| 张晓芳,于好强,罗羲,张于福,李晚忱,付凤玲.玉米MYB转录因子靶基因的全基因组预测及验证[J].干旱地区农业研究,2018,36(3):59~65 |
| 玉米MYB转录因子靶基因的全基因组预测及验证 |
| Genome-wide prediction and verification for target genes of MYB transcription factor in maize |
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| DOI：10.7606/j.issn.1000-7601.2018.03.09 |
| 中文关键词: 基因组 玉米 MYB转录因子 支持向量机 靶基因 |
| 英文关键词:genome maize MYB transcription factor support vector machine target gene |
| 基金项目:国家科技重大专项（2016ZX08003-004）；国家自然科学基金（31071433） |
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| 中文摘要: |
| MYB转录因子参与调控植物的生长发育及逆境应答过程。为预测MYB靶基因，本研究将HexDIFF算法与支持向量机结合，根据已验证的MYB识别位点的核心序列及其侧翼序列构建分类模型，在玉米全基因组范围内预测MYB靶基因及其启动子。结果表明，共预测到435个MYB结合位点，其下游的424个基因判定为MYB靶基因，涉及众多生长发育过程。为验证预测结果，经凝胶迁移实验检测玉米MYB-IF25蛋白与30个预测位点的体外结合，结果有27个预测位点可以与MYB-IF25蛋白互作。GUS瞬时表达实验表明，渗透胁迫下，预测的MYB逆境相关靶基因启动子能够启动GUS基因表达，说明其具有启动活性。以上结果证明，此预测方法可靠性高，可为预测转录因子靶基因提供借鉴。 |
| 英文摘要: |
| The MYB transcription factor are involved in the regulation of plant growth, and stress response. To predict the MYB target genes and their promoters within the whole genome of maize., the HexDIFF algorithm was combined with support vector machines to construct a classification model based on the verified core sequences of MYB recognition sites and their flanking sequences.The results showed that a total of 435 MYB binding sites were obtained and 424 genes downstream of them were identified as MYB target genes, involving in various growth and development processes.To verify the prediction results,the electrophoretic mobility shift assay was performed to detect the combination between maize MYB-IF25 protein and 30 predicted binding sites. As a result,27 binding sites could interact with MYB-IF25 protein. GUS transient expression showed that the promoters of predicted MYB stress\|related target genes could initiate the GUS gene expression, indicating that these promoters possessed driving activity. The above results prove that the predicion method has high reliablity and can provide a reference for predicting the target gene of transcription factor. |
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