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Cited by 749RNA Research and SplicingRNA regulation and diseaseGenetics and Neurodevelopmental Disorders

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

Open access
Irimia, Manuel, Weatheritt, Robert J., Ellis, Jonathan D., Parikshak, Neelroop N., Gonatopoulos-Pournatzis, Thomas, Babor, Mariana, Quesnel-Vallières, Mathieu, Tapial, Javier +9 more·2014·Cell
DOI 10.1016/j.cell.2014.11.035PMC PMC4390143
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Abstract

Summary Alternative splicing (AS) generates vast transcriptomic and proteomic complexity. However, which of the myriad of detected AS events provide important biological functions is not well understood. Here, we define the largest program of functionally coordinated, neural-regulated AS described to date in mammals. Relative to all other types of AS within this program, 3-15 nucleotide ‘microexons’ display the most striking evolutionary conservation and switch-like regulation. These microexons modulate the function of interaction domains of proteins involved in neurogenesis. Most neural microexons are regulated by the neuronal-specific splicing factor nSR100/SRRM4, through its binding to adjacent intronic enhancer motifs. Neural microexons are frequently misregulated in the brains of individuals with autism spectrum disorder, and this misregulation is associated with reduced levels of nSR100. The results thus reveal a highly conserved program of dynamic microexon regulation associated with the remodeling of protein interaction networks during neurogenesis, the misregulation of which is linked to autism.

AI snapshot

Written from the paper’s full text.

TL;DR

This paper defines a large neural-regulated alternative splicing program in mammals, showing that 3–27 nucleotide microexons are exceptionally conserved, dynamically regulated during neuronal differentiation, and often controlled by nSR100/SRRM4. It further reports that microexons are frequently misregulated in autistic brains and that this misregulation correlates with reduced nSR100 expression.

Key findings

  • Across human and mouse cell/tissue datasets, the authors identified about 2,500 neural-regulated AS events per species; microexons showed stronger neural-specific inclusion than longer exons (60.7% of microexons with ΔPSI>15 versus 9.5% of longer exons).
  • Of 308 human neural-regulated microexons, 225 (73.5%) were also neural-differentially spliced in mouse, compared with 527 of 1,390 (37.9%) longer neural-regulated exons; many microexons were deeply conserved across vertebrates.
  • During mouse ES-cell-to-cortical-neuron differentiation, 151 of 219 profiled neural-regulated microexons (69%) showed a PSI switch ≥50, and 65 (30%) showed a switch ≥90; nSR100 knockdown/overexpression affected more than half of profiled microexons.
  • In ASD post-mortem superior temporal gyrus samples, 126 of 504 detected microexons (30%) had mean ΔPSI>10 between ASD and control, versus 825 of 15,405 longer exons (5.4%); nSR100 mRNA was downregulated on average by about 10% in ASD samples (p=0.014).

Methods

  • The authors developed an RNA-Seq analysis pipeline to detect all AS classes, including microexons, and applied it to deep datasets from more than 50 human and mouse cell/tissue types, developmental stages, and several vertebrate species.
  • They analyzed microexon regulation across six time points of mouse embryonic stem cell differentiation into cortical glutamatergic neurons, and used knockdown/overexpression plus PAR-iCLIP data to test nSR100/SRRM4 regulation.
  • Protein interaction effects were tested with LUMIER assays and co-immunoprecipitation-western blotting for Apbb1 and AP1S2 microexons; ASD analyses used 24 autistic individuals and 24 matched controls, with 12 ASD samples showing the strongest ASD-associated expression signature and 12 controls selected for downstream comparisons.

Limitations

  • The paper does not state a dedicated limitations section.
  • Evident from the text: the ASD splicing analysis focused on a selected subset of 12 ASD and 12 control samples stratified by a pre-existing ASD gene-expression signature, so findings may not generalize to all autistic individuals.
  • Evident from the text: the link between reduced nSR100 and microexon misregulation in ASD is correlational, and the authors do not establish causation; microexon detection also depends on a specialized pipeline and sufficient RNA-Seq read coverage.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/j.cell.2014.11.035

Cites

113 of 113 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 47 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    The authors' analysis defines the largest known program of functionally coordinated, neural-regulated alternative splicing in mammals.

