrated that IPA1 could directly bind to the promoter of rice TEOSINTE BRANCHED1, a negative regulator of tiller bud outgrowth, to suppress rice tillering, and directly and positively regulate DENSE AND ERECT PANICLE1, an important gene regulating panicle architecture, to influence plant height and panicle length. The elucidation of target genes of IPA1 genome-wide will contribute to understanding the molecular mechanisms underlying plant architecture and to facilitating the breeding of elite varieties with ideal plant architecture.

水稻转录激活因子IPA1的全基因组结合分析表明存在一个复杂的网络控制水稻株型

IPA1在调控水稻株型方面非常重要,它能显著增加水稻产量。为了深入了解其分子机制,我们首次确认IPA1是一个有功能的转录激活因子,通过全基因染色质免疫沉淀测序分析(Chip-Seq)发现,在水稻茎尖SAs和幼穗组织YPs中发现有1067和2185基因与IPA1结合位点有关。SBP-box(SQUAMOSA启动子结合蛋白框)直接结合核心基序GTAC在IPA1结合峰中高度富集,有趣的是,之前报道的未知的间接结合基序TGGGCC/T也通过IPA1与增殖细胞核抗原启动子结合因子(PCF1)和(PCF2)的互作显著富集。通过RNA重测序对全基因组表达谱进一步分析显示IPA1参与调控多个生长发育过程。而且,我们结果表明IPA1能与控制水稻分蘖侧芽生长的负调控因子OsTB1的启动子直接结合,抑制水稻分蘖发生,还通过直接正调控水稻株型重要基因DEP1,调节水稻株高和穗长。通过对IPA1全基因组的靶基因的阐释,有助于我们对水稻株型的分子机制认识并且有利于培育优良品种的选育。


基因列表
  Squamosa启动子结合蛋白基因 OsSPL14; IPA1;WFP