Hagfish genome reveals parallel evolution of 7SL RNA-derived SINEs

Kenji K Kojima

doi:10.1186/s13100-020-00210-2

Abstract

BackgroundShort interspersed elements (SINEs) are ubiquitous components of eukaryotic genomes. SINEs are composite transposable elements that are mobilized by non-long terminal repeat (non-LTR) retrotransposons, also called long interspersed elements (LINEs). The 3′ part of SINEs usually originated from that of counterpart non-LTR retrotransposons. The 5′ part of SINEs mostly originated from small RNA genes. SINE1 is a group of SINEs whose 5′ part originated from 7SL RNA, and is represented by primate Alu and murine B1. Well-defined SINE1 has been found only from Euarchontoglires, a group of mammals, in contrast to the wide distribution of SINE2, which has a tRNA-derived sequence, from animals to plants to protists. Both Alu and B1 are mobilized by L1-type non-LTR retrotransposons, which are the only lineage of autonomous non-LTR retrotransposons active in these mammalian lineages.ResultsHere a new lineage of SINE1 is characterized from the seashore hagfish Eptatretus burgeri genome. This SINE1 family, designated SINE1-1_EBu, is young, and is transposed by RTE-type non-LTR retrotransposon, not L1-type. Comparison with other SINE families from hagfish indicated the birth of SINE1-1_EBu through chimera formation of a 7SL RNA-derived sequence and an older tRNA-derived SINE family. It reveals parallel evolution of SINE1 in two vertebrate lineages with different autonomous non-LTR retrotransposon partners. The comparison between two SINE1 lineages supports that the RNA secondary structure of the Alu domain of 7SL RNA is required for the efficient retrotransposition.ConclusionsThe hagfish SINE1 is the first evident SINE1 family found outside of Euarchontoglires. Independent evolution of SINE1 with similar RNA secondary structure originated in 7SL RNA indicates the functional importance of 7SL RNA-derived sequence in the proliferation of SINEs.

Highlights

Short interspersed elements (SINEs) are composite mobile elements that can mobilize dependent on the help of counterpart long interspersed elements (LINEs), called non-long terminal repeat retrotransposons [1, 2]
Well-defined examples of SINE1 are only found in one lineage of mammals, Euarchontoglires, which is composed of 5 orders: primates, flying lemurs, Kojima Mobile DNA (2020) 11:18 tree shrews, rodents, and lagomorphs [7]
One copy of 7SL RNA gene was characterized from the hagfish genome, and it is more similar to SINE1-1_ EBu than to the human 7SL RNA gene

Summary

Introduction

Short interspersed elements (SINEs) are composite mobile elements that can mobilize dependent on the help of counterpart long interspersed elements (LINEs), called non-long terminal repeat (non-LTR) retrotransposons [1, 2]. SINEs are composed of several independently-originated regions, called head, body, and tail These three regions are not always present in all SINEs, and sometimes, more than one independently derived sequences constitute one of these regions. SINEs with tRNA-originated heads, called SINE2, are the most common SINEs and widely distributed among eukaryotes [6]. Well-defined SINE1 has been found only from Euarchontoglires, a group of mammals, in contrast to the wide distribution of SINE2, which has a tRNA-derived sequence, from animals to plants to protists. Both Alu and B1 are mobilized by L1-type non-LTR retrotransposons, which are the only lineage of autonomous non-LTR retrotransposons active in these mammalian lineages

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