SR proteins regulate V6 exon splicing of CD44 pre-mRNA

CD44 pre-mRNA includes 20 exons, of which exons 1-5 (C₁-C₅) and exons 16-20 (C₆-C₁₀) are constant exons, whereas exons 6-15 (V₁-V₁₀) are variant exons. V₆-exon-containing isoforms have been known to be implicated in tumor cell invasion and metastasis. In the present study, we performed a SR protein screen for CD44 V₆ splicing using overexpression and lentivirus-mediated shRNA treatment. Using a CD44 V₆ minigene, we demonstrate that increased SRSF3 and SRSF4 expression do not affect V₆ splicing, but increased expression of SRSF1, SRSF6 and SRSF9 significantly inhibit V₆ splicing. In addition, using a constitutive exon-specific primer set, we could not detect alterations of CD44 splicing after SR protein-targeting shRNA treatment. However, using a V₆ specific primer, we identified that reduced SRSF2 expression significantly reduced the V₆ isoform, but increased V_6-10 and V_6,7-10 isoforms. Our results indicate that SR proteins are important regulatory proteins for CD44 V₆ splicing. [BMB Reports 2016; 49(11): 612-616].