    “Here, we define the largest program of functionally coordinated, neural-regulated AS described to date in mammals.”
    • Also stated in: § Global features of neural-regulated AS · plain
      “These data reveal the largest program of neural-regulated AS events defined to date, and that this program is associated with a broader range of functional processes and pathways linked to nervous system biology than previously detected (Boutz et al., 2007; Fagnani et al., 2007; Ule et al., 2005).”
    Quote in the paperSubstantial claim
  • Findingown data

    There is a striking inverse relationship between the length of an alternative exon and its propensity to be specifically included in neural tissues.

    “Further analysis of the neural-regulated AS program revealed a striking inverse relationship between the length of an alternative exon and its propensity to be specifically included in neural tissues.”
    Quote in the paperSubstantial claim
  • Findingown data

    Nearly half of neural-regulated alternative splicing events, including alternative retained introns, are predicted to generate protein isoforms both when the alternative sequence is included and skipped.

    “Nearly half of the neural-regulated AS events, including alternative retained introns, are predicted to generate protein isoforms both when the alternative sequence is included and skipped.”
    Quote in the paperNot a substantial claim
  • Findingown data

    Only about 20% of non-neural alternative splicing events have the potential to generate alternative protein isoforms.

    “In contrast, only ∼20% of AS events not subject to neural regulation (hereafter ‘non-neural’ events) have the potential to generate alternative protein isoforms (Figure 1B; p=2.7×10-248, proportion test).”
    Quote in the paperSubstantial claim
  • Findingown data

    The analysis identified approximately 2,500 neural-regulated alternative splicing events in each of human and mouse.

    “By applying this pipeline to more than 50 diverse cell and tissue types each from human and mouse (Table S1), we identified ∼2,500 neural-regulated AS events in each species (Figure 1A and Table S2; Extended Experimental Procedures).”
    Quote in the paperSubstantial claim
  • May combine two claims. 28
  • Classified as probably not a substantial claim. 19

  • May combine two claims.

    Findingown data

    Within the neural-regulated alternative splicing program, 3-15 nucleotide microexons show the strongest evolutionary conservation and switch-like regulation compared with all other alternative splicing types.

    “Relative to all other types of AS within this program, 3-15 nucleotide ‘microexons’ display the most striking evolutionary conservation and switch-like regulation.”
    • Also stated in: § Introduction · boosted
      “Strikingly, neural-included microexons represent the most highly conserved and dynamically-regulated component of this program, and the corresponding genes are highly enriched in neuronal functions.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    There is little overlap (8.5%) between genes with neural-regulated alternative splicing and mRNA expression, although these subsets are highly enriched in overlapping Gene Ontology terms (40% in common).

    “Consistent with previous results (Fagnani et al., 2007; Pan et al., 2004), there is little overlap (8.5%) between genes with neural-regulated AS and mRNA expression, although these subsets of genes are highly enriched in overlapping GO terms (40% in common; Figure S1).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Fagnani et al., 2007 source

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    • cites Pan et al., 2004 source

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  • May combine two claims.

    Findingown data

    60.7% of alternative microexons show increased neural percent spliced in (ΔPSI>15) versus 9.5% of longer (average ~135 nt) alternative exons.

    “60.7% of alternative microexons show increased neural ‘percent spliced in’ (PSI) (ΔPSI>15) versus 9.5% of longer (average ∼135 nt) alternative exons (p=1.9×10-220, proportion test).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Among 49 available and de novo-modeled tertiary protein structures containing microexons, the corresponding residues are largely surface accessible and unlikely to significantly affect the folding of the overlapping or adjacent protein domains.

    “Supporting this view, among 49 available and de novo-modeled tertiary protein structures containing microexons, the corresponding residues are largely surface accessible amd unlikely to significantly affect the folding of the overlapping or adjacent protein domains (Figure S6A; Extended Experimental Procedures).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Microexons are significantly more often conserved at the levels of genomic sequence, detection in alternatively spliced transcripts, and neural-differential regulation.

