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      Autistic traits in myotonic dystrophy type 1 due to MBNL inhibition and RNA mis-splicing

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          Abstract

          Tandem repeat expansions are enriched in autism spectrum disorder, including CTG expansion in the DMPK gene that underlines myotonic muscular dystrophy type 1. Although the clinical connection of autism to myotonic dystrophy is corroborated, the molecular links remained unknown. Here, we show a mechanistic path of autism via repeat expansion in myotonic dystrophy. We found that inhibition of muscleblind-like (MBNL) splicing factors by expanded CUG RNAs alerts the splicing of autism-risk genes during brain development especially a class of autism-relevant microexons. To provide in vivo evidence that the CTG expansion and MBNL inhibition axis leads to the presentation of autistic traits, we demonstrate that CTG expansion and MBNL-null mouse models recapitulate autism-relevant mis-splicing profiles and demonstrate social deficits. Our findings indicate that DMPK CTG expansion-associated autism arises from developmental mis-splicing. Understanding this pathomechanistic connection provides an opportunity for greater in-depth investigations of mechanistic threads in autism.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            STAR: ultrafast universal RNA-seq aligner.

            Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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              Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference

              We introduce Salmon, a method for quantifying transcript abundance from RNA-seq reads that is accurate and fast. Salmon is the first transcriptome-wide quantifier to correct for fragment GC content bias, which we demonstrate substantially improves the accuracy of abundance estimates and the reliability of subsequent differential expression analysis. Salmon combines a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: MethodologyRole: SoftwareRole: ValidationRole: Formal AnalysisRole: InvestigationRole: Data CurationRole: Writing – Original DraftRole: VisualizationRole: SupervisionRole: Project AdministrationRole: Funding Acquisition
                Role: SoftwareRole: Formal Analysis
                Role: Formal AnalysisRole: Investigation
                Role: Investigation
                Role: Investigation
                Role: Funding Acquisition
                Role: MethodologyRole: ValidationRole: ResourcesRole: Funding Acquisition
                Role: MethodologyRole: ValidationRole: InvestigationRole: Resources
                Role: ResourcesRole: Funding Acquisition
                Role: MethodologyRole: ValidationRole: ResourcesRole: Data CurationRole: Funding Acquisition
                Journal
                Res Sq
                ResearchSquare
                Research Square
                American Journal Experts
                14 August 2023
                : rs.3.rs-3221704
                Affiliations
                University of Nevada, Las Vegas
                the hospital for sick children
                University of Florida
                Adam Mickiewicz University
                University of Florida
                Adam Mickiewicz University in Poznań
                Hospital for Sick Children
                Adam Mickiewicz University
                University of Florida
                University of Florida
                the hospital for sick children
                Author notes
                Author information
                http://orcid.org/0000-0001-6822-6485
                http://orcid.org/0000-0001-9545-4205
                http://orcid.org/0000-0001-6245-5367
                http://orcid.org/0000-0001-7273-4968
                Article
                10.21203/rs.3.rs-3221704
                10.21203/rs.3.rs-3221704/v1
                10462192
                37645891
                4ae503a5-4006-40e0-91ed-17f23aeab822

                This work is licensed under a Creative Commons Attribution 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.

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                Article

                asd,autism spectrum disorder,myotonic dystrophy,short tandem repeat expansion,microexon,alternative splicing,dmpk,mbnl,srrm4,ank2

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