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Cited by 2,072Genetics and Neurodevelopmental DisordersRNA and protein synthesis mechanismsRNA Research and Splicing

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

Open access
Darnell, Jennifer C., Van Driesche, Sarah J., Zhang, Chaolin, Hung, Ka Ying Sharon, Mele, Aldo, Fraser, Claire E., Stone, Elizabeth F., Chen, Cynthia +5 more·2011·Cell
DOI 10.1016/j.cell.2011.06.013PMC PMC3232425
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Abstract

Summary FMRP loss-of-function causes Fragile X Syndrome (FXS) and autistic features. FMRP is a polyribosome-associated neuronal RNA-binding protein, suggesting that it plays a key role in regulating neuronal translation, but there has been little consensus regarding either its RNA targets or mechanism of action. Here we use high throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) to identify FMRP interactions with mouse brain polyribosomal mRNAs. FMRP interacts with the coding region of transcripts encoding pre- and postsynaptic proteins, and transcripts implicated in autism spectrum disorders (ASD). We developed a brain polyribosome-programmed translation system, revealing that FMRP reversibly stalls ribosomes specifically on its target mRNAs. Our results indicate that loss of a translational brake on the synthesis of a subset of synaptic proteins may contribute to FXS. In addition, they provide insight into the molecular basis of the cognitive and allied defects in FXS and ASD, and suggest multiple targets for clinical intervention.

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Crossref · 10.1016/j.cell.2011.06.013

Cites

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Claims the paper makes

0 of 43 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    661 novel FMRP mRNA targets not found previously were conservatively identified.

    “our data conservatively identified 661 novel FMRP mRNA targets not found previously.”
    Quote in the paperSubstantial claim
  • Findingown data

    Comparison with 83 APRA targets revealed only 6 in common (p=0.28).

    “comparison with 83 targets obtained using the APRA method (Miyashiro et al., 2003) revealed only 6 in common (p=0.28; Tables S2C and S3A).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Miyashiro et al., 2003 source

      Not checked in the free run.

  • Findingown data

    FMRP-bound transcripts are enriched for proteins related to neuronal and synaptic transmission and regulation of small GTPase mediated signaling.

    “In both analyses, proteins encoded by FMRP-bound transcripts were enriched in those related to neuronal and synaptic transmission and regulation of small GTPase mediated signaling.”
    Quote in the paperSubstantial claim
  • Findingown data

    The number of FMRP tags per transcript showed little correlation with transcript abundance or length.

    “Importantly, the number of FMRP tags per transcript showed little correlation with transcript abundance or length (Figure S1E–F).”
    Quote in the paperSubstantial claim
  • Findingown data

    FMRP CLIP results were reproducible, with high correlations between exonic tag number per gene across different anti-FMRP antibodies, purification protocols and sequencing platforms.

    “The results were very reproducible, with high correlations seen between exonic tag number per gene in CLIP experiments using different anti-FMRP antibodies, purification protocols and sequencing platforms (Figure S1A–B).”
    Quote in the paperSubstantial claim
  • May combine two claims. 33
  • The quote only partly states this claim. 1
  • Classified as probably not a substantial claim. 11

  • May combine two claims.

    Findingown data

    54% of RIP-CHIP targets were present in the FMRP CLIP target list (p=2.4 × 10−121), accounting for 24% of CLIP targets.

    “54% of RIP-CHIP targets (p=2.4 × 10−121; Tables S2C and S3A) were present in the FMRP CLIP target list, accounting for 24% of CLIP targets.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The 842 FMRP targets were detectable with both antibodies, both CLIP protocols, different sequencing platforms, and were biologically reproducible in at least 6 of 7 experiments for 99% of targets.

    “These FMRP targets were detectable with both antibodies (100%), using both CLIP protocols (100%), different sequencing platforms (100%), and were biologically reproducible (99% were detectable in at least 6 out of 7 experiments).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Addition of kcRNA after run-off did not cause a shift in mRNA distribution, ruling out the possibility that observed changes were due to loss of the mass of FXRPs alone.

    “Significantly, addition of kcRNA after run-off did not cause a shift in the distribution of mRNAs, ruling out the possibility that observed changes in mRNA distributions were due to the loss of the mass of FXRPs alone (Figure S4C).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Labeling of puromycin-resistant complexes by EGFP-FMRP was dependent on FMRP relative to an EGFP negative control, demonstrating physical association of FMRP with stalled polyribosomes in vivo.