    “They are also significantly more often conserved at the levels of genomic sequence, detection in alternatively spliced transcripts, and neural-differential regulation (Figure 2D; Figure S2E, neural-regulated exons; p<0.001 for all pairwise comparisons, proportion tests.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Knockdown and overexpression of nSR100 had the strongest effect on microexon regulation, with more than half of the profiled microexons displaying a pronounced change in inclusion level compared to controls.

    “Among several analyzed splicing regulators (Extended Experimental Procedures), knockdown and overexpression of nSR100 had the strongest effect on microexon regulation, with more than half of the profiled microexons displaying a pronounced change in inclusion level compared to controls (Figure 4A and S4A-S4H).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Proteins containing microexons are significantly more often central in protein-protein interaction networks and detected in protein complexes compared to proteins with other types of alternative exons.

    “Moreover, proteins containing microexons are significantly more often central in protein-protein interaction networks and detected in protein complexes compared to proteins with other types of alternative exons (Figures 5H and S5O,P, p≤0.004 for all comparisons, Wilcoxon Rank Sum test).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Of 308 neural-regulated microexons in human, 225 (73.5%) are neural-differentially spliced in mouse, compared to 527 of 1390 (37.9%) longer neural-regulated exons.

    “Of 308 neural-regulated microexons in human, 225 (73.5%) are neural-differentially spliced in mouse, compared to only 527 of 1390 (37.9%) longer neural-regulated exons.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Each cluster revealed significant enrichment of specific Gene Ontology terms including regulation of GTPase activity (Cluster I), glutamate receptor binding and actin cytoskeleton organization (Cluster V).

    “Despite the small number of genes representing clusters of kinetically-distinct sets of regulated microexons, each cluster revealed significant enrichment of specific GO terms including “regulation of GTPase activity” (Cluster I), “glutamate receptor binding” and “actin cytoskeleton organization” (Cluster V) (Table S4).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    While microexons represent only about 1% of all alternative splicing events, they comprise approximately one third of all neural-regulated alternative splicing events conserved between human and mouse that are predicted to generate alternative protein isoforms.

    “Remarkably, while microexons represent only ∼1% of all AS events, they comprise approximately one third of all neural-regulated AS events conserved between human and mouse that are predicted to generate alternative protein isoforms (Figure S2F).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Microexon residues overlapping protein domains are significantly more often surface-accessible and enriched in charged residues than residues overlapping longer neural or non-neural exons.

    “In contrast, microexon residues overlapping protein domains are significantly more often surface-accessible and enriched in charged residues (Figures 5C,D, and S5F-I; p<10-7 for all comparisons, proportion test) than are residues overlapping longer neural or non-neural exons.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Substitution of both microexon residues with alanine also enhanced the Kat5 interaction, although to a lesser extent than the presence of Arg and Glu.

    “Substitution of both microexon residues with alanine also enhanced the Kat5 interaction, although to a lesser extent than the presence of Arg and Glu (Figure 6C).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Inclusion of the Apbb1 microexon significantly enhances the interaction with Kat5, whereas there is little to no effect on the interaction with App.

    “LUMIER and co-immunoprecipitation-western analysis reveals that inclusion of the microexon significantly enhances the interaction with Kat5, whereas there is little to no effect on the interaction with App (Figures 6C,D and Figure S6B,C).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    These late stages correspond to maturing post-mitotic neurons when pan-neuronal markers are already expressed, and are subsequent to the expression of most neurogenic transcription factors.

    “These stages correspond to maturing post-mitotic neurons when pan-neuronal markers are already expressed, and are subsequent to the expression of most neurogenic transcription factors (Figure S3A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Of 219 neural-regulated microexons with sufficient read coverage across time points, 151 (69%) displayed a PSI switch of at least 50 between embryonic stem cells and mature neurons, and 65 (30%) a switch of at least 90.

    “Remarkably, of 219 neural-regulated microexons with sufficient read coverage across time points, 151 (69%) displayed a PSI switch ≥ 50 between ES cells and mature neurons, and 65 (30%) a switch of ≥ 90 (Figure 3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Comparable numbers of alternative microexons were detected in all analyzed vertebrate species, the majority of which are also strongly neural-specifically included.

