title: Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia.
abstract: Most non-long terminal repeat (non-LTR) retrotransposons encoding a restriction-like endonuclease show target-specific integration into repetitive sequences such as ribosomal RNA genes and microsatellites. However, only a few target-specific lineages of non-LTR retrotransposons are distributed widely and no lineage is found across the eukaryotic kingdoms. Here we report the most widely distributed lineage of target sequence-specific non-LTR retrotransposons, designated Utopia. Utopia is found in three supergroups of eukaryotes: Amoebozoa, SAR, and Opisthokonta. Utopia is inserted into a specific site of U2 small nuclear RNA genes with different strength of specificity for each family. Utopia families from oomycetes and wasps show strong target specificity while only a small number of Utopia copies from reptiles are flanked with U2 snRNA genes. Oomycete Utopia families contain an "archaeal" RNase H domain upstream of reverse transcriptase (RT), which likely originated from a plant RNase H gene. Analysis of Utopia from oomycetes indicates that multiple lineages of Utopia have been maintained inside of U2 genes with few copy numbers. Phylogenetic analysis of RT suggests the monophyly of Utopia, and it likely dates back to the early evolution of eukaryotes.
authors.affiliation: Genetic Information Research Institute, Los Altos, California, United States of America.|Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan.|Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan.
authors.forename: Kenji K
authors.initials: KK
authors.lastname: Kojima
authors.affiliation: Genetic Information Research Institute, Los Altos, California, United States of America.
authors.forename: Jerzy
authors.initials: J
authors.lastname: Jurka
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D056890:Eukaryota / Q000235:genetics*; D018628:Gene Dosage; D008969:Molecular Sequence Data; D009868:Oomycetes / Q000235:genetics; D010802:Phylogeny; D012342:RNA, Small Nuclear / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D012342:RNA, Small Nuclear; D018626:Retroelements; C405484:U2 small nuclear RNA