title: A New Class of SINEs with snRNA Gene-Derived Heads.
abstract: Eukaryotic genomes are colonized by various transposons including short interspersed elements (SINEs). The 5' region (head) of the majority of SINEs is derived from one of the three types of RNA genes--7SL RNA, transfer RNA (tRNA), or 5S ribosomal RNA (rRNA)--and the internal promoter inside the head promotes the transcription of the entire SINEs. Here I report a new group of SINEs whose heads originate from either the U1 or U2 small nuclear RNA gene. These SINEs, named SINEU, are distributed among crocodilians and classified into three families. The structures of the SINEU-1 subfamilies indicate the recurrent addition of a U1- or U2-derived sequence onto the 5' end of SINEU-1 elements. SINEU-1 and SINEU-3 are ancient and shared among alligators, crocodiles, and gharials, while SINEU-2 is absent in the alligator genome. SINEU-2 is the only SINE family that was active after the split of crocodiles and gharials. All SINEU families, especially SINEU-3, are preferentially inserted into a family of Mariner DNA transposon, Mariner-N4_AMi. A group of Tx1 non-long terminal repeat retrotransposons designated Tx1-Mar also show target preference for Mariner-N4_AMi, indicating that SINEU was mobilized by Tx1-Mar.
authors.affiliation: Genetic Information Research Institute, Los Altos, CA kojima@girinst.org.
authors.forename: Kenji K
authors.initials: KK
authors.lastname: Kojima
mesh_terms: D000489:Alligators and Crocodiles / Q000235:genetics; D000818:Animals; D012342:RNA, Small Nuclear / Q000235:genetics*; D020086:Short Interspersed Nucleotide Elements; D014158:Transcription, Genetic
chemical_list: D012342:RNA, Small Nuclear; C405483:U1 small nuclear RNA; C405484:U2 small nuclear RNA
keywords: Mariner-N4_AMi; SINEU; Tx1; Tx1-Mar; U1; U2; alligator; crocodile; crocodilians; gharial; transposable elements