A new class of SINEs with snRNA gene-derived heads

Kenji K. Kojima

Research output: Contribution to journalArticlepeer-review

16 Citations (Scopus)


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 theU1orU2 small nuclear RNA gene. These SINEs, named SINEU, are distributed amongcrocodilians and classified into three families. The structures of the SINEU-1 subfamilies indicate the recurrent addition of aU1- 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 forMariner-N4-AMi, indicating that SINEU was mobilized by Tx1-Mar.

Original languageEnglish
Pages (from-to)1702-1712
Number of pages11
JournalGenome Biology and Evolution
Issue number6
Publication statusPublished - 2015 Jun

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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