Minimal regulatory spaces in yeast genomes
Minimal regulatory spaces in yeast genomes
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DOI：
10.1186/1471-2164-12-320
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发表时间：
2011-06-16
期刊：
影响因子：
4.4
通讯作者：
Lercher, Martin J.
中科院分区：
文献类型：
--
作者：
Chen, Wei-Hua;Wei, Wu;Lercher, Martin J.
背景：启动子区域DNA中编码的调控信息通常在相邻基因的编码区域之间强制规定了一个最小的非零距离。然而，这个最小调控空间的大小通常是未知的。特别是，最小启动子大小在不同物种之间以及单向和双向作用的调控区域之间是否存在差异尚不清楚。
结果：通过分析11种酵母的基因组，我们表明含启动子区域的下限大小在相对较窄的范围内（80 - 255bp）因物种而异。这个大小限制同样适用于在一条或两条链上起始转录的区域，这表明双向启动子和单向启动子受到类似的限制。我们还发现，年轻的、物种特异性区域平均比古老区域长得多，这表明酵母中要么存在缺失偏向，要么存在对基因组紧凑性的选择。虽然无启动子的基因间区域的长度演化可以用一个简单的、纯中性模型很好地描述，但含启动子的区域通常有过多的异常长区域。两侧为反向转录基因的区域具有双峰长度分布，较短长度在古老区域中更常见。这些古老的短区域可能包含进化上保守的双向活性启动子。令人惊讶的是，11个物种中的两个（酿酒酵母和瓦尔蒂酵母）中一些进化上最年轻的区域比在古老区域中观察到的下限还要短。
结论：转录调控所需的最小染色体空间在酵母物种间似乎相对相似，并且对于单向和双向启动子是相同的。由基因组重排产生的新基因间区域往往朝着在古老区域中发现的更窄的大小分布演化。
Background: The regulatory information encoded in the DNA of promoter regions usually enforces a minimal, non-zero distance between the coding regions of neighboring genes. However, the size of this minimal regulatory space is not generally known. In particular, it is unclear if minimal promoter size differs between species and between uni- and bi-directionally acting regulatory regions.Results: Analyzing the genomes of 11 yeasts, we show that the lower size limit on promoter-containing regions is species-specific within a relatively narrow range (80-255 bp). This size limit applies equally to regions that initiate transcription on one or both strands, indicating that bi-directional promoters and uni-directional promoters are constrained similarly. We further find that young, species-specific regions are on average much longer than older regions, suggesting either a bias towards deletions or selection for genome compactness in yeasts. While the length evolution of promoter-less intergenic regions is well described by a simplistic, purely neutral model, regions containing promoters typically show an excess of unusually long regions. Regions flanked by divergently transcribed genes have a bi-modal length distribution, with short lengths found preferentially among older regions. These old, short regions likely harbor evolutionarily conserved bi-directionally active promoters. Surprisingly, some of the evolutionarily youngest regions in two of the eleven species (S. cerevisiae and K. waltii) are shorter than the lower limit observed in older regions.Conclusions: The minimal chromosomal space required for transcriptional regulation appears to be relatively similar across yeast species, and is the same for uni-directional and bi-directional promoters. New intergenic regions created by genome rearrangements tend to evolve towards the more narrow size distribution found among older regions.