Alu-Derived Alternative Splicing Events Specific to Macaca Lineages in CTSF Gene
Ja-Rang Lee1,3, Sang-Je Park1,3, Young-Hyun Kim1,2,3, Se-Hee Choe1,2, Hyeon-Mu Cho1,2, Sang-Rae Lee1,2, Sun-Uk Kim1,2, Ji-Su Kim1,2, Bo-Woong Sim1, Bong-Seok Song1, Kang-Jin Jeong1, Youngjeon Lee1, Yeung Bae Jin1, Philyong Kang1, Jae-Won Huh1,2,*, and Kyu-Tae Chang1,2,*
1National Primate Research Center, 2University of Science & Technology (UST), National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea, 3These authors contributed equally to this work.
*Correspondence: huhjw@kribb.re.kr (JWH); changkt@kribb.re.kr (KTC)
Received August 26, 2016; Revised January 4, 2017; Accepted January 4, 2017.; Published online February 14, 2017.
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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 crabeating 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 Aluderived 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.
Keywords: Alternative splicing, Alu, CTSF, exonization, primate


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