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Combining data derived from a meta-analysis of human disease-associated 5′ splice site GT>GC (i.e., +2T>C) variants and a cell culture-based full-length gene splicing assay (FLGSA) of forward engineered +2T>C substitutions, we recently estimated that ∼15–18% of +2T>C variants can generate up to 84% wild-type transcripts relative to their wild-type counterparts. Herein, we analyzed the splicing outcomes of 20 +2T>C variants that generate some wild-type transcripts in two minigene assays. We found a high discordance rate in terms of the generation of wild-type transcripts, not only between FLGSA and the minigene assays but also between the different minigene assays. In the pET01 context, all 20 wild-type minigene constructs generated the expected wild-type transcripts; of the 20 corresponding variant minigene constructs, 14 (70%) generated wild-type transcripts. In the pSPL3 context, only 18 of the 20 wild-type minigene constructs generated the expected wild-type transcripts whereas 8 of the 18 (44%) corresponding variant minigene constructs generated wild-type transcripts. Thus, in the context of a particular type of variant, we raise awareness of the limitations of minigene splicing assays and emphasize the importance of sequence context in regulating splicing. Whether or not our findings apply to other types of splice-altering variant remains to be investigated.

Combining data derived from a meta-analysis of human disease-associated 5′ splice site GT>GC (i.e., +2T>C) variants and a cell culture-based full-length gene splicing assay (FLGSA) of forward engineered +2T>C substitutions, we recently estimated that ∼15–18% of +2T>C variants can generate up to 84% wild-type transcripts relative to their wild-type counterparts. Herein, we analyzed the splicing outcomes of 20 +2T>C variants that generate some wild-type transcripts in two minigene assays. We found a high discordance rate in terms of the generation of wild-type transcripts, not only between FLGSA and the minigene assays but also between the different minigene assays. In the pET01 context, all 20 wild-type minigene constructs generated the expected wild-type transcripts; of the 20 corresponding variant minigene constructs, 14 (70%) generated wild-type transcripts. In the pSPL3 context, only 18 of the 20 wild-type minigene constructs generated the expected wild-type transcripts whereas 8 of the 18 (44%) corresponding variant minigene constructs generated wild-type transcripts. Thus, in the context of a particular type of variant, we raise awareness of the limitations of minigene splicing assays and emphasize the importance of sequence context in regulating splicing. Whether or not our findings apply to other types of splice-altering variant remains to be investigated. [ABSTRACT FROM AUTHOR]

We identified a novel homozygous mutation in the splice site donor (SSD) of intron 30 (c.5866 + 1G > A) in consanguineous Japanese SPG11 siblings showing late-onset spastic paraplegia using the whole-exome sequencing. Phenotypic variability was observed, including age-at-onset, dysarthria and pes cavus . Coding DNA sequencing revealed that the mutation affected the recognition of the constitutive SSD of intron 30, splicing upstream onto a nearby cryptic SSD in exon 30. The use of constitutive splice sites of intron 29 was confirmed by sequencing. The mutant transcripts are mostly subject to degradation by the nonsense-mediated mRNA decay system. SPG11 transcripts, escaping from the nonsense-mediated mRNA decay pathway, would generate a truncated protein (p.Tyr1900Phefs5X) containing the first 1899 amino acids and followed by 4 aberrant amino acids. This study showed a successful clinical application of whole-exome sequencing in spastic paraplegia and demonstrated a further evidence of allelic heterogeneity in SPG11. The confirmation of aberrant transcript by splice site mutation is a prerequisite for a more precise molecular diagnosis. [ABSTRACT FROM AUTHOR]

Hereditary hemorrhagic telangiectasia (HHT) occasionally can be discovered in patients with cerebrovascular disease. Pulmonary arteriovenous malformation (PAVM) is one of the complications in HHT and occasionally is causative for life-threatening embolic stroke. Several genetic defects have been reported in patients with HHT. The broad spectrum of phenotype and intrafamilial phenotype variations, including age-at-onset of vascular events, often make an early diagnosis difficult. We present here a Japanese family with a novel intronic heterozygous mutation of ENG , which was identified using whole exome sequencing (WES). The intronic mutation, IVS3 + 4delAGTG, results in in-frame deletion of exon 3 and would produce a shorter ENG protein lacking the extracellular forty-seven amino acid sequences, which is located within the orphan domain. Our findings highlight the importance of the domain for the downstream signaling pathway of transforming growth factor-beta and bone morphogenesis protein superfamily receptors. Considering the phenotype variations and the available treatment for vascular complications, an early diagnosis using genetic testing, including WES, should be considered for individuals at risk of HHT. [ABSTRACT FROM AUTHOR]

Efficient gene silencing tools are extremely important for genomics and biotechnology applications. A number of aberrant RNA species induce silencing of homologous genes; however, only the inverted repeat RNA is widely utilized for targeted gene silencing in plants. Development of additional silencing constructs would not only provide an alternative technology for single targets, it may also serve as a simpler platform for multi-target silencing. The present study found that aberrantly terminated sense transcripts serve as efficient inducers of gene silencing. A construct initially designed to carry out homologous recombination into the Phytochrome A locus of Arabidopsis induced instead a high rate of Phytochrome A silencing, resulting in a strong mutant phenotype. Attempts to decipher the silencing determinant of the construct revealed that absence of a proper transcription termination signal contributed to the silencing efficiency of the construct. Furthermore, silencing of an additional gene, Phytochrome B, was conferred by a separate construct of a similar design. Proper placement of a transcription termination signal in the silencing construct abolished its silencing ability. Therefore, transcription of aberrantly terminated transcripts was deduced to be the cause of the elevated rate of silencing observed in transgenic lines. These transcripts could be produced either by direct transcription or read-through transcription. Since silencing resulted in strong mutant phenotypes in the majority of transgenic lines, terminator-less constructs are proposed to serve as efficient tools for knocking out endogenous targets. [ABSTRACT FROM AUTHOR]

