Alu-Derived Alternative Splicing Events Specific to Macaca Lineages in CTSF Gene

Abstract

Cathepsin F, which is encoded by CTSF, is a cysteine proteinase ubiquitously expressed in several tissues. In a previous study, novel transcripts of the CTSF gene were identified in the crab-eating monkey deriving from the integration of an Alu element–AluYRa1. The occurrence of AluYRa1-derived alternative transcripts and the mechanism of exonization events in the CTSF gene of human, rhesus monkey, and crab-eating monkey were investigated using PCR and reverse transcription PCR on the genomic DNA and cDNA isolated from several tissues. Results demonstrated that AluYRa1 was only integrated into the genome of Macaca species and this lineage-specific integration led to exonization events by producing a conserved 3′ splice site. Six transcript variants (V1–V6) were generated by alternative splicing (AS) events, including intron retention and alternative 5′ splice sites in the 5′ and 3′ flanking regions of CTSF_AluYRa1. Among them, V3–V5 transcripts were ubiquitously expressed in all tissues of rhesus monkey and crab-eating monkey, whereas AluYRa1-exonized V1 was dominantly expressed in the testis of the crab-eating monkey, and V2 was only expressed in the testis of the two monkeys. These five transcript variants also had different amino acid sequences in the C-terminal region of CTSF, as compared to reference sequences. Thus, species-specific Alu-derived exonization by lineage-specific integration of Alu elements and AS events seems to have played an important role during primate evolution by producing transcript variants and gene diversification.

Cooperative evolution of two different TEs results in lineage-specific novel transcripts in the BLOC1S2 gene

“…Several disease-causing mechanisms have been identified such as insertional mutagenesis and aberrant splicing [25, 28]. On the other hand, TEs can be advantageous elements that increase genomic diversity, and have a tremendous impact on evolution at the DNA and RNA levels by transduction-mediated gene formation, gene retrotransposition, alternative splicing, alternative polyadenylation, and the actions of alternative promoters, enhancers, and silencer elements [11, 18, 25]. In the present study, for the first time, we identified and validated that MIR_ Alu Sp combined sequences induced lineage-specific alternative splicing events and played an important role in diversifying BLOC1S2 gene transcripts, especially in the crab-eating monkey, rhesus monkey, and African green monkey.…”

“…Specifically, Alu and MIR, which belong to the SINE family, are known to contribute to alternative splicing [16]. The Alu element, the most abundant TE in the human genome, is primate specific and composed of two similar monomers, the left and right arms, and these arms in the antisense orientation provide potential 5′- and 3′-splicing sites that can be recognized by the spliceosome [17, 18]. Moreover, a previous study has shown that Alu creates ~ 5% of the alternatively spliced exons in the human genome; thus, it is considered crucial for AS events [19].…”

Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation

“…This element is about 300 bases long, formed from two similar monomers, called "leftarm" and "right-arm" 18,21 . Antisense Alu in the genic region tends to provide potential splicing donor (GT) and acceptor (AG) sites, creating a new exon for the transcript 10,22 . This Alu-involved AS event accounts for ~ 5% of all internal alternative exons in the human genome 23 .…”