IGFL, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France.
Cells. 2021 Nov 2;10(11):2983. doi: 10.3390/cells10112983.
It is recognized that a large proportion of eukaryotic RNAs and proteins is not produced from conventional genes but from short and alternative (alt) open reading frames (ORFs) that are not captured by gene prediction programs. Here we present an in silico prediction of altORFs by applying several selecting filters based on evolutionary conservation and annotations of previously characterized altORF peptides. Our work was performed in the (), which was one of the first genomic regions described to contain long non-coding RNAs in . We showed that several altORFs could be predicted from coding and non-coding sequences of . In addition, the selected altORFs encode for proteins that contain several interesting molecular features, such as the presence of transmembrane helices or a general propensity to be rich in short interaction motifs. Of particular interest, one altORF encodes for a protein that contains a peptide sequence found in specific isoforms of two Hox proteins. Our work thus suggests that several altORF proteins could be produced from a particular genomic region known for its critical role during embryonic development. The molecular signatures of these altORF proteins further suggests that several of them could make numerous protein-protein interactions and be of functional importance in vivo.
人们认识到，很大一部分真核 RNA 和蛋白质不是由传统基因产生的，而是来自短的和替代（alt）开放阅读框（ORF），这些 ORF 不能被基因预测程序捕获。在这里，我们通过应用几种基于进化保守性和先前表征的 altORF 肽注释的选择过滤器，在计算机上预测 altORF。我们的工作是在 （）中进行的，这是第一个被描述为包含 的长非编码 RNA 的基因组区域之一。我们表明，可以从 的编码和非编码序列中预测出几个 altORF。此外，选定的 altORF 编码的蛋白质包含几个有趣的分子特征，例如存在跨膜螺旋或普遍富含短相互作用基序的倾向。特别有趣的是，一个 altORF 编码的蛋白质包含在两个 Hox 蛋白的特定同工型中发现的肽序列。因此，我们的工作表明，几个 altORF 蛋白可以从其在 胚胎发育过程中关键作用的特定基因组区域产生。这些 altORF 蛋白的分子特征进一步表明，其中许多蛋白可能进行大量的蛋白质-蛋白质相互作用，并在体内具有重要的功能意义。
