Université Montpellier 2, UMR DAP, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.
BMC Genomics. 2011 Aug 1;12:387. doi: 10.1186/1471-2164-12-387.
In rice, the major part of the post-embryonic root system is made of stem-derived roots named crown roots (CR). Among the few characterized rice mutants affected in root development, crown rootless1 mutant is unable to initiate crown root primordia. CROWN ROOTLESS1 (CRL1) is induced by auxin and encodes an AS2/LOB-domain transcription factor that acts upstream of the gene regulatory network controlling CR development.
To identify genes involved in CR development, we compared global gene expression profile in stem bases of crl1 mutant and wild-type (WT) plants. Our analysis revealed that 250 and 236 genes are down- and up-regulated respectively in the crl1 mutant. Auxin induces CRL1 expression and consequently it is expected that auxin also alters the expression of genes that are early regulated by CRL1. To identify genes under the early control of CRL1, we monitored the expression kinetics of a selected subset of genes, mainly chosen among those exhibiting differential expression, in crl1 and WT following exogenous auxin treatment. This analysis revealed that most of these genes, mainly related to hormone, water and nutrient, development and homeostasis, were likely not regulated directly by CRL1. We hypothesized that the differential expression for these genes observed in the crl1 mutant is likely a consequence of the absence of CR formation. Otherwise, three CRL1-dependent auxin-responsive genes: FSM (FLATENNED SHOOT MERISTEM)/FAS1 (FASCIATA1), GTE4 (GENERAL TRANSCRIPTION FACTOR GROUP E4) and MAP (MICROTUBULE-ASSOCIATED PROTEIN) were identified. FSM/FAS1 and GTE4 are known in rice and Arabidopsis to be involved in the maintenance of root meristem through chromatin remodelling and cell cycle regulation respectively.
Our data showed that the differential regulation of most genes in crl1 versus WT may be an indirect consequence of CRL1 inactivation resulting from the absence of CR in the crl1 mutant. Nevertheless some genes, FAS1/FSM, GTE4 and MAP, require CRL1 to be induced by auxin suggesting that they are likely directly regulated by CRL1. These genes have a function related to polarized cell growth, cell cycle regulation or chromatin remodelling. This suggests that these genes are controlled by CRL1 and involved in CR initiation in rice.
在水稻中，后胚胎根系的主要部分由茎衍生的根组成，称为冠根（CR）。在少数特征明确的根发育受影响的水稻突变体中，冠根缺失 1 突变体无法启动冠根原基。冠根缺失 1（CRL1）由生长素诱导，编码一个 AS2/LOB 结构域转录因子，该因子在上游调控控制 CR 发育的基因调控网络中起作用。
为了鉴定参与 CR 发育的基因，我们比较了 crl1 突变体和野生型（WT）植物茎基部的全局基因表达谱。我们的分析表明，CRL1 突变体中分别有 250 个和 236 个基因下调和上调。生长素诱导 CRL1 的表达，因此可以预期生长素也会改变 CRL1 早期调控的基因的表达。为了鉴定早期受 CRL1 控制的基因，我们监测了外源性生长素处理后 crl1 和 WT 中选定基因子集的表达动力学。该分析表明，这些基因中的大多数，主要是那些表现出差异表达的基因，与激素、水和养分、发育和内稳态有关，不太可能直接受 CRL1 调控。我们假设在 crl1 突变体中观察到的这些基因的差异表达可能是由于缺乏 CR 形成的结果。否则，三个 CRL1 依赖性生长素响应基因：FSM（FLATENNED SHOOT MERISTEM）/FAS1（FASCIATA1）、GTE4（GENERAL TRANSCRIPTION FACTOR GROUP E4）和 MAP（MICROTUBULE-ASSOCIATED PROTEIN）被鉴定出来。在水稻和拟南芥中，FSM/FAS1 和 GTE4 分别通过染色质重塑和细胞周期调控被认为参与维持根分生组织。
我们的数据表明，在 crl1 与 WT 之间，大多数基因的差异调控可能是 CRL1 失活的间接结果，这是由于 crl1 突变体中缺乏 CR。然而，一些基因，如 FAS1/FSM、GTE4 和 MAP，需要 CRL1 被生长素诱导，这表明它们可能直接受 CRL1 调控。这些基因的功能与极化细胞生长、细胞周期调控或染色质重塑有关。这表明这些基因受 CRL1 控制，并参与水稻 CR 的启动。
