title: Disease-causing mutations improving the branch site and polypyrimidine tract: pseudoexon activation of LINE-2 and antisense Alu lacking the poly(T)-tail.
abstract: Cryptic exons or pseudoexons are typically activated by point mutations that create GT or AG dinucleotides of new 5' or 3' splice sites in introns, often in repetitive elements. Here we describe two cases of tetrahydrobiopterin deficiency caused by mutations improving the branch point sequence and polypyrimidine tracts of repeat-containing pseudoexons in the PTS gene. In the first case, we demonstrate a novel pathway of antisense Alu exonization, resulting from an intronic deletion that removed the poly(T)-tail of antisense AluSq. The deletion brought a favorable branch point sequence within proximity of the pseudoexon 3' splice site and removed an upstream AG dinucleotide required for the 3' splice site repression on normal alleles. New Alu exons can thus arise in the absence of poly(T)-tails that facilitated inclusion of most transposed elements in mRNAs by serving as polypyrimidine tracts, highlighting extraordinary flexibility of Alu repeats in shaping intron-exon structure. In the other case, a PTS pseudoexon was activated by an A>T substitution 9 nt upstream of its 3' splice site in a LINE-2 sequence, providing the first example of a disease-causing exonization of the most ancient interspersed repeat. These observations expand the spectrum of mutational mechanisms that introduce repetitive sequences in mature transcripts and illustrate the importance of intronic mutations in alternative splicing and phenotypic variability of hereditary disorders.
authors.affiliation: Division of Clinical Chemistry and Biochemistry, University Children's Hospital Zürich, Switzerland.
authors.forename: David
authors.initials: D
authors.lastname: Meili
authors.forename: Jana
authors.initials: J
authors.lastname: Kralovicova
authors.forename: Julian
authors.initials: J
authors.lastname: Zagalak
authors.forename: Luisa
authors.initials: L
authors.lastname: Bonafé
authors.forename: Laura
authors.initials: L
authors.lastname: Fiori
authors.forename: Nenad
authors.initials: N
authors.lastname: Blau
authors.forename: Beat
authors.initials: B
authors.lastname: Thöny
authors.forename: Igor
authors.initials: I
authors.lastname: Vorechovsky
mesh_terms: D020087:Alu Elements / Q000235:genetics*; D001483:Base Sequence; D002460:Cell Line; D016373:DNA, Antisense / Q000235:genetics*; D004194:Disease / Q000235:genetics*; D005091:Exons / Q000235:genetics*; D005260:Female; D006801:Humans; D007231:Infant, Newborn; D007438:Introns / Q000235:genetics; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D008297:Male; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D009687:Nuclear Proteins / Q000378:metabolism; D009690:Nucleic Acid Conformation; D019761:Phosphorus-Oxygen Lyases / Q000235:genetics / Q000378:metabolism; D011071:Poly T / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism; D017384:Sequence Deletion / Q000235:genetics; D000068103:Serine-Arginine Splicing Factors
chemical_list: D016373:DNA, Antisense; D009687:Nuclear Proteins; D022821:RNA Splice Sites; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D000068103:Serine-Arginine Splicing Factors; D011071:Poly T; D019761:Phosphorus-Oxygen Lyases; C043497:6-pyruvoyltetrahydropterin synthase