The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation.
The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation.
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DOI：
10.1186/1471-2164-11-581
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发表时间：
2010-10-19
期刊：
影响因子：
4.4
通讯作者：
Li WH
中科院分区：
文献类型：
--
作者：
Lin Z;Wu WS;Liang H;Woo Y;Li WH
转录因子结合位点（TFBSs）在启动子区域的分布对基因调控具有重要意义。以往的研究以翻译起始密码子作为参考点来推断TFBS的分布。然而，使用转录起始位点（TSS）作为参考点在生物学上更具相关性。在本研究中，我们重新审视了TFBS的空间分布，研究了可能影响其分布的各种启动子特征，并研究了TFBS分布对转录调控的影响。我们发现TFBSs在TSS上游~115 bp处有一个明显的分布峰，但以翻译起始密码子为参照点时没有明显的分布峰。我们对63株酵母菌的序列变异数据进行了分析，发现分布峰与TSS之间的缺失多态性非常低，表明TSS与TFBSs之间的距离在进化过程中受到了选择性的限制。与之前的研究一样，我们发现核小体的占用和启动子区域TATA-box的存在/不存在影响TFBS的分布模式。此外，我们发现5'UTR长度与TFBS分布模式之间存在相关性，并表明TFBS分布模式影响基因转录水平和可塑性。以TSS为参考点得到的TFBSs的空间分布峰比以翻译起始密码子为参考点得到的分布峰要尖锐得多。TFBS分布模式受核小体占用和TATA-box存在的影响，影响基因的转录水平和转录可塑性。
How the transcription factor binding sites (TFBSs) are distributed in the promoter region have implications for gene regulation. Previous studies used the translation start codon as the reference point to infer the TFBS distribution. However, it is biologically more relevant to use the transcription start site (TSS) as the reference point. In this study, we reexamined the spatial distribution of TFBSs, investigated various promoter features that may affect the distribution, and studied the effect of TFBS distribution on transcriptional regulation. We found a sharp peak for the distribution of TFBSs at ~115 bp upstream of the TSS, but no clear peak when the translation start codon was used as the reference point. Our analysis of sequence variation data among 63 yeast strains revealed very low deletion polymorphisms in the region between the distribution peak and the TSS, suggesting that the distances between TFBSs and the TSS have been selectively constrained in evolution. As in previous studies, we found that the nucleosome occupancy and the presence/absence of TATA-box in the promoter region affect the TFBS distribution pattern. In addition, we found that there exists a correlation between the 5'UTR length and the TFBS distribution pattern and we showed that the TFBS distribution pattern affects gene transcription level and plasticity. The spatial distribution of TFBSs obtained using the TSS as the reference point shows a much sharper peak than does the distribution obtained using the translation start codon as the reference point. The TFBS distribution pattern is affected by nucleosome occupancy and presence of TATA-box and it affects the transcription level and transcription plasticity of the gene.
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影响因子：
16
作者：
Badis, Gwenael;Chan, Esther T.;van Bakel, Harm;Pena-Castillo, Lourdes;Tillo, Desiree;Tsui, Kyle;Carlson, Clayton D.;Gossett, Andrea J.;Hasinoff, Michael J.;Warren, Christopher L.;Gebbia, Marinella;Talukder, Shaheynoor;Yang, Ally;Mnaimneh, Sanie;Terterov, Dimitri;Coburn, David;Yeo, Ai Li;Yeo, Zhen Xuan;Clarke, Neil D.;Lieb, Jason D.;Ansari, Aseem Z.;Nislow, Corey;Hughes, Timothy R.
通讯作者：
Hughes, Timothy R.
影响因子：
3.5
作者：
Pesole, G;Mignone, F;Liuni, S
通讯作者：
Liuni, S
影响因子：
64.5
作者：
Basehoar, AD;Zanton, SJ;Pugh, BF
通讯作者：
Pugh, BF
影响因子：
14.9
作者：
Hansen L;Mariño-Ramírez L;Landsman D
通讯作者：
Landsman D
影响因子：
64.8
作者：
Schacherer J;Shapiro JA;Ruderfer DM;Kruglyak L
通讯作者：
Kruglyak L