    “The labeling of these complexes was dependent on FMRP, relative to an overexpressed negative control (EGFP alone; Figure S7B), demonstrating the physical association of FMRP with stalled polyribosomes in vivo (Figure 7C).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    62% of mGluR5 receptor complex proteins and 34% of NMDAR receptor complex proteins are FMRP targets.

    “Strikingly, a significant fraction of the mGluR5 (62%, p=5.8 × 10−22; Tables S3A and S3D) and NMDAR (34%, p=7.4 × 10−23; Tables S3A and S3E) receptor complex proteins were FMRP targets.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    PABP and Hu shifted to lighter fractions after run-off, as did FMRP when EDTA was added to dissociate ribosomes.

    “In contrast, PABP or Hu shifted to lighter fractions, as did FMRP when EDTA was added to dissociate ribosomes (Figure 3C).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In two biological replicate CLIP experiments, FMRP was crosslinked to the same target transcripts and with the same coding sequence distribution in puromycin-insensitive (stalled) and steady-state complexes.

    “In two biological replicate CLIP experiments, we found that FMRP was crosslinked to the same target transcripts (Figure 7I; Table S7) and with the same CDS distribution in puromycin-insensitive (stalled) and steady-state complexes (Figure 7J).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    After micrococcal nuclease treatment, the majority of FMRP pelleted with ribosomes, PABP was readily released, and rpP0 was MN resistant.

    “Incubation of sucrose-gradient purified polyribosomes with MN, followed by separation of ribosomes from released material on a sucrose cushion, revealed that the majority of FMRP pelleted with the ribosomes (Figure 7D–E). As controls, PABP (bound to mRNA poly(A) tails) was readily released from polyribosomes by MN, while rpP0 was MN resistant.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    There was some correlation between coding sequence length and RRS among all transcripts (R2=0.41), largely due to FMRP targets (R2=0.56 for targets; R2=0.17 for non-targets), consistent with FMRP stalling ribosomes across the length of the coding sequence of its target transcripts.

    “We observed some correlation between coding sequence (CDS) length and RRS among all transcripts (R2=0.41); this was largely due to FMRP targets (Figure 6E, R2=0.56 for targets; R2=0.17 for non-targets), consistent with FMRP stalling ribosomes across the length of the CDS of its target transcripts.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The FMRP-induced stall is dynamic and can be rapidly reversed by RNA decoys in run-off assays.

    “it is likely to be dynamic, as it can be acutely reversed by RNA decoys in run-off assays.”
    Quote in the paperSubstantial claim

  • The quote only partly states this claim.

    Findingown data

    25 of 196 candidate autism susceptibility genes in duplicated loci are FMRP targets (p=0.001).

    “Restricting our analysis to loci containing 5 or fewer protein-coding genes, we found a significant number (25/196) of candidate autism susceptibility genes in duplicated loci are FMRP targets (Tables S3A and S5, p=0.001).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The SFARI autism candidate gene list provides a valid set of ASD susceptibility genes.

  • May combine two claims.

    Findingown data

    No loss of polyribosome integrity was observed in IVTEBP reactions incubated with cycloheximide at 30°C for up to 45 minutes, indicating that ribosome run-off could not be explained by nuclease activity.

    “No loss of polyribosome integrity was observed in parallel reactions incubated with cycloheximide (CHX) at 30°C for up to 45 minutes, indicating that ribosome run-off could not be explained by nuclease activity.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    35S-methionine incorporation in the IVTEBP system was time- and brain polyribosome-dependent and was not increased if hippuristanol was omitted, indicating that elongation can occur on pre-existing brain polyribosome-associated mRNAs without initiation.

    “This run-off was accompanied by 35S-methionine incorporation in a time- and brain polyribosome-dependent manner that was not increased if hippuristanol was omitted (Figure S3B–C), indicating that elongation can occur on pre-existing brain polyribosome-associated mRNAs in the absence of initiation in the IVTEBP system.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    66% of FMRP mRNA binding was within the coding sequence, with no specific position relative to start and stop codons and lower tag density in the 3′ or 5′ UTRs.

    “Strikingly, 66% of FMRP mRNA binding was within the coding sequence (CDS), with no specific position relative to the start and stop codons, and with lower tag density in the 3′ or 5′ UTRs; in comparison, RNA tags of the neuronal Hu proteins mapped predominantly to the 3′ UTR of target transcripts (Figure 2C).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    There was a small but significant increase in protein synthesis of two FMRP targets (Camk2a and Lingo1) in the absence of functional FMRP, with no significant change in overall protein synthesis or in synthesis of the non-target PABP.

