Abstract
BackgroundThe BLOC1S2 gene encodes the multifunctional protein BLOS2, a shared subunit of two lysosomal trafficking complexes: i) biogenesis of lysosome-related organelles complex-1 and i) BLOC-1-related complex. In our previous study, we identified an intriguing unreported transcript of the BLOC1S2 gene that has a novel exon derived from two transposable elements (TEs), MIR and AluSp. To investigate the evolutionary footprint and molecular mechanism of action of this transcript, we performed PCR and RT-PCR experiments and sequencing analyses using genomic DNA and RNA samples from humans and various non-human primates.ResultsThe results showed that the MIR element had integrated into the genome of our common ancestor, specifically in the BLOC1S2 gene region, before the radiation of all primate lineages and that the AluSp element had integrated into the genome of our common ancestor, fortunately in the middle of the MIR sequences, after the divergence of Old World monkeys and New World monkeys. The combined MIR and AluSp sequences provide a 3′ splice site (AG) and 5′ splice site (GT), respectively, and generate the Old World monkey-specific transcripts. Moreover, branch point sequences for the intron removal process are provided by the MIR and AluSp combination.ConclusionsWe show for the first time that sequential integration into the same location and sequence divergence events of two different TEs generated lineage-specific transcripts through sequence collaboration during primate evolution.
Highlights
The BLOC1S2 gene encodes the multifunctional protein BLOS2, a shared subunit of two lysosomal trafficking complexes: i) biogenesis of lysosome-related organelles complex-1 and i) biogenesis of lysosome- related organelles complex 1 (BLOC-1)-related complex
Comparative analysis of the structure of the BLOC1S2 gene in humans and non-human primates In a previous study, a large-scale transcriptome sequencing analysis of the genome of the crab-eating monkey enabled us to detect a new partial exon, which is located on the 4th intron of the BLOC1S2 gene, overlapping sequences of two transposable elements (TEs), AluSp, and MIR (Fig. 1) [22]
Prior to identification and experimental validation of this partial exon, we investigated the BLOC1S2 mRNA sequence of the crabeating monkey and analyzed its structure comparatively with that of the rhesus monkey and human mRNA sequences
Summary
The BLOC1S2 gene encodes the multifunctional protein BLOS2, a shared subunit of two lysosomal trafficking complexes: i) biogenesis of lysosome-related organelles complex-1 and i) BLOC-1-related complex. We identified an intriguing unreported transcript of the BLOC1S2 gene that has a novel exon derived from two transposable elements (TEs), MIR and AluSp. To investigate the evolutionary footprint and molecular mechanism of action of this transcript, we performed PCR and RT-PCR experiments and sequencing analyses using genomic DNA and RNA samples from humans and various non-human primates. BLOC1S2, located on human chromosome 10q24.31, encodes the multifunctional protein BLOS2 that is a shared subunit of two lysosomal trafficking complexes. An alternatively spliced exon can be generated by three different molecular mechanisms: exon shuffling, transition of a constitutive exon to an alternative exon, and exonization of intronic sequences [10,11,12]
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