Corà Davide, Di Cunto Ferdinando, Caselle Michele, Provero Paolo
Dept of Theoretical Physics, University of Turin and INFN, Turin, Italy.
BMC Bioinformatics. 2007 May 24;8:174. doi: 10.1186/1471-2105-8-174.
3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become increasingly clear in the last few years.
We propose two complementary approaches to the statistical analysis of oligonucleotide frequencies in mammalian 3' UTRs aimed at the identification of candidate binding sites for regulatory elements. The first method is based on the identification of sets of genes characterized by evolutionarily conserved overrepresentation of an oligonucleotide. The second method is based on the identification of oligonucleotides showing statistically significant strand asymmetry in their distribution in 3' UTRs.
Both methods are able to identify many previously known binding sites located in 3'UTRs, and in particular seed regions of known miRNAs. Many new candidates are proposed for experimental verification.
3'非翻译区（3'UTR）包含许多调控元件的结合位点，尤其是微小RNA（miRNA）的结合位点。在过去几年中，miRNA介导的转录后调控的重要性日益明显。
我们提出了两种互补的方法，用于对哺乳动物3'UTR中的寡核苷酸频率进行统计分析，旨在识别调控元件的候选结合位点。第一种方法基于鉴定以寡核苷酸的进化保守性过表达为特征的基因集。第二种方法基于鉴定在3'UTR中的分布显示出统计学上显著的链不对称性的寡核苷酸。
两种方法都能够识别位于3'UTR中的许多先前已知的结合位点，特别是已知miRNA的种子区域。提出了许多新的候选位点以供实验验证。
