Phenotypic consequences of branch point substitutions

Královičová, Jana; Lei, Hetian; Vořechovský, Igor

doi:10.1002/humu.20362

Cited by 39 publications

(41 citation statements)

References 81 publications

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“…We can readily envisage at least three consequences of SNPs within extended AGEZs. First, sequence variants of a distant BP may affect the degree of exon inclusion, as they do for canonically positioned BPs (Kralovicova et al 2004(Kralovicova et al , 2006. Second, splicing regulatory elements may be affected, with possible tissue-specific consequences on alternative splicing.…”

Section: Snps and Agezsmentioning

confidence: 99%

Four exons of the serotonin receptor 4 gene are associated with multiple distant branch points

Hallegger

Sobala²,

Smith³

2010

RNA

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Splicing of vertebrate introns involves recognition of three consensus elements at the 39 end. The branch point (BP) and polypyrimidine tract (PPT) are usually located within 40 nucleotides (nt) of the 39 splice site (39 ss), AG, but can be much more distant. A characteristic of the region between distant BPs (dBPs) and the 39 ss is the absence of intervening AG dinucleotides, leading to its designation as the ''AG exclusion zone'' (AGEZ). The human HTR4 gene, which encodes serotonin receptor 4 and has been associated with schizophrenia, bipolar disease, and gastrointestinal disorders, has four exons with extensive AGEZs. We have mapped the BPs for HTR4 exons 3, 4, 5, and g generated by in vitro splicing, and validated them by mutagenesis in exon-trapping vectors. All exons used dBPs up to 273 nt upstream of the exon. Strikingly, exons 4 and 5 used combinations of both distant and conventionally located BPs, suggesting that successful splicing of these exons can occur by distinct pathways. Our results emphasize the importance for single nucleotide polymorphism resequencing projects to take account of potential dBPs, as the extended AGEZs are vulnerable to mutations that could affect splicing itself or regulation of alternative splicing.

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Section: Snps and Agezsmentioning

confidence: 99%

Four exons of the serotonin receptor 4 gene are associated with multiple distant branch points

Hallegger

Sobala²,

Smith³

2010

RNA

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“…28 Other A4G branch point substitutions had been observed in various Mendelian disorders, which caused reduced expression of the normal transcripts. 29 However, this A4G transversion does not fall in a typical branch point sequence.…”

Section: Homozygosity Mapping For the Disease-causing Genementioning

confidence: 95%

Limb girdle myasthenia with digenic RAPSN and a novel disease gene AK9 mutations

et al. 2016

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Though dysfunction of neuromuscular junction (NMJ) is associated with congenital myasthenic syndrome (CMS), the proteins involved in neuromuscular transmission have not been completely identified. In this study, we aimed to identify a novel CMS gene in a consanguineous family with limb-girdle type CMS. Homozygosity mapping of the novel CMS gene was performed using high-density single-nucleotide polymorphism microarrays. The variants in CMS gene were identified by whole-exome sequencing (WES) and Sanger sequencing. A 20 MB-region of homozygosity (ROH) was mapped on chromosome 6q15-21. This was the only ROH that present in all clinically affected siblings and absent in all clinically unaffected siblings. WES showed a novel variant of AK9 gene located in this ROH. This variant was a start-gain mutation and introduced a cryptic 5′-UTR signal in intron 5 of the AK9 gene. The normal splicing signal would be interfered by the cryptic translation signal leading to defective splicing. Another 25 MB-ROH was found on chromosome 11p13-q12 in all siblings. WES showed a homozygous RAPSN pathogenic variant in this ROH. Since RAPSN-associated limb-girdle type CMS was only manifested in AK9 homozygous variant carriers, the disease phenotype was of digenic inheritance, and was determined by the novel disease modifier AK9 which provides NTPs for N-glycosylation. This is the first time that this specific genotype-phenotype correlation is reported. Importantly, the AK9-associated nucleotide deficiency may replete by dietary supplements. Since AK9 is a disease modifier, enhancing N-glycosylation by increasing dietary nucleotides may be a new therapeutic option for CMS patients.

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Section: Splicing Reporter Constructsmentioning

confidence: 99%

“…17,73 The SMN2 minigene 17 was a gift from Drs Ravi and Nathalia Singh, Iowa University. The F9 minigene had a substitution of the branch point adenine 73 to obtain similar levels of exon inclusion and skipping. The L1CAM minigene 73 contained the MIR hairpin at 2 different positions of the central exon to create reporters L1CAM(r1)-FGB and L1CAM(r2)-FGB.…”

Section: Splicing Reporter Constructsmentioning

confidence: 99%

The role of short RNA loops in recognition of a single-hairpin exon derived from a mammalian-wide interspersed repeat

et al. 2015

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Splice-site selection is controlled by secondary structure through sequestration or approximation of splicing signals in primary transcripts but the exact role of even the simplest and most prevalent structural motifs in exon recognition remains poorly understood. Here we took advantage of a single-hairpin exon that was activated in a mammalian-wide interspersed repeat (MIR) by a mutation stabilizing a terminal triloop, with splice sites positioned close to each other in a lower stem of the hairpin. We first show that the MIR exon inclusion in mRNA correlated inversely with hairpin stabilities. Employing a systematic manipulation of unpaired regions without altering splice-site configuration, we demonstrate a high correlation between exon inclusion of terminal tri-and tetraloop mutants and matching tri-/ tetramers in splicing silencers/enhancers. Loop-specific exon inclusion levels and enhancer/silencer associations were preserved across primate cell lines, in 4 hybrid transcripts and also in the context of a distinct stem, but only if its loopclosing base pairs were shared with the MIR hairpin. Unlike terminal loops, splicing activities of internal loop mutants were predicted by their intramolecular Watson-Crick interactions with the antiparallel strand of the MIR hairpin rather than by frequencies of corresponding trinucleotides in splicing silencers/enhancers. We also show that splicing outcome of oligonucleotides targeting the MIR exon depend on the identity of the triloop adjacent to their antisense target. Finally, we identify proteins regulating MIR exon recognition and reveal a distinct requirement of adjacent exons for C-terminal extensions of Tra2a and Tra2b RNA recognition motifs.

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Phenotypic consequences of branch point substitutions

Cited by 39 publications

References 81 publications

Four exons of the serotonin receptor 4 gene are associated with multiple distant branch points

Four exons of the serotonin receptor 4 gene are associated with multiple distant branch points

Limb girdle myasthenia with digenic RAPSN and a novel disease gene AK9 mutations

The role of short RNA loops in recognition of a single-hairpin exon derived from a mammalian-wide interspersed repeat

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