    “Furthermore, comparable numbers of alternative microexons were detected in all analyzed vertebrate species, the majority of which are also strongly neural-specifically included (Figure 2E; Supplemental Information for details).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    Alternative microexons show the highest genomic sequence conservation, tissue-specific regulatory conservation, and frame-preservation potential among all classes of alternative splicing detected so far in vertebrates.

    “alternative microexons display the highest degrees of genomic sequence conservation, tissue-specific regulatory conservation, and frame-preservation potential, relative to all other classes of AS detected to date in vertebrate species”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Many of the genes with ASD-associated microexon misregulation act in shared pathways and/or physically interact through protein-protein interactions.

    “Many of the corresponding genes act in common pathways and/or physically interact through protein-protein interactions (Figure 7F)”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The ASD and control brain samples analyzed are representative of the broader ASD and control populations.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Many cell- and tissue-type- and developmentally regulated alternative splicing events are coordinately controlled by individual RNA binding proteins, and these events are enriched in genes operating in common biological processes and pathways.

    “An important advance that is facilitating a more general understanding of the role of individual AS events is the observation that many cell/tissue type- and developmentally-regulated AS events are coordinately controlled by individual RBPs, and that these events are significantly enriched in genes that operate in common biological processes and pathways (Calarco et al., 2011; Irimia and Blencowe,”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Calarco et al., 2011 source

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    • cites Irimia and Blencowe, 2012

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    • cites Licatalosi and Darnell, 2010

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Alternative splicing expands the functional and regulatory capacity of metazoan genomes.

    “Alternative splicing (AS) – the process by which different pairs of splice sites are selected in precursor mRNA to generate multiple mRNA and protein products – is responsible for greatly expanding the functional and regulatory capacity of metazoan genomes (Braunschweig et al., 2013; Chen and Manley, 2009; Kalsotra and Cooper, 2011).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Braunschweig et al., 2013 source

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    • cites Chen and Manley, 2009

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    • cites Kalsotra and Cooper, 2011

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  • May combine two claims.

    Interpretationreasoning

    The results reveal a highly conserved program of dynamic microexon regulation associated with remodeling of protein interaction networks during neurogenesis, whose misregulation is linked to autism.

    “The results thus reveal a highly conserved program of dynamic microexon regulation associated with the remodeling of protein interaction networks during neurogenesis, the misregulation of which is linked to autism.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Among analyzed neural-specific exons enriched in disordered regions, about one third promoted or disrupted interactions with partner proteins.

    “Indeed, among a set of analyzed neural-specific exons enriched in disordered regions, approximately one third promoted or disrupted interactions with partner proteins (Ellis et al., 2012).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Ellis et al., 2012 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Changes in the expression of RBFOX1 have been linked to misregulation of alternative splicing in the brains of individuals with autism spectrum disorder.

    “changes in the expression of the RBP RBFOX1 have been linked to misregulation of AS in the brains of individuals with autism spectrum disorder (ASD) (Voineagu et al., 2011).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Voineagu et al., 2011 source

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  • May combine two claims.

    Interpretationown data

    The data reveal the largest program of neural-regulated alternative splicing events defined to date, associated with a broader range of functional processes and pathways linked to nervous system biology than previously detected.

    “These data reveal the largest program of neural-regulated AS events defined to date, and that this program is associated with a broader range of functional processes and pathways linked to nervous system biology than previously detected (Boutz et al., 2007; Fagnani et al., 2007; Ule et al., 2005).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Boutz et al., 2007 source

      Not checked in the free run.

    • cites Fagnani et al., 2007 source

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    • cites Ule et al., 2005 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Human disease mutations often disrupt cis-elements that control splicing and result in aberrant alternative splicing patterns.

    “Human disease mutations often disrupt cis-elements that control splicing and result in aberrant AS patterns (Cartegni et al., 2002).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Cartegni et al., 2002 source

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  • Classified as probably not a substantial claim.

    Premisecitation

    The function of the vast majority of detected alternative splicing events is unknown.

