Department of Biosciences and Bioinformatics, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin, Gyeonggi-do, 17060, Republic of Korea.
Genomics Genetics Institute, GreenGene BioTech Inc., 16-4 Dongbaekjungang-ro 16beon-gil, Giheung-gu, Yongin, Gyeonggi-do, 17015, Republic of Korea.
Planta. 2021 Jan 21;253(2):40. doi: 10.1007/s00425-021-03572-w.
The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Transcription factors (TFs) regulate gene expression at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas in the functional analysis of TFs in the postgenomic era. Although many methods have been developed to address this challenge, many TFs still have unknown DNA-binding motifs. In this study, we designed RPBM with 40-bp probes and 20-bp of overlap, yielding 49 probes spanning the 1-kb upstream region before the translation start site of each gene in the entire genome. To confirm the efficiency of RPBM technology, we selected two previously studied TFs, OsWOX13 and OsSMF1, and an uncharacterized TF, OsWRKY34. We identified the ATTGATTG and CCACGTCA DNA-binding sequences of OsWOX13 and OsSMF1, respectively. In total, 635 and 932 putative feature genes were identified for OsWOX13 and OsSMF1, respectively. We discovered the CGTTGACTTT DNA-binding sequence and 195 putative feature genes of OsWRKY34. RPBM could be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in the promoter and 5' upstream CDS regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements.
本研究表明，水稻（Oryza sativa）特异性蛋白质结合微阵列（RPBM）可用于分析 DNA 结合基序与 TF，其中结合在扩展的天然启动子区域中进行评估。该分析可通过顺式元件促进鉴定 TF 及其下游基因，并构建基因网络。转录因子（TF）通过结合特定的 DNA 序列在转录水平上调节基因表达。因此，预测 TF 的 DNA 结合基序是在后基因组时代对 TF 的功能进行分析的最重要领域之一。尽管已经开发了许多方法来解决这一挑战，但许多 TF 仍然具有未知的 DNA 结合基序。在本研究中，我们设计了具有 40 个碱基探针和 20 个碱基重叠的 RPBM，产生了 49 个探针，跨越整个基因组中每个基因翻译起始位点之前的 1kb 上游区域。为了确认 RPBM 技术的效率，我们选择了两个先前研究过的 TF，OsWOX13 和 OsSMF1，以及一个未被表征的 TF，OsWRKY34。我们分别鉴定了 OsWOX13 和 OsSMF1 的 ATTGATTG 和 CCACGTCA DNA 结合序列。总共为 OsWOX13 和 OsSMF1 鉴定了 635 和 932 个假定特征基因。我们发现了 OsWRKY34 的 CGTTGACTTT DNA 结合序列和 195 个假定特征基因。RPBM 可适用于在启动子和 5'上游 CDS 区域中评估结合的 TF 的 DNA 结合基序分析。该分析可通过顺式元件促进鉴定 TF 及其下游基因，并构建基因网络。
