酵母基因上游与内含子可能存在的转录协同作用

Potential Transcriptional Synergy Between Upstream Regions and Introns of Yeast Genes

前期研究表明,酵母高转录基因内含子与低转录基因内含子的序列结构有较大差异,高转录基因内含子中存在一些潜在的正调控位点,而且这些内含子非常靠近基因上游区,有的内含子甚至位于5'-UTR区. 这些结果提示,高转录基因内含子可能参与转录调控,并可能与上游转录调控有协同作用. 为探索内含子与上游区的协同作用,将基因上游序列(翻译起始点上游800 bp或两个相邻基因之间部分)取出,仍使用寡核苷酸频率比较方法,抽提出高转录基因上游区可能的转录正调控元件,这些元件与实验所得结果吻合得较好. 然后定义“寡核苷酸对”,其中一个位于上游区,另一个位于内含子,对“最近距离”在一定范围内(84 bp)的寡核苷酸对进行分析,抽提出匹配基因数显著高于随机匹配数的寡核苷酸对(主要是四核苷酸对和五核苷酸对),分析这些寡核苷酸对的相互作用模式(位置分布及可能的作用因子,如RAP1,ABF1和TAF等),获得了酵母基因上游与内含子之间可能存在的一些转录协同作用模式. 这些结果有助于对基因转录调控机制的认识.

Previous work indicated that there was a large difference of the sequence features of introns between highly- and lowly-transcribed yeast genes. Some potential positive transcriptional regulatory motifs in the highly-transcribed introns were extracted. It was found that these introns were very close to the upstream regions of genes, and several introns even located within 5'-UTR. These results show that introns of yeast genes may regulate the transcriptional efficiencies and cooperate with upstream regions. To understand the synergy between upstream regions and introns of highly-transcribed yeast genes, the upstream regions (800 bp upstream of translation start sites, or the regions of two adjacent genes) of these two sets of genes were retrieved, and some potential positive transcriptional motifs in the upstream of highly-transcribed genes were extracted using the statistical comparative analysis approach developed before. Most of the potential motifs extracted were supported by literature search of experimental analyses. Then, every pair of oligonucleotides, one in the upstream region and the other in the intron, was defined as an 'oligonucleotide pair', i.e. a motif pair. Considering the motif pairs with the 'nearest distance' not larger than 84 bp, the motif pairs, mainly tetra- and penta-nucleotide pairs, occurring in the highly-transcribed genes non-randomly were extracted and the synergistic pattern of these motif pairs including position distributions and binding transcription factors such as RAP1, ABF1 and TAF was analyzed. Some potential patterns of transcriptional synergy were observed. These results could help people to understand the mechanism of transcriptional regulation and provide evidence for biological verification.