    “However, the function of the vast majority of AS events detected to date are not known, and new landscapes of AS regulation remain to be discovered and characterized(Braunschweig et al., 2014; Eom et al., 2013).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Braunschweig et al., 2014 source

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    • cites Eom et al., 2013 source

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    Premisecitation

    Disease changes can affect the activity or expression of RNA binding proteins, causing entire programs of alternative splicing to be misregulated.

    “Other disease changes affect the activity or expression of RBPs, causing entire programs of AS to be misregulated.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Polymenidou et al., 2012 source

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    • cites Voineagu et al., 2011 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Cell- and tissue-differentially regulated alternative splicing events are under-represented in folded protein domains and enriched in disordered, surface-accessible regions that embed short linear interaction motifs.

    “While cell and tissue differentially-regulated AS events are significantly under-represented in functionally defined, folded domains in proteins, they are enriched in regions of protein disorder that typically are surface accessible and embed short linear interaction motifs (Buljan et al., 2012; Ellis et al., 2012; Romero et al., 2006).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Buljan et al., 2012 source

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    • cites Ellis et al., 2012 source

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    • cites Romero et al., 2006 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    nSR100 promotes the inclusion of a subset of longer neural exons via binding to intronic UGC motifs proximal to suboptimal 3′ splice sites.

    “Recently, we have shown that nSR100 promotes the inclusion of a subset of (longer) neural exons via binding to intronic UGC motifs proximal to suboptimal 3′ splice sites (Raj et al., 2014).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Raj et al., 2014 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Mutations in AP1S2 have been previously implicated in phenotypic features associated with autism spectrum disorder and X-linked mental retardation.

    “Interestingly, mutations in AP1S2 have been previously implicated in phenotypic features associated with ASD and X-linked mental retardation (Borck et al., 2008; Tarpey et al., 2006).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Borck et al., 2008 source

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    • cites Tarpey et al., 2006 source

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  • Classified as probably not a substantial claim.

    Interpretationreasoning

    The properties of microexons suggest that their misregulation could be associated with neurological disorders.

    “The properties of microexons described above suggest that their misregulation could be associated with neurological disorders.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Misregulation of alternative splicing frequently causes or contributes to human disease.

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    The AP1 complex functions in intracellular transport of cargo proteins between the trans-Golgi apparatus and endosomes by linking clathrin to cargo proteins during vesicle membrane formation, and is important for somatodendritic transport of proteins required for neuronal polarity.

    “The AP1 complex functions in the intracellular transport of cargo proteins between the trans-Golgi apparatus and endosomes by linking clathrin to the cargo proteins during vesicle membrane formation (Kirchhausen, 2000), and is important for the somatodendritic transport of proteins required for neuronal polarity (Farias et al., 2012).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Kirchhausen, 2000 source

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    • cites Farias et al., 2012 source

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    Premisecitation

    Apbb1 contains two phosphotyrosine binding domains, PTB1 and PTB2, which bind Kat5 and App, respectively.

    “Apbb1 contains two phosphotyrosine binding domains, PTB1 and PTB2, which bind Kat5 and App, respectively (Cao and Sudhoff, 2001).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Cao and Sudhoff, 2001

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  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Sample selection was independent of any information on splicing changes.

    “Sample selection was independent of any information on splicing changes.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    An alternative microexon overlapping the SH3A domain of Intersectin 1 promotes interaction with Dynamin 1 and was proposed to modulate Itsn1 roles in endocytosis, cell signaling, and/or actin-cytoskeleton dynamics.

    “an alternative microexon overlapping the SH3A domain of Intersectin 1 (Itsn1) has been reported to promote an interaction with Dynamin 1, and was proposed to modulate roles of Itsn1 in endocytosis, cell signaling and/or actin-cytoskeleton dynamics (Dergai et al., 2010)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Dergai et al., 2010 source

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  • Classified as probably not a substantial claim.

    Interpretationreasoning

    The discovery and characterization of widespread, neural-regulated microexons in this study enables systematic investigation of new and highly conserved mechanisms controlling protein interaction networks associated with vertebrate nervous system development and neurological disorders.