Abstract: To evaluate whether the tumour suppressor gene, PPP2R1B, is involved in pathogenesis of hepatocellular carcinoma (HCC), reverse transcription-polymerase chain reaction (RT-PCR) and cDNA sequencing were performed. Eleven of 38 (29%) tumours and 1 of 34 (3%) corresponding non-tumour tissues showed coexpression of wild-type and aberrant mRNA. Various deletions were found in aberrant transcripts. Southern blot analysis did not show gene deletion in tumours, suggesting abnormal RNA splicing may be involved. These data suggest the possibility that aberrant transcripts of PPP2R1B might be associated with the development of HCC. [Copyright &y& Elsevier]

Petal and stamen identity of the Antirrhinum majus flower is under the genetic control of the floral homeotic gene DEFICIENS ( DEF). To isolate factors involved in the regulation of DEF gene activity, a promoter segment of this B-function gene, containing cis-acting regulatory elements, was used to identify the novel trans-acting factor ROSINA (RSI). RSI does not show an extended similarity with any gene product present in the database. Rather RSI constitutes a protein that contains domains similar to known proteins from organisms of different phyla. The capacity of RSI to bind a sequence element of the DEF promoter, its spatial and temporal expression pattern together with the phenotype of RSI-RNAi interference plants as well as RSI over-expression in Arabidopsis thaliana suggest that RSI is a putative regulator of DEF gene activity in A. majus. [ABSTRACT FROM AUTHOR]

The zebrafish no tail gene ( ntl) is indispensable for the formation of the notochord and the tail structure. In a wild-type zebrafish population, we occasionally observed adult zebrafish with a narrow or no tailfin. This led us to examine the hypothesis that the activity of ntl was somehow genetically unstable. Here we present two findings regarding the gene. First, approximately 3% of ntl transcripts were aberrant; most of them carried deletions at various positions. Second, free, DNA double-stranded ends (DSEs) were formed at an AT dinucleotide repeat in ntl. DSEs were also generated in another zebrafish gene, noggin2 ( nog2). DSEs in ntl and nog2 had common characteristics, which suggested that the AT repeats in these genes elicited DSEs by blocking progression of the replication. [ABSTRACT FROM AUTHOR]

Inactivation of the TSG101 gene has been shown to induce cellular transformation of NIH3T3 fibroblasts, and aberrant TSG101 transcripts have been observed not only in various human solid tumors but also in hematopoietic malignant disorders. In the present study, we performed nested reverse transcription/polymerase chain reaction (RT-PCR) analysis to identify aberrant TSG101 transcripts in 43 human leukemia and lymphoma cell lines. We could detect only a single band of the wild-type transcript with the expected size in virtually all cell lines after the first round of PCR. As in the case with various human solid tumors, the smaller TSG101 transcripts appeared in most of these cell lines after the second round of PCR. Thus, the expression level of the variant transcripts was extremely low as compared with that of the wild-type transcript, and this finding was also confirmed by Northern blot analysis. Identification of various truncated transcripts with extensive deletions in the TSG101 coding region was confirmed by means of sequencing analysis, and expression of these transcripts did not appear to be associated with a specific type of hematopoietic malignant disorder. Southern blot analysis did not indicate any gross TSG101 gene rearrangement. The truncated transcripts were also detected in normal peripheral blood leukocytes. Our results suggest that the truncated TSG101 transcripts are definitely detectable in various human leukemia and lymphoma cell lines, but do not support the notion that the variant transcripts may have a major functional relevance in the pathogenesis of human hematopoietic malignant disorder. [ABSTRACT FROM AUTHOR]

Tuberous sclerosis complex (TSC) is a rare autosomal dominant disorder characterized by non-cancerous tumors in multiple organs including the brain, kidney, lung, heart, and skin. We encountered a Japanese family consisting of two siblings (a four-year-old boy and a one-year-old girl) with multiple cardiac rhabdomyomas conveying a high risk of TSC and apparently unaffected sibling (a two-year-old girl) and parents. Whole exome sequencing and application of Integrative Genomic Viewer revealed an identical intragenic TSC1 deletion with the breakpoints on intron 15 and exon 19 in the affected siblings, but not in the apparently unaffected sibling and parents. Subsequently, PCR-based analyses were performed using primers flanking the deletion, showing that the deletion was also present in the father and that the deletion occurred between chr9:135,777,038 (bp) and chr9:135,780,540 (bp) in association with a one bp overlap. Furthermore, RT-PCR analyses were carried out using lymphoblastoid cell lines, revealing a major in-frame insertion/deletion transcript produced by aberrant splicing using a cryptic ″ag″ splice acceptor motif at intron 15 (r.1998_2438delinsTTCATTAGGTGG) and a minor frameshift transcript generated by aberrant splicing between exon 15 and exon 20 (r.1998_2502del, p.Lys666Asnfs*15) in the affected siblings. These findings imply that the intragenic deletion producing two aberrant transcripts was generated as a somatic pathogenic variant involving the germline in the father and was transmitted to the affected siblings. [ABSTRACT FROM AUTHOR]