    “We found a small but significant increase in protein synthesis of both FMRP targets in the absence of functional FMRP, similar to results reported for Camk2a by Bear and colleagues in slice cultures (Osterweil et al., 2010), with no significant change in either overall protein synthesis or in the synthesis of the non-target PABP (Figure 6G and Figure S6).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Osterweil et al., 2010 source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    RRS was not dependent on transcript abundance (R2=0.01) or on how many ribosomes were associated with the transcript in the steady state (R2=0.07).

    “The RRS was not dependent on transcript abundance (R2=0.01), nor how many ribosomes were associated with the transcript in the steady state (R2=0.07).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the IVTEBP system, puromycin-induced ribosomal run-off was evident within 2 minutes, reached a plateau by 15 minutes, and was saturable.

    “in the presence of puromycin at 30°C, ribosomal run-off was evident within 2 minutes, reached a plateau by 15 minutes, and was saturable, as neither a ten-fold increase in puromycin nor incubation for up to 45 minutes caused additional run-off.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    FMRP co-immunoprecipitated with rpP0-containing complexes, as did ribosomal proteins rpL5 and rpS6, demonstrating a direct association of FMRP with ribosome-containing complexes.

    “FMRP co-IP’d with rpP0-containing complexes, as did the ribosomal proteins rpL5 and rpS6 (Figure 7H), demonstrating a direct association of FMRP with ribosome-containing complexes, reminiscent of previous findings in cultured cells (Khandjian et al., 1996; Siomi et al., 1996).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Khandjian et al., 1996 source

      Not checked in the free run.

    • cites Siomi et al., 1996 source

      Not checked in the free run.

  • May combine two claims.

    Findingcitation

    ERK1 and the mTOR inhibitors Pten, Nf1 and Tsc2 are FMRP targets.

    “FMRP also targets ERK1 and the mTOR inhibitors Pten, Nf1 and Tsc2”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Rai1 and Ube3a carried FMRP CLIP tags in 6/7 and 3/7 experiments, respectively.

    “Rai1 and Ube3a, harbored FMRP CLIP tags in 6/7 and 3/7 experiments, respectively”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    FMRP targets belong to several functional categories, and their overlap with ASD candidate genes is enriched in categories such as synaptic cell adhesion molecules, the NMDAR complex, the mTOR pathway, and small GTPase regulators.

    “We find that FMRP targets fall into several functional categories, as do ASD candidate genes (Sebat et al., 2007; Pinto et al., 2010) and the overlap is enriched in several inter-related functional categories, including synaptic cell adhesion molecules, the NMDAR complex, the mTOR pathway, and regulators of the small GTPases.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Sebat et al., 2007 source

      Not checked in the free run.

    • cites Pinto et al., 2010 source

      Not checked in the free run.

  • May combine two claims.

    Findingreasoning

    FMRP targets include mGluR5 and NMDAR subunits, along with many other proteins in their synaptic complexes.

    “mGluR5 and the NMDAR subunits, the only glutamate receptors known to mediate protein-synthesis dependent long-term synaptic plasticity, are themselves FMRP targets, as are many other protein components of their macromolecular complexes at the synapse.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisenone given

    Loss of FMRP function causes Fragile X Syndrome and autistic features.

    “FMRP loss-of-function causes Fragile X Syndrome (FXS) and autistic features.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Verkerk et al., 1991 source

      Not checked in the free run.

    • cites Hagerman and Hagerman, 2002

      Not checked in the free run.

    • cites Hernandez et al., 2009 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    FMRP is a neuronal RNA-binding protein that is largely associated with polyribosomes.

    “FMRP is a polyribosome-associated neuronal RNA-binding protein, suggesting that it plays a key role in regulating neuronal translation, but there has been little consensus regarding either its RNA targets or mechanism of action.”
    • Also stated in: § Introduction · plain
      “the majority of FMRP is associated with polyribosomes (Feng et al., 1997b; Khandjian et al., 2004; Stefani et al., 2004).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Feng et al., 1997b

      Not checked in the free run.

    • cites Khandjian et al., 2004 source

      Not checked in the free run.

    • cites Stefani et al., 2004 source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    In brain, 85-90% of FMRP is associated with polyribosomes.

