title: Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut site (IVS4+1A>G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda.
abstract: X-linked spondyloepiphyseal dysplasia tarda can be caused by mutations in the SEDL gene. This study describes an interesting novel mutation (IVS4+1A>G) located exactly at the rare noncanonical AT-AC consensus splicing donor point of SEDL, which regained the canonical GT-AG consensus splicing junction in addition to several other rarer noncanonical splice patterns. The mutation activated several cryptic splice sites and generated the production of seven erroneous splicing isoforms, which we confirmed by sequencing of RT-PCR products and resequencing of cDNA clones. All the practical splice donors/acceptors were further assessed using FSPLICE 1.0 and SPL(M) Platforms to predict potential splice sites in genomic DNA. Subsequently, the expression levels of SEDL among the affected patients, carriers and controls were estimated using real-time quantitative PCR. Expression analyses showed that the expression levels of SEDL in both patients and carriers were decreased. Taken together, these results illustrated how disruption of the AT donor site in a rare AT-AC intron, leading to a canonical GT donor site, resulted in a multitude of aberrant transcripts, thus impairing exon definition. The unexpected splicing patterns resulting from the special mutation provide additional challenges and opportunities for understanding splicing mechanisms and specificity.
authors.affiliation: Children's Hospital of Chongqing Medical University, Central District, Chongqing, PR China.
authors.forename: Feng
authors.initials: F
authors.lastname: Xiong
authors.forename: Jianjun
authors.initials: J
authors.lastname: Gao
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Yun
authors.initials: Y
authors.lastname: Liu
authors.forename: Guoyin
authors.initials: G
authors.lastname: Feng
authors.forename: Wenli
authors.initials: W
authors.lastname: Fang
authors.forename: Hongfen
authors.initials: H
authors.lastname: Chang
authors.forename: Jiang
authors.initials: J
authors.lastname: Xie
authors.forename: Haitao
authors.initials: H
authors.lastname: Zheng
authors.forename: Tingyu
authors.initials: T
authors.lastname: Li
authors.forename: Lin
authors.initials: L
authors.lastname: He
mesh_terms: D001483:Base Sequence; D041321:Chromosomes, Human, X / Q000235:genetics; D004252:DNA Mutational Analysis; D040181:Genetic Diseases, X-Linked / Q000235:genetics*; D006801:Humans; D026901:Membrane Transport Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation; D010009:Osteochondrodysplasias / Q000235:genetics*; D020033:Protein Isoforms / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics*; D012326:RNA Splicing; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D026901:Membrane Transport Proteins; D020033:Protein Isoforms; D022821:RNA Splice Sites; C120759:TRAPPC2 protein, human; D014157:Transcription Factors