Role of Hfq-binding aptamers in antisense transcripts opposite to start and stop sites of protein coding genes in E. coli

为了使细胞以受控的方式生长，其基因产物的合成必须受到严格的调节。迄今为止，对基因表达调控的研究主要集中在调控蛋白上。然而，近年来，数以百计的调控rna被发现在各个水平上调控基因表达。使用基因组SELEX作为发现新rna的替代方法，我们鉴定了大量基因组Hfq适体，这些适体映射到大肠杆菌中蛋白质编码基因的反义链。这些适体富集于翻译起始位点和操纵子中基因间的干预序列相反的位置。我们假设这些适体可能参与调节同源mrna的翻译或稳定性，或通过加工参与多顺反子mrna中基因的差异表达。另外，Hfq适体可能负责保持反义转录物的低表达。我们希望通过表征反义转录组并揭示Hfq适体在大肠杆菌转录组调控中的作用来验证这些假设。这项工作可能会建立大反义转录物作为控制翻译和/或转录沉默的额外一类RNA分子。

For a cell to grow in a controlled way, the synthesis of its gene products has to be tightly regulated. Until recently, studies on the regulation of gene expression were mainly focusing on regulatory proteins. However, in recent years, hundreds of regulatory RNAs have been discovered that regulate gene expression at all levels. Using genomic SELEX as an alternative approach to discover novel RNAs, we identified a large number of genomic Hfq aptamers that map to the antisense strand of protein coding genes in E. coli. These aptamers are enriched opposite to translation initiation sites and opposite to intervening sequences between genes in operons. We hypothesize that these aptamers might be involved in regulating translation or stability of their cognate mRNAs or in the differential expression of genes in polycistronic mRNAs by processing. Alternatively, Hfq aptamers might be responsible to keep the expression of antisenses transcripts low. We want to test these hypotheses by characterizing the antisense transcriptome and revealing the role of Hfq aptamers in the regulation of the E. coli transcriptome. This work might establish large antisense transcripts as an additional class of RNA molecules that control translation and/or transcriptional silencing.