    “we first took advantage of the observation that 85–90% of FMRP is associated with polyribosomes in the brain (Figure 1B–D) as a purification step (Stefani et al., 2004).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Stefani et al., 2004 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The I304N missense mutation in FMRP's second RNA-binding domain abolishes polyribosome association and causes a Fragile X phenotype in mice and humans.

    “a missense mutation in the second RNA binding domain (I304N) abolishes FMRP polyribosome association (Zang et al., 2009; Feng et al., 1997a) and causes a Fragile X phenotype in mice (Zang et al., 2009) and humans (DeBoulle et al., 1993).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Zang et al., 2009 source

      Not checked in the free run.

    • cites Feng et al., 1997a

      Not checked in the free run.

    • cites DeBoulle et al., 1993

      Not checked in the free run.

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

    Premisecitation

    FMRP is present in the neuronal cell body, proximal dendrites and axons.

    “In the brain, FMRP is present in the neuronal cell body, proximal dendrites and axons (Christie et al., 2009)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Christie et al., 2009 source

      Not checked in the free run.

  • May combine two claims.

    Premisereasoning

    Earlier approaches to identify FMRP target mRNAs had limited success in deriving a consensus target set, validating targets genetically, or defining FMRP function.

    “The net result is that they have met with limited success either in deriving a consensus set of FMRP mRNA targets, in identifying mRNAs that can be validated as targets in genetic systems, or in defining FMRP function.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    FMRP binds RNA in vitro with high affinity for kissing complex and G-quadruplex motifs through its KH and RGG-type RNA-binding domains.

    “FMRP binds to RNA in vitro (Siomi et al., 1993) with high affinity for kissing complex and G-quadruplex motifs mediated through its KH and RGG-type RNA binding domains, respectively (Darnell et al., 2005a; Darnell et al., 2001).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Siomi et al., 1993

      Not checked in the free run.

    • cites Darnell et al., 2005a

      Not checked in the free run.

    • cites Darnell et al., 2001 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Ribosomes are stalled on FMRP-bound mRNAs in an FMRP-dependent manner in vivo, with stalling relieved in mice carrying either of two different FMRP loss-of-function mutations.

    “suggesting that ribosomes are stalled on FMRP-bound mRNAs in an FMRP-dependent manner in vivo, with stalling relieved in mice harboring either of two different FMRP loss-of function mutations.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The Fmr1 knockout and I304N mouse models faithfully represent the translational consequences of FMRP loss in human FXS.

  • May combine two claims.

    Interpretationown data

    FMRP appears to associate with the coding sequence of transcripts on which some ribosomes may be stalled, suggesting a role in regulating elongation.

    “Thus FMRP appears to associate with the CDS of transcripts on which some of the ribosomes may be stalled, suggesting that FMRP might play a role in regulating translation at the level of elongation.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    Stalled ribosomes might shield mRNA from degradation while it is transported or stored.

    “Stalled ribosomes may also protect mRNA from degradation during transport or storage.”
    Quote in the paperNot a substantial claim

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

    Premisecitation

    A substantial portion of cellular mRNA can be translated in subcellular compartments.

    “It is increasingly recognized that a large fraction of cellular mRNA may be translated within subcellular domains (Martin and Ephrussi, 2009)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Martin and Ephrussi, 2009

      Not checked in the free run.

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

    Premisecitation

    FXS is the leading monogenic cause of ASDs, accounting for up to 5% of all cases, and 90% of affected males show autistic behaviors.

    “FXS is the leading monogenic cause of ASDs, accounting for up to 5% of all cases (Kelleher and Bear, 2008), and 90% of affected males show autistic behaviors (Hernandez et al., 2009).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Kelleher and Bear, 2008 source

      Not checked in the free run.

    • cites Hernandez et al., 2009 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    FMRP-mediated ribosomal stalling can be functional and dynamic, because acutely relieving it leads to increased synthesis of new protein.

    “Therefore FMRP-mediated ribosomal stalling can be functional and dynamic, as acutely relieving it leads to increased synthesis of new protein.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationcitation

    A single stalled ribosome quickly lowers protein output, and recycled ribosomes re-initiate to rebuild the loaded state.

    “The stalling of a single ribosome almost immediately slows protein production, while recycled ribosomes continue to re-initiate and restore the “loaded” state (Figure 7C) (Wolin and Walter, 1988).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Wolin and Walter, 1988

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    FMRP might participate in homeostatic synaptic plasticity by suppressing activity-driven translation, creating a feedback loop that restrains neuronal responses.

