title: Characterization of the Regulation of CD46 RNA Alternative Splicing.
abstract: Here we present a detailed analysis of the alternative splicing regulation of human CD46, which generates different isoforms with distinct functions. CD46 is a ubiquitous membrane protein that protects host cells from complement and plays other roles in immunity, autophagy, and cell adhesion. CD46 deficiency causes an autoimmune disorder, and this protein is also involved in pathogen infection and cancer. Before this study, the mechanisms of CD46 alternative splicing remained unexplored even though dysregulation of this process has been associated with autoimmune diseases. We proved that the 5' splice sites of CD46 cassette exons 7 and 8 encoding extracellular domains are defined by noncanonical mechanisms of base pairing to U1 small nuclear RNA. Next we characterized the regulation of CD46 cassette exon 13, whose inclusion or skipping generates different cytoplasmic tails with distinct functions. Using splicing minigenes, we identified multiple exonic and intronic splicing enhancers and silencers that regulate exon 13 inclusion via trans-acting splicing factors like PTBP1 and TIAL1. Interestingly, a common splicing activator such as SRSF1 appears to repress CD46 exon 13 inclusion. We also report that expression of CD46 mRNA isoforms is further regulated by non-sense-mediated mRNA decay and transcription speed. Finally, we successfully manipulated CD46 exon 13 inclusion using antisense oligonucleotides, opening up opportunities for functional studies of the isoforms as well as for therapeutics for autoimmune diseases. This study provides insight into CD46 alternative splicing regulation with implications for its function in the immune system and for genetic disease.
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
authors.forename: Sze Jing
authors.initials: SJ
authors.lastname: Tang
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
authors.forename: Shufang
authors.initials: S
authors.lastname: Luo
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
authors.forename: Jia Xin Jessie
authors.initials: JXJ
authors.lastname: Ho
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
authors.forename: Phuong Thao
authors.initials: PT
authors.lastname: Ly
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
authors.forename: Eling
authors.initials: E
authors.lastname: Goh
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore. Electronic address: xroca@ntu.edu.sg.
authors.forename: Xavier
authors.initials: X
authors.lastname: Roca
mesh_terms: D017398:Alternative Splicing; D001483:Base Sequence; D004742:Enhancer Elements, Genetic; D005091:Exons; D020868:Gene Silencing; D057809:HEK293 Cells; D006801:Humans; D051916:Membrane Cofactor Protein / Q000235:genetics*; D012313:RNA / Q000235:genetics*
chemical_list: D051916:Membrane Cofactor Protein; D012313:RNA
keywords: alternative splicing; complement system; exonic splicing enhancer; exonic splicing silencer; lymphocyte; molecular genetics