    “The discovery and characterization of widespread, neural-regulated microexons in the present study thus enables a systematic investigation of new and highly conserved mechanisms controlling protein interaction networks associated with vertebrate nervous system development and neurological disorders.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    A neural-specific microexon in Protrudin/Zfyve27 increases interaction with VAP and promotes neurite outgrowth.

    “A neural-specific microexon in Protrudin/Zfyve27 was recently shown to increase its interaction with the vesicle-associated membrane protein-associated protein (VAP), and to promote neurite outgrowth (Ohnishi et al., 2014)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ohnishi et al., 2014 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Recent reports have linked individual microexons with neurodevelopmental disorders, including ASD, schizophrenia, and epilepsy.

    “recent reports have begun to link individual microexons with neurodevelopmental disorders, including ASD (Zhu et al., 2014), schizophrenia (Ovadia and Shifman, 2011) and epilepsy (Rusconi et al., 2014)”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Zhu et al., 2014 source

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    • cites Ovadia and Shifman, 2011

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    • cites Rusconi et al., 2014

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    nSR100 promotes neurite outgrowth.

    “we have previously shown that nSR100 promotes neurite outgrowth (Calarco et al., 2009)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Calarco et al., 2009 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Apbb1 is an adapter protein that functions in neurite outgrowth and synaptic plasticity, processes linked to neurological disorders including ASD.

    “Apbb1 is an adapter protein that functions in neurite outgrowth (Cheung et al., 2014; Ikin et al., 2007) and synaptic plasticity (Sabo et al., 2003), processes that have been linked to neurological disorders including ASD (Hussman et al., 2011)”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Cheung et al., 2014 source

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    • cites Ikin et al., 2007 source

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    • cites Sabo et al., 2003 source

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  • May combine two claims.

    Interpretationreasoning

    The results suggest that misregulation of microexons, and of longer alternative exons, may affect protein interaction networks needed for normal neuronal development and synaptic function.

    “the results suggest that the misregulation of microexons, as well as of longer alternative exons (Corominas et al., 2014; Voineagu et al., 2011), may impact protein interaction networks that are required for normal neuronal development and synaptic function”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Corominas et al., 2014 source

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    • cites Voineagu et al., 2011 source

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    • Rests on an assumption: The ASD and control brain samples analyzed are representative of the broader ASD and control populations.
41 of 41

  • The paper relies on this without support.

    Misregulation of alternative splicing frequently causes or contributes to human disease.

    “since the misregulation of AS frequently causes or contributes to human disease, there is a pressing need to systematically define the functions of splice variants in disease contexts.”

  • The paper relies on this without support.

    Gene prediction algorithms, high-throughput RNA sequencing analysis methods, and RNA-Seq datasets generally lack the sensitivity and/or depth required to detect specific types of alternative splicing.

    “Gene prediction algorithms, high-throughput RNA sequencing (RNA-Seq) analysis methods, and RNA-Seq datasets generally lack the sensitivity and/or depth required to detect specific types of AS.”

  • The paper relies on this without support.

    It is generally not known which disease-misregulated alternative splicing events cause or contribute to disease phenotypes.

    “As is the case with assessing the normal functions of AS, it is generally not known which disease-misregulated AS events cause or contribute to disease phenotypes.”

  • The paper relies on this without support.

    Several genes with misregulated microexons have been linked to learning or intellectual disability.

    “Other genes with misregulated microexons have been linked to learning or intellectual disability (e.g. APBB1, TRAPPC9, RAB3GAP1)”

  • The paper relies on this without support.

    The ASD and control brain samples analyzed are representative of the broader ASD and control populations.

    “We analyzed 24 autistic individuals and 24 controls matched by age and gender.”

  • The paper relies on this without support.

    nSR100 mRNA expression levels reflect nSR100 protein activity or functional nSR100 levels.

    “nSR100 mRNA expression is, on average, significantly downregulated in the brains of the analyzed ASD versus control subjects”
6 of 6

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • SRRM4 and RBFOX1 expression are positively correlated, and PTBP1 and SRRM4 expression are anticorrelated.

