Conserved noncoding sequences in the grasses
Conserved noncoding sequences in the grasses
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DOI：
10.1101/gr.1280703
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发表时间：
2003-09-01
期刊：
影响因子：
7
通讯作者：
Freeling, M
中科院分区：
文献类型：
--
作者：
Inada, DC;Bashir, A;Freeling, M
随着相关物种的同源基因随着时间的推移而分化，一些序列在非编码区是保守的。在哺乳动物中，大的系统发育足迹或保守的非编码序列(CNS)是已知的基因的共同特征。在这里，我们提出了第一个大规模的植物基因的CNSS分析。我们使用了玉米和水稻，这是单子叶植物中分歧最大的成员。使用局部序列比对集仅提供显著的比对，我们在大多数被研究的基因的非编码区发现了一个或多个CNS。与哺乳动物基因相比，GRASS基因的CNS数量要少得多，也要小得多。27%的草基因比对显示没有CNS。与编码酶或结构蛋白的基因相比，发挥上游调控作用的基因，如转录因子，在CNS中得到了极大的丰富。此外，我们还表明，结1同源盒基因内含子中的CNS簇作为负调控位点。我们发现ADH1基因中的CNS与已知的顺式作用位点无关。我们讨论了CNS的潜在含义以及它们作为分析工具和进化特征的价值。我们提出的想法是，许多CNS的功能锁定基因调控决定。
As orthologous genes from related species diverge over time, some sequences are conserved in noncoding regions. In mammals, large phylogenetic footprints, or conserved noncoding sequences (CNSs), are known to be common features of genes. Here we present the first large-scale analysis of plant genes for CNSs. We used maize and rice, maximally diverged members of the grass family of monocots. Using a local sequence alignment set to deliver only significant alignments, we found one or more CNSs in the noncoding regions of the majority of genes studied. Grass genes have dramatically fewer and much smaller CNSs than mammalian genes. Twenty-seven percent of grass gene comparisons revealed no CNSs. Genes functioning in upstream regulatory roles, such as transcription factors, are greatly enriched for CNSs relative to genes encoding enzymes or structural proteins. Further, we show that a CNS Cluster in an intron of the knotted1 homeobox gene serves as a site of negative regulation. We show that CNSs in the adh1 gene do not correlate with known cis-acting sites. We discuss the potential meanings of CNSs and their value as analytical tools and evolutionary characters. We advance the idea that many CNSs function to lock-in gene regulatory decisions.