Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea.
Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea.
Gene. 2019 Mar 1;687:238-245. doi: 10.1016/j.gene.2018.11.043. Epub 2018 Nov 16.
Horses (Equus caballus) have been domesticated and bred to enhance speed, strength, and agility. Members of the Equus caballus Endogenous Retrovirus (EqERV) family affect several of these abilities in horses. EqERV elements have been integrated in the horse genome during evolution and generate repeat elements such as long terminal repeats (LTRs). LTR sequences are involved in retrovirus replication and play an essential function in post-transcriptional control mechanisms, such as by providing binding sites for microRNAs (miRNAs) or generating miRNA precursors. In this study, we identified a novel miRNA derived from EqERV-E1 LTR using various bioinformatics tools. To examine the relationship between EqERV-E1 LTR and similar elements, we used BLAST2seq and phylogenetic analysis. LTR sequences were located in the untranslated region (UTR) of mRNAs and also formed the stem-loop secondary structure. The sequence was registered in the DDBJ database as LTR derived miRNA under the accession number corresponding to LC383797 (referred to eca-miR-1804). Quantitative polymerase chain reaction (qPCR) to confirm the expression of eca-miR-1804 and the similar miR-1255a, showed an almost identical expression pattern in eight different equine tissues. Therefore, these data imply that the LTR could function as an miRNA, which is expressed in the examined equine tissues. In addition, the current study provides inputs for additional functional studies concerning the LTR of other EqERV families.
马（Equus caballus）经过驯化和选育，以提高速度、力量和敏捷性。马类内源性逆转录病毒（EqERV）家族的成员影响着马的这些能力。EqERV 元件在进化过程中已整合到马的基因组中，并产生重复元件，如长末端重复（LTR）。LTR 序列参与逆转录病毒复制，并在转录后调控机制中发挥重要功能，例如为 microRNAs（miRNAs）提供结合位点或产生 miRNA 前体。在本研究中，我们使用各种生物信息学工具从 EqERV-E1 LTR 中鉴定出一种新的 miRNA。为了研究 EqERV-E1 LTR 与类似元件的关系，我们使用了 BLAST2seq 和系统发育分析。LTR 序列位于 mRNA 的非翻译区（UTR）中，也形成茎环二级结构。该序列已在 DDBJ 数据库中注册为 LTR 衍生的 miRNA，登录号对应 LC383797（称为 eca-miR-1804）。定量聚合酶链反应（qPCR）用于验证 eca-miR-1804 和类似的 miR-1255a 的表达，在八种不同的马组织中显示出几乎相同的表达模式。因此，这些数据表明 LTR 可以作为 miRNA 发挥作用，在检测的马组织中表达。此外，本研究为其他 EqERV 家族的 LTR 的进一步功能研究提供了依据。
