Arata Yukinobu, Jurica Peter, Parrish Nicholas, Sako Yasushi
Cellular Informatics Laboratory, Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan.
Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
Bioinform Biol Insights. 2024 Dec 20;18:11779322241304668. doi: 10.1177/11779322241304668. eCollection 2024.
Transposable elements (TEs) or transposons are thought to play roles in animal physiological processes, such as germline, early embryonic, and brain development, as well as aging. However, their roles have not been systematically investigated through experimental studies. In this study, we created a catalog of genes directly involved in replication, excision, or integration of transposon-coding DNA, which we refer to as transposon DNA processing genes (TDPGs). Specifically, to bridge the gap to experimental studies, we sought potentially functional TDPGs which maintain intact open reading frames and the amino acids at their catalytic cores on the latest long-read genome assembly of , VC2010. Among 52 519 TE loci, we identified 145 potentially functional TDPGs encoded in long terminal repeat elements, long interspersed nuclear elements, terminal inverted repeat elements, Helitrons, and Mavericks/Polintons. Our TDPG catalog, which contains a feasible number of genes, allows for the experimental manipulation of TE mobility , regardless of whether the TEs are autonomous or non-autonomous, thereby potentially promoting the study of the physiological functions of TE mobility.
转座元件（TEs）或转座子被认为在动物生理过程中发挥作用，如生殖系、早期胚胎和大脑发育以及衰老过程。然而，它们的作用尚未通过实验研究进行系统调查。在本研究中，我们创建了一个直接参与转座子编码DNA复制、切除或整合的基因目录，我们将其称为转座子DNA加工基因（TDPGs）。具体而言，为了弥合与实验研究之间的差距，我们在最新的长读长基因组组装VC2010上寻找具有完整开放阅读框且其催化核心氨基酸保持完整的潜在功能性TDPGs。在52519个TE位点中，我们在长末端重复元件、长散在核元件、末端反向重复元件、Helitrons以及Mavericks/Polintons中鉴定出145个潜在功能性TDPGs。我们的TDPG目录包含数量可行的基因，允许对TE迁移进行实验操作，无论TE是自主型还是非自主型，从而有可能促进对TE迁移生理功能的研究。
