Suppression of 5′ splice-sites through multiple exonic motifs by hnRNP L

Selection of 5′ splice-sites (5′SS) in alternative splicing plays an important role in gene regulation. Although regulatory mechanisms of heterogeneous nuclear ribonucleoprotein L (hnRNP L), a well-known splicing regulatory protein, have been studied in a substantial level, its role in 5′SS selection is not thoroughly defined. By using a KLF6 pre-mRNA alternative splicing model, we demonstrate in this report that hnRNP L inhibits proximal 5′SS but promotes two consecutive distal 5′SS splicing, antagonizing SRSF1 roles in KLF6 pre-mRNA splicing. In addition, three consecutive CA-rich sequences in a CA cassette immediately upstream of the proximal 5′SS are all required for hnRNP L functions. Importantly, the CA-cassette locations on the proximal exon do not affect hnRNP L roles. We further show that the proximal 5′SS but not the two distal 5′SSs are essential for hnRNP L activities. Notably, in a Bcl-x pre-mRNA model that contains two alternative 5′SS but includes CA-rich elements at distal exon, we demonstrate that hnRNP L also suppresses nearby 5′SS activation. Taken together, we conclude that hnRNP L suppresses 5′SS selection through multiple exonic motifs. •hnRNP L inhibits proximal 5’SS but promotes two consecutive distal 5’SS splicing.•Three consecutive CA-rich sequences immediately upstream of the proximal 5’SS are all required for hnRNP L functions.•The CA-cassette locations on the proximal exon do not affect hnRNP L roles.•The proximal 5’SS but not the two distal 5’SSs are essential for hnRNP L activities.•hnRNP L also suppresses nearby 5’SS activation in Bcl-x pre-mRNA.