Kojima Kenji K
Genetic Information Research Institute, Cupertino, CA 95014, USA.
Biology (Basel). 2022 Jan 20;11(2):166. doi: 10.3390/biology11020166.
is a unique superfamily of DNA transposons, inserted specifically in multicopy RNA genes. The zebrafish genome harbors five families of transposons, whose targets are U6 and U1 snRNA genes, and tRNA-Ala and tRNA-Leu genes. , which is inserted specifically in U6 snRNA genes, is found in four animal phyla, but other target-specific lineages have been reported only from one or two species. Here, vertebrate genomes and transcriptomes were surveyed to characterize families with new target specificities, and over 120 families were characterized from the genomes of actinopterygian fish. They were classified into 12 groups with confirmed target specificities. Newly characterized families target tRNA genes for Asp, Asn, Arg, Gly, Lys, Ser, Tyr, and Val, and 5S rRNA genes. Targeted positions inside of tRNA genes are concentrated in two regions: around the anticodon and the A box of RNA polymerase III promoter. Phylogenetic analysis revealed the relationships among actinopterygian families, and one domestication event in the common ancestor of carps and minnows belonging to Cyprinoidei, Cypriniformes. Sequences targeted by phylogenetically related families show sequence similarities, indicating that the target specificity of is accomplished through the recognition of primary nucleotide sequences.
是一个独特的DNA转座子超家族，专门插入多拷贝RNA基因中。斑马鱼基因组含有五个转座子家族，其靶标是U6和U1 snRNA基因以及tRNA - Ala和tRNA - Leu基因。专门插入U6 snRNA基因的在四个动物门中被发现，但其他靶标特异性谱系仅在一两个物种中被报道过。在这里，对脊椎动物的基因组和转录组进行了调查，以表征具有新靶标特异性的家族，并且从辐鳍鱼的基因组中表征了120多个家族。它们被分为12个具有确定靶标特异性的组。新表征的家族靶向天冬氨酸、天冬酰胺、精氨酸、甘氨酸、赖氨酸、丝氨酸、酪氨酸和缬氨酸的tRNA基因以及5S rRNA基因。tRNA基因内部的靶向位置集中在两个区域：反密码子周围和RNA聚合酶III启动子的A框。系统发育分析揭示了辐鳍鱼家族之间的关系，以及鲤形目鲤亚目的鲤鱼和 minnows共同祖先中的一次驯化事件。系统发育相关家族靶向的序列显示出序列相似性，表明的靶标特异性是通过对初级核苷酸序列的识别来实现的。
