A single mutation in the ACTR8 gene associated with lineage-specific expression in primates

Se-Hee Choe,Sang-Je Park,Young-Hyun Kim,Ja-Rang Lee,Hyeon-Mu Cho,Jae-Won Huh,Hye-Ri Park

doi:10.1186/s12862-020-01620-9

Abstract

BackgroundAlternative splicing (AS) generates various transcripts from a single gene and thus plays a significant role in transcriptomic diversity and proteomic complexity. Alu elements are primate-specific transposable elements (TEs) and can provide a donor or acceptor site for AS. In a study on TE-mediated AS, we recently identified a novel AluSz6-exonized ACTR8 transcript of the crab-eating monkey (Macaca fascicularis). In the present study, we sought to determine the molecular mechanism of AluSz6 exonization of the ACTR8 gene and investigate its evolutionary and functional consequences in the crab-eating monkey.ResultsWe performed RT-PCR and genomic PCR to analyze AluSz6 exonization in the ACTR8 gene and the expression of the AluSz6-exonized transcript in nine primate samples, including prosimians, New world monkeys, Old world monkeys, and hominoids. AluSz6 integration was estimated to have occurred before the divergence of simians and prosimians. The Alu-exonized transcript obtained by AS was lineage-specific and expressed only in Old world monkeys and apes, and humans. This lineage-specific expression was caused by a single G duplication in AluSz6, which provides a new canonical 5′ splicing site. We further identified other alternative transcripts that were unaffected by the AluSz6 insertion. Finally, we observed that the alternative transcripts were transcribed into new isoforms with C-terminus deletion, and in silico analysis showed that these isoforms do not have a destructive function.ConclusionsThe single G duplication in the TE sequence is the source of TE exonization and AS, and this mutation may suffer a different fate of ACTR8 gene expression during primate evolution.

Highlights

Alternative splicing (AS) generates various transcripts from a single gene and plays a significant role in transcriptomic diversity and proteomic complexity
Structural analysis of the actin-related protein 8 homolog (ACTR8) gene in various primates We conducted a structural analysis of the ACTR8 gene in nine primates, including hominoids, Old world monkeys, New world monkeys, and prosimians, using DNA and mRNA sequences from the NCBI genome database
Obtained DNA sequences were screened for repetitive elements using the RepeatMasker Program, which revealed that AluSz6 is located in the 7th intron region in antisense orientation (Fig. 1a)

Summary

Introduction

Alternative splicing (AS) generates various transcripts from a single gene and plays a significant role in transcriptomic diversity and proteomic complexity. We sought to determine the molecular mechanism of AluSz6 exonization of the ACTR8 gene and investigate its evolutionary and functional consequences in the crab-eating monkey. TEs are mobile genetic elements that can change their position in the genome and can affect the sequence and structure of genes They can modulate gene functions in a relatively short time and are considered as an evolutionary driving force [12, 13]. Alu elements generally consist of distinct monomeric left and right arms, an A-rich linker, and a poly(A) tail [19] These features facilitate the regulation of gene expression by alternative polyadenylation and non-allelic Alu/ Alu recombination, causing genomic instability and eventually contributing to primate genome divergence [20,21,22]. Alu exonization contributes to novel functions and genome evolution in primates [20, 24]

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