    “These observations suggest that FMRP may play a role in homeostatic synaptic plasticity (Turrigiano, 2008). In this model, FMRP would act to repress the translation stimulated by neuronal activity to generate a feedback loop limiting neuronal responses to activity at the level of the neuron rather than a specific synapse.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Turrigiano, 2008 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Acute loss of polyribosome-associated FMRP yields the same relief of translational repression as long-term loss of function in mouse models, indicating that ribosome stalling is likely caused directly and reversibly by FMRP.

    “Taken together, these results demonstrate that acute loss of polyribosome-associated FMRP yields the same relief of translational repression as long-term loss of function in mouse models, indicating that ribosome stalling is likely to be caused directly and reversibly by FMRP.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The Fmr1 knockout and I304N mouse models faithfully represent the translational consequences of FMRP loss in human FXS.

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

    Study design and conductown data

    Reproducibility was 4/4, 2/2, and one replicate for kcRNA decoy, I304N, and KO models, respectively; overall results were consistent in 7/7 experiments across the three loss-of-function models.

    “Experiments gave reproducible results in 4/4, 2/2 and one biologic replicate with kcRNA decoy, I304N mice, and KO mice, respectively. In sum, these results were consistent in 7/7 experiments using three loss of function models.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    FMRP effects were assessed with three loss-of-function models: Fmr1 knockout, I304N knock-in, and kcRNA decoy.

    “The effects of FMRP were measured using three loss-of-function models including the Fmr1 KO and I304N point mutant knock-in mice, and where indicated, addition of in vitro transcribed kcRNA (Darnell et al., 2005a) as a competitive RNA ligand (decoy)”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Darnell et al., 2005a

      Not checked in the free run.

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

    Study design and conductown data

    The experimental findings were replicated in several independent experiments.

    “experimental results were reproduced in multiple independent experiments as noted throughout.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    Control mice in the experiments were littermates.

    “Mice used as experimental controls were littermates”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    A nonparametric ranking of FMRP targets incorporated both total tags per gene from seven CLIP experiments and reproducibility.

    “FMRP targets were ranked using a nonparametric method that considered both the total number of tags/gene in seven different CLIP experiments and experimental reproducibility.”
    Quote in the paperNot a substantial claim
43 of 43

  • The paper relies on this without support.

    The Fmr1 knockout and I304N mouse models faithfully represent the translational consequences of FMRP loss in human FXS.

    “Studies of Fmr1 knockout (KO) and I304N mice have documented a number of defects in synaptic plasticity (Pfeiffer and Huber, 2009; Zang et al., 2009).”

  • The paper relies on this without support.

    The SFARI autism candidate gene list provides a valid set of ASD susceptibility genes.

    “Comparison of the 842 FMRP target genes with 117 evaluable candidate genes from the SFARI database of autism candidate genes (http://gene.sfari.org (Basu et al., 2009)) revealed a highly significant overlap with 28 FMRP targets (24%, p=1.0 × 10−8; Table S3A), including several well-studied autism candidate genes such NLGN3, NRXN1, SHANK3, PTEN, TSC2, and NF1 (Table S5).”

  • The paper relies on this without support.

    The P8-P25 mouse brain developmental window is relevant to human FXS.

    “our results clearly demonstrate that on a cell population level there is no FMRP-dependent difference in steady state mRNA polysome distribution in the P8-P25 mouse brain.”

  • The paper relies on this without support.

    Learning and memory depend on changes in long-term synaptic strength and on new protein synthesis.

    “Learning and memory almost certainly involve changes in long-term synaptic strength and require new protein synthesis.”

  • The paper relies on this without support.

    The molecular basis of symptom overlap between Fragile X Syndrome and autism is not well understood.

    “The molecular basis for the overlap in symptoms between Fragile X Syndrome and autism is poorly understood.”
5 of 5

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?

  • In the mouse brain, Cyfip2 mRNA (but not Cyfip1 mRNA) is a target of FMRP that represses its translation.

    “Indeed, in the mouse brain, Cyfip2 mRNA (but not Cyfip1 mRNA) was reported to be a target of FMRP that represses its translation (Darnell et al., 2011).”

