Splicing Outcomes of 5' Splice Site GT>GC Variants That Generate Wild-Type Transcripts Differ Significantly Between Full-Length and Minigene Splicing Assays.
Jin-Huan Lin,Hao Wu,Wen-Bin Zou,Emmanuelle Masson,Yann Fichou,Gérald Le Gac,David Neil Cooper,Claude Férec,Zhuan Liao,Jian-Min Chen +9 more
TLDR
In this article, 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) is presented.Abstract:
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.read more
Citations
More filters
Journal ArticleDOI
Characterization of a possible founder synonymous variant in TECTA in multiple individuals with autosomal recessive hearing loss
Robert Chen,Maria A. Diaz-Miranda,Erfan Aref-Eshghi,Tiffiney R. Hartman,Christopher C. Griffith,Jennifer L Morrison,Patricia G. Wheeler,Erin Torti,Gabriele Richard,Margaret A. Kenna,Elizabeth T. DeChene,Nancy B. Spinner,Renkui Bai,Laura K. Conlin,Ian D. Krantz,Samir S. Amr,Minjie Luo +16 more
TL;DR: This study demonstrates that synonymous variants need careful splicing assessment and support from additional testing methodologies to determine their clinical impact, and suggests that this synonymous variant is likely pathogenic for TECTA-associated autosomal recessive hearing loss.
Journal ArticleDOI
Minigene splicing assays reveal new insights into exonic variants of the <i>SLC12A3</i> gene in Gitelman syndrome
TL;DR: Wang et al. as discussed by the authors analyzed 342 previously presumed SLC12A3 missense variants using bioinformatics programs and identified candidate variants that may alter the splicing of pre-mRNA through minigene assays.
Journal ArticleDOI
Counteracting the Common Shwachman–Diamond Syndrome-Causing SBDS c.258+2T>C Mutation by RNA Therapeutics and Base/Prime Editing
L Peretto,Elena Tonetto,Iva Maestri,Valentino Bezzerri,Roberto Valli,Marco Cipolli,Mirko Pinotti,Dario Balestra +7 more
TL;DR: In this article , the authors investigated the molecular mechanisms underlying aberrant SBDS splicing and showed that SBDS exon 2 is dense in splicing regulatory elements and cryptic splice sites, complicating proper 5′ss selection.
Posted ContentDOI
HiFENS: High-throughput FISH detection of endogenous pre-mRNA splicing isoforms
TL;DR: High throughput FISH Detection of ENdogenous Splicing Isoforms, a high-throughput imaging assay based on hybridization chain reaction and used to screen for cellular factors that regulate alternative splicing of endogenous genes to demonstrate optimized detection with high specificity of endogenous splicing isoforms and multiplexing of probes for accurate detection of splicing outcomes with single cell resolution.
Journal ArticleDOI
HiFENS: high-throughput FISH detection of endogenous pre-mRNA splicing isoforms
TL;DR: HiFENS as mentioned in this paper is a high throughput FISH detection of endogenous splicing isoforms, a high-throughput imaging assay based on hybridization chain reaction (HCR) and used HiFENS to screen for cellular factors that regulate alternative splicing of endogenous genes.
References
More filters
Journal ArticleDOI
RNA and Disease
TL;DR: The discovery of disease-causing mutations in RNAs is yielding a wealth of new therapeutic targets, and the growing understanding of RNA biology and chemistry is providing new RNA-based tools for developing therapeutics.
Journal ArticleDOI
Predicting Splicing from Primary Sequence with Deep Learning.
Kishore Jaganathan,Sofia Kyriazopoulou Panagiotopoulou,Jeremy F. McRae,Siavash Fazel Darbandi,David A. Knowles,Yang I. Li,Jack A. Kosmicki,Jack A. Kosmicki,Juan Arbelaez,Wenwu Cui,Grace Schwartz,Eric D. Chow,Efstathios Kanterakis,Hong Gao,Amirali Kia,Serafim Batzoglou,Stephen Sanders,Kyle Kai-How Farh +17 more
TL;DR: A deep neural network is described that accurately predicts splice junctions from an arbitrary pre-mRNA transcript sequence, enabling precise prediction of noncoding genetic variants that cause cryptic splicing.
Journal ArticleDOI
HGVS Recommendations for the Description of Sequence Variants: 2016 Update
Johan T. den Dunnen,Raymond Dalgleish,Donna Maglott,Reece K. Hart,Marc S. Greenblatt,Jean McGowan-Jordan,Anne-Françoise Roux,Timothy D. Smith,Stylianos E. Antonarakis,Peter E.M. Taschner +9 more
TL;DR: The current recommendations, HGVS version 15.11, are presented, and briefly summarize the changes that were made since the 2000 publication, with most focus on removing inconsistencies and tightening definitions allowing automatic data processing.
Journal ArticleDOI
RNA mis-splicing in disease
TL;DR: An overview of RNA splicing mechanisms is provided followed by a discussion of disease-associated errors, with an emphasis on recently described mutations that have provided new insights into splicing regulation.
Journal ArticleDOI
Context-dependent control of alternative splicing by RNA-binding proteins
Xiang-Dong Fu,Manuel Ares +1 more
TL;DR: Some of the emerging rules that govern the highly context-dependent and combinatorial nature of alternative splicing regulation are described.