Pseudoexons provide a mechanism for allele-specific expression of APC in familial adenomatous polyposis.
Allele-specific expression (ASE) of the Adenomatous Polyposis Coli (APC) gene occurs in up to one-third of families with adenomatous polyposis (FAP) that have screened mutation-negative by conventional techniques. To advance our understanding of the genomic basis of this phenomenon, 54 APC mutation-negative families (21 with classical FAP and 33 with attenuated FAP, AFAP) were investigated. We focused on four families with validated ASE and scrutinized these families by sequencing of the blood transcriptomes (RNA-seq) and genomes (WGS). Three families, two with classical FAP and one with AFAP, revealed deep intronic mutations associated with pseudoexons. In all three families, intronic mutations (c.646-1806T>G in intron 6, c.1408+729A>G in intron 11, and c.1408+731C>T in intron 11) created new splice donor sites resulting in the insertion of intronic sequences (of 127 bp, 83 bp, and 83 bp, respectively) in the APC transcript. The respective intronic mutations were absent in the remaining polyposis families and the general population. Premature stop of translation as the predicted consequence as well as co-segregation with polyposis supported the pathogenicity of the pseudoexons. We conclude that next generation sequencing on RNA and genomic DNA is an effective strategy to reveal and validate pseudoexons that are regularly missed by traditional screening methods and is worth considering in apparent mutation-negative polyposis families.
University of Helsinki, Medical and Clinical Genetics, Helsinki, Finland.
Taina T
TT
Nieminen
University of Helsinki, Medical and Clinical Genetics, Helsinki, Finland.|Laboratorio de Citogenética y Mutagénesis, Instituto Multidisciplinario de Biología Celular (IMBICE-CONICET-CICPBA), La Plata, Argentina.
Walter
W
Pavicic
University of Helsinki, Medical and Clinical Genetics, Helsinki, Finland.
Noora
N
Porkka
University of Helsinki, Institute for Molecular Medicine Finland, Helsinki, Finland.
Matti
M
Kankainen
Second Department of Surgery, Helsinki University Central Hospital, Helsinki, Finland.
Heikki J
HJ
Järvinen
Department of Colorectal Surgery, Abdominal Center, Helsinki University Hospital, Helsinki, Finland.
Anna
A
Lepistö
University of Helsinki, Medical and Clinical Genetics, Helsinki, Finland.
Päivi
P
Peltomäki
D011125:Adenomatous Polyposis Coli / Q000235:genetics*; D025601:Adenomatous Polyposis Coli Protein / Q000235:genetics*; D000293:Adolescent; D000328:Adult; D000368:Aged; D000483:Alleles; D002648:Child; D015331:Cohort Studies; D004252:DNA Mutational Analysis; D005387:Finland; D020869:Gene Expression Profiling; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007438:Introns / Q000235:genetics*; D008875:Middle Aged; D009154:Mutation; D010375:Pedigree; D011401:Promoter Regions, Genetic; D012326:RNA Splicing / Q000235:genetics*; D017423:Sequence Analysis, RNA; D000073336:Whole Genome Sequencing; D055815:Young Adult
C555337:APC protein, human; D025601:Adenomatous Polyposis Coli Protein
APC; RNA-seq; allele-specific expression; familial adenomatous polyposis; pseudoexon
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