    “the known positive correlation between SRRM4 and RBFOX1 and anticorrelation between PTBP1 and SRRM4 (refs 14,19)”

    From Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism (2016) · cites this paper as [14]

  • Previous studies identified alterations in local splicing events in ASD and in smaller cohorts in SCZ and BD.

    “Previous studies have identified alterations in local splicing events in ASD (19, 30) and in smaller cohorts in SCZ (2, 24) and BD (31).”

    From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [30]

  • Several studies have demonstrated that genes carrying microexons are preferentially expressed in brain and their splicing is dysregulated in autism spectrum disorder.

    “several studies have demonstrated that genes carrying microexons are preferentially expressed in brain and their splicing is dysregulated in ASD (30, 82, 83).”

    From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [30]

  • nSR100 controls alternative splicing of 3-15 nucleotide microexons during neurogenesis, and reduced nSR100 and dysregulated neuronal microexons are implicated in some cases of autism.

    “nSR100 controls alternative splicing of 3–15 nucleotide “microexons,” which in turn alters protein-protein interactions, during neurogenesis. Reduced levels of nSR100 and dysregulated neuronal microexons are implicated in some cases of autism (Irimia et al., 2014).”

    From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Irimia et al., 2014

  • Recent studies have highlighted the importance of aberrant alternative splicing of mRNA in the brains of subjects with an ASD diagnosis.

    “Recent studies have highlighted the importance of aberrant alternative splicing of mRNA in the brains of subjects with an ASD diagnosis (Corominas et al., 2014; Gandal et al., 2018; Irimia et al., 2014; Parikshak et al., 2016; Voineagu et al., 2011).”

    From Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice (2019) · cites this paper as Irimia et al., 2014

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

  • ASD microexon misregulation rate is overstated

    Major

    The stated count is 126 of 504 microexons, which is 25%, not 30%. This overstates a rate used to describe the extent of ASD-associated misregulation.

    Reported 30 · recomputed 25

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Authors
Irimia, M., Weatheritt, R. J., Ellis, J. D., Parikshak, N. N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallières, M., Tapial, J., Raj, B., O’Hanlon, D., Barrios-Rodiles, M., Sternberg, M. J. E., Cordes, S. P., Roth, F. P., Wrana, J. L., Geschwind, D. H., & Blencowe, B. J.
Affiliations
  • University of Toronto (CA)
  • MRC Laboratory of Molecular Biology (GB)
  • University of California, Los Angeles (US)
  • Centre for Genomic Regulation (ES)
  • Imperial College London (GB)
  • Mount Sinai Hospital (CA)
  • Canadian Institute for Advanced Research (CA)
Corresponding author
  • Irimia, Manuel
  • Blencowe, Benjamin J.
ORCID
Venue
Cell
Publisher
Elsevier BV
Published
2014-12
Volume
159
Issue
7
Pages
1511-1523
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2014.11.035
PMC
PMC4390143
OpenAlex
W2139480055
Semantic Scholar
50b56e7b67ca01c7c25009821818d9e4a479c378
Cited by
693
References
117
Citations by year
2026: 59 · 2025: 63 · 2024: 64 · 2023: 62 · 2022: 59 · 2021: 87 · 2020: 69 · 2019: 49 · 2018: 56 · 2017: 47 · 2016: 40 · 2015: 32 · 2014: 4 · 2013: 1
FWCI
16.82
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
Funders
  • National Institutes of Health (5r01mh094714-04)
  • Canadian Institutes of Health Research
  • National Institute of Mental Health (5R01MH094714, R01-MH094714, F30MH099886, R37MH060233)
  • National Human Genome Research Institute (U01HG001715, R01HG003224, P50HG004233)
  • National Institute of General Medical Sciences (T32GM008042)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
Keywords
microexons, alternative splicing, autism spectrum disorder, SRRM4, neurogenesis, protein-protein interaction domains, evolutionary conservation, brain transcriptome
MeSH terms
Animals, Child Development Disorders, Pervasive, Humans, Models, Molecular, Nerve Tissue Proteins, Neurons, Temporal Lobe, Alternative Splicing, Sequence Analysis, RNA, Mice, Protein Interaction Domains and Motifs, Neurogenesis

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-06.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-06.

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