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Analysis of transcriptional synergy between upstream regions and introns in ribosomal protein genes of yeast

机译:酵母核糖体蛋白基因上游区域与内含子的转录协同分析

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摘要

Transcriptional regulation in eukaryotic genes generally requires combinatorial binding on DNA of multiple transcription factors. Though many analyses have been performed for identification of combinatorial patterns in promoter sequences, there are few studies concerned with introns of genes. Here our study focuses on the transcriptional synergistic (cooperative) regulation between upstream promoters and introns of ribosomal protein (RP) genes in Saccharomyces cerevisiae yeast. We first extract some potential transcriptional regulatory motifs based on a statistical comparative analysis. 98% of these motifs are accordance with experimental analyses. Then by pairing these motifs each other, we identify some potential synergistic motif pairs between upstream regions and introns of yeast RP genes (RPGs). Among 48 detected motif pairs, 44 match the binding sites for interacting transcriptional factors known from experiments or predictions. Checking the positions of these motif pairs in yeast RPGs, it is found that both motifs of the detected motif pairs are enriched in specific regions of upstream regions and introns, respectively. Some motif pairs present distance and orientation preferences, which may be favorable for transcription factors to bind simultaneously to DNA. These results will be helpful to understand the mechanism of synergistic regulation in yeast RPGs.
机译:真核基因中的转录调控通常需要对多种转录因子的DNA进行组合结合。尽管已经进行了许多分析以鉴定启动子序列中的组合模式,但是很少有研究涉及基因的内含子。在这里,我们的研究集中在酿酒酵母酵母上游启动子和核糖体蛋白(RP)基因内含子之间的转录协同(合作)调控。我们首先根据统计比较分析提取一些潜在的转录调控基序。这些基序中的98%与实验分析一致。然后通过将这些基序彼此配对,我们在酵母RP基因(RPG)的上游区域和内含子之间鉴定了一些潜在的协同基序对。在48个检测到的基序对中,有44个与结合位点匹配,这些结合位点是相互作用的转录因子(从实验或预测中得知)。检查酵母RPG中这些基序对的位置,发现检测到的基序对的两个基序分别富集在上游区域和内含子的特定区域中。一些基序对具有距离和方向偏好,这可能有利于转录因子同时与DNA结合。这些结果将有助于理解酵母RPG中的协同调节机制。

著录项

  • 来源
    《Computational biology and chemistry》 |2010年第2期|106-114|共9页
  • 作者

    Jun Hu; Huimin Li; Jing Zhang;

  • 作者单位

    Laboratory for Conservation and Utilization of Bio-resources, Yunnan University. Kunming 650091, China School of Science and Information Engineering, Yunnan Agricultural University, Kunming 650201, China;

    Laboratory for Conservation and Utilization of Bio-resources, Yunnan University. Kunming 650091, China;

    School of Mathematics and Statistics, Yunnan University, No. 2, North Cuihu Road, Kunming, Yunnan 650091, China;

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  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    transcriptional regulation; upstream regions; introns; ribosomal protein genes; yeast;

    机译:转录调控;上游地区;内含子核糖体蛋白基因;酵母;

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