Inada Dan Choffnes, Bashir Ali, Lee Chunghau, Thomas Brian C, Ko Cynthia, Goff Stephen A, Freeling Michael
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA.
Genome Res. 2003 Sep;13(9):2030-41. doi: 10.1101/gr.1280703.
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 showthat 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.
随着相关物种的直系同源基因随时间发生分歧，一些序列在非编码区域得以保留。在哺乳动物中，大型系统发育足迹或保守非编码序列（CNSs）是基因的常见特征。在此，我们首次对植物基因的CNSs进行大规模分析。我们使用了单子叶植物禾本科中分歧最大的成员玉米和水稻。通过设置仅提供显著比对结果的局部序列比对，我们在所研究的大多数基因的非编码区域中发现了一个或多个CNSs。禾本科植物基因的CNSs比哺乳动物基因的显著更少且更小。27%的禾本科植物基因比对未发现CNSs。相对于编码酶或结构蛋白的基因，在转录因子等上游调控中起作用的基因，其CNSs显著富集。此外，我们发现knotted1同源异型盒基因内含子中的一个CNSs簇作为负调控位点发挥作用。我们还发现adh1基因中的CNSs与已知的顺式作用位点不相关。我们讨论了CNSs的潜在意义及其作为分析工具和进化特征的价值。我们提出许多CNSs的功能是锁定基因调控决策这一观点。