    From New insights into the regulatory function of CYFIP1 in the context of WAVE- and FMRP-containing complexes (2017) · cites this paper as Darnell et al., 2011

    The Results describe FMRP target mRNAs in mouse brain, and the Discussion says FMRP stalls ribosomes on its targets, repressing translation. But our copy does not identify Cyfip2 mRNA as a target or establish the claimed contrast with Cyfip1 mRNA (searched both names). (LLM, conf=0.80)

    Experimental — accuracy not yet measured

  • In Mnk1-null neurons, altered expression of a subset of proteins was observed, including 26 proteins whose encoding mRNAs are bound by FMRP in translating ribosomes.

    “In particular, in Mnk1-null neurons, altered expression of a subset of proteins was observed, including 26 proteins whose encoding mRNAs are bound by FMRP in translating ribosomes (Genheden et al., 2016; Darnell et al., 2011).”

    From New insights into the regulatory function of CYFIP1 in the context of WAVE- and FMRP-containing complexes (2017) · cites this paper as Darnell et al., 2011

  • FMRP acts as an overall suppressor of protein synthesis by regulating nuclear-cytoplasmic translocation and translation of various mRNAs, many of which are associated with synapse function.

    “FMRP acts as an overall suppressor of protein synthesis (Laggerbauer et al., 2001), a function which it achieves by regulating nuclear-cytoplasmic translocation (Feng et al., 1997; Kim et al., 2009) and translation of various mRNAs. Many of these RNAs are associated with synapse function (Darnell et al., 2011).”

    From Astrocytes in fragile X syndrome (2024) · cites this paper as Darnell et al., 2011

  • In mouse, CYFIP2 has been described both as a co-effector and a downstream target of FMRP.

    “It is interesting to notice that in mouse, while we are describing CYFIP1 as an antagonist of FMRP, CYFIP2 has been described both as a co-effector (e.g. depletion of CYFIP2 worsens some phenotypes of Fmr1-knockout mouse) (Han et al., 2015) and a downstream target of FMRP.”

    From New insights into the regulatory function of CYFIP1 in the context of WAVE- and FMRP-containing complexes (2017) · cites this paper as Darnell et al., 2011

    The Introduction and Results describe FMRP regulation of mouse-brain mRNA targets, but the passages found for “CYFIP2” and a targeted search for its transcript do not identify CYFIP2 as one of them. The co-effector example is separately attributed to Han et al. (2015) in the citing sentence. Our copy therefore does not verify the CYFIP2-specific claim attributed to this paper. (LLM, conf=0.73)

    Experimental — accuracy not yet measured

  • mRNA translation of BRSK2, ITSN1, and RALGAPB in neurons is predicted to be regulated by FMR1 protein.

    “mRNA translation of BRSK2, ITSN1, and RALGAPB in neurons is predicted to be regulated by FMR1 protein.35”

    From Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes (2019) · cites this paper as [35]

Cites

Flagged first, then by citations

Research works printed but not linked: 14

  1. Brown, 2001, Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome, Cell, 107, 477, 10.1016/s0092-8674(01)00568-2 · DOI · Paper page
  2. Cahoy, 2008, A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function, J. Neurosci., 28, 264, 10.1523/jneurosci.4178-07.2008 · DOI · Paper page
  3. Darnell, 2005, FMRP RNA targets: identification and validation, Genes Brain Behav., 4, 341, 10.1111/j.1601-183x.2005.00144.x · DOI
  4. Miyashiro, 2003, RNA cargoes associating with FMRP reveal deficits in cellular functioning in Fmr1 null mice, Neuron, 37, 417, 10.1016/s0896-6273(03)00034-5 · DOI · Paper page
  5. Stefani, 2004, Fragile X mental retardation protein is associated with translating polyribosomes in neuronal cells, J. Neurosci., 24, 7272, 10.1523/jneurosci.2306-04.2004 · DOI · Paper page
  6. Abul-Husn, N.S., Bushlin, I., Morón, J.A., Jenkins, S.L., Dolios, G., Wang, R., Iyengar, R., Ma'ayan, A., and Devi, L.A. (2009). Systems approach to explore components and interactions in the presynapse. Proteomics 9, 3303–3315. · DOI · Paper page
  7. Basu, S.N., Kollu, R., and Banerjee-Basu, S. (2009). AutDB: a gene reference resource for autism research. Nucleic Acids Res. 37 (Database issue), D832–D836. · DOI · Paper page
  8. Croning, M.D., Marshall, M.C., McLaren, P., Armstrong, J.D., and Grant, S