Bai Yongsheng, Casola Claudio, Betrán Esther
Department of Biology, Box 19498, University of Texas-Arlington, Arlington, TX 76019, USA.
Genomics. 2009 Jan;93(1):83-9. doi: 10.1016/j.ygeno.2008.09.006. Epub 2008 Oct 23.
Retrogenes are processed copies of genes that are inserted into new genomic regions and that acquire new regulatory elements from the sequences in their surroundings. Here we use a comparative approach of phylogenetic footprinting and a non-comparative approach of measuring motif over-representation in retrogenes in order to describe putative elements present in cis-regulatory regions of 94 retrogenes recently described in Drosophila. The detailed examination of the motifs found in the core promoter regions of retrogenes reveals an abundance of the DNA replication-related element (DRE), the Initiator (Inr), and a new over-represented motif that we call the GCT motif. Parental genes also show an abundance of DRE and Inr motifs, but these do not seem to have been carried over with retrogenes. In particular, we also examined motifs upstream of retrogenes expressed in adult testis and were able to identify 6 additional over-represented motifs. Comparative analyses provide data on the conservation and origin of some of these motifs and reveal 15 additional conserved motifs in these retrogenes. Some of those conserved motifs are sequences bound by known transcription factors, while others are novel motifs. In this report we provide the first genome-wide data on which specific cis-regulatory regions can be recruited by retrogenes after they are inserted into new coding regions in the genome. Future experiments are needed to determine the function and role of the new elements presented here.
逆转录基因是插入到新基因组区域的基因加工拷贝，它们从周围序列中获取新的调控元件。在这里，我们使用系统发育足迹法的比较方法和测量逆转录基因中基序过度表达的非比较方法，来描述最近在果蝇中描述的94个逆转录基因的顺式调控区域中存在的假定元件。对逆转录基因核心启动子区域中发现的基序进行详细检查，发现大量与DNA复制相关的元件（DRE）、起始子（Inr）以及一个我们称为GCT基序的新的过度表达基序。亲本基因也显示出大量的DRE和Inr基序，但这些似乎并没有随着逆转录基因一起遗传下来。特别是，我们还检查了在成年睾丸中表达的逆转录基因上游的基序，并能够识别出另外6个过度表达的基序。比较分析提供了关于其中一些基序的保守性和起源的数据，并揭示了这些逆转录基因中另外15个保守基序。其中一些保守基序是已知转录因子结合的序列，而其他一些则是新的基序。在本报告中，我们提供了首个全基因组数据，表明逆转录基因插入基因组新编码区域后可募集哪些特定的顺式调控区域。需要进一步的实验来确定这里呈现的新元件的功能和作用。
