Plant Genome. 2019 Mar;12(1). doi: 10.3835/plantgenome2017.09.0081.
Transcription factors (TFs) regulate plant gene expression in different tissues. To investigate TF genes in rice ( L.), a genome-wide TF identification was conducted with the japonica rice genome. This study identified 3078 putative TFs in 59 families. The TF number of the top 10 TF families accounted for 58% of the 3078 rice TFs. The three largest TF families were the myeloblastosis (MYB) superfamily, basic helix-loop-helix (bHLH), and far-red-impaired response (FAR1), which contained 413, 228, and 210 TF members, respectively. The expression profiles of the 3078 TF genes were surveyed with the RNA sequencing (RNA-seq) data of 13 rice tissue types. Based on these expression profiles, we validated 1087 TFs expressed in 13 rice tissue types, which accounted for 35.32% of the 3078 putative TFs. We further analyzed the tissue-specific TFs in rice. In total, 28, 14, 14, 10, 9, 5, 5, 4, 3, 3, 2, 11, and 1 tissue-specific TF sequences were identified in the dry seed, pistil, spikelet, aleurone, anther, ovules, embryo 25 d after pollination (DAP), seed 5 DAP, root, leaf, seed 10 DAP, shoot, and endosperm 25 DAP, respectively. Moreover, we constructed RicetissueTFDB (), a comprehensive and public rice TF database that integrates tissue expression characters, genomic location, and Gene Ontology (GO) terms for each TF. The RicetissueTFDB database will facilitate the identification of target TFs and the functional studies about rice TFs.
转录因子（TFs）在不同组织中调节植物基因表达。为了研究水稻（L.）中的 TF 基因，利用粳稻基因组进行了全基因组 TF 鉴定。本研究在 59 个家族中鉴定了 3078 个推定 TF。前 10 个 TF 家族的 TF 数量占 3078 个水稻 TF 的 58%。最大的三个 TF 家族是髓细胞瘤（MYB）超家族、碱性螺旋-环-螺旋（bHLH）和远红受损反应（FAR1），分别包含 413、228 和 210 个 TF 成员。使用 13 种水稻组织类型的 RNA 测序（RNA-seq）数据调查了 3078 个 TF 基因的表达谱。基于这些表达谱，我们验证了在 13 种水稻组织类型中表达的 1087 个 TF，占 3078 个推定 TF 的 35.32%。我们进一步分析了水稻中的组织特异性 TF。总共在干种子、雌蕊、小穗、糊粉层、花药、胚珠、授粉后 25 天胚乳、种子 5 天、根、叶、种子 10 天、茎和胚乳 25 天中鉴定了 28、14、14、10、9、5、5、4、3、3、2、11 和 1 个组织特异性 TF 序列。此外，我们构建了 RicetissueTFDB（），这是一个综合的公共水稻 TF 数据库，整合了每个 TF 的组织表达特征、基因组位置和基因本体（GO）术语。RicetissueTFDB 数据库将有助于鉴定靶 TF 和研究水稻 TF 的功能。
