雷蒙德氏棉和拟南芥基因启动子中顺式作用元件的分布

随着雷蒙德氏棉(Gossypium raimondii)基因组草图的完成, 相关的基因组学研究已经全面展开。文章利用已公布的雷蒙德氏棉和拟南芥基因组序列, 结合顺式作用元件(cis-regulatory element, CRE)数据库PLACE中的CRE序列信息, 对两个物种中带有5′UTR注释的基因启动子上游1 000 bp序列进行CRE扫描和统计。结果表明, 雷蒙德氏棉和拟南芥基因组中分别有44(12.3%)和57(15.5%)个CRE在启动子的特定位置呈峰状分布, 其中在两个基因组均呈峰状分布的有34个, 这些CRE又可以根据核心序列分为4大类。TATABOX类CRE顶峰在启动子中出现的位置和其真实位置(~ -30 bp)具有一致性, 预示CRE真实位置在不同基因启动子中相对保守, 从而推测本研究中呈峰状分布CRE的顶峰位置可能就是转录因子和该CRE结合的真实位置。而同一CRE在两个基因组中存在的位置差异则主要源于雷蒙德氏棉基因的5′UTR长度变异大于拟南芥。另外, 文章还发现绝大多数峰状分布的CRE的位置都集中在-110 bp~0 bp之间, 这种集中的分布可能更有利于转录因子之间相互作用, 从而调控下游基因的表达。     

Computational predictions of common transcription factor binding sites on the genes of proline metabolism in plants

Proline, an imino acid, has been well documented to be associated with the stress response induced by abiotic factors such as drought, cold and salinity in plants and biotic factors such as bacterial and fungal attacks. However, the regulatory mechanisms controlling proline metabolism, intercellular and intracellular transport and connections of proline to other metabolic pathways are poorly understood. F-MATCH analysis combined with composite module analysis (CMA) revealed that the binding sites matching matrices for O2 and OCSBF-1 were overrepresented in the promoters of differentially expressed proline metabolism genes. The presence of MYBAS1 consensus binding sites occurring in combination with O2 and OCSBF1 in the promoters of genes of proline biosynthesis pathway and SBF1 and GT1 consensus binding sites occurring in combination with O2 and OCSBF1 in the promoters of proline catabolic pathway genes suggest their involvement in modulation of proline metabolism and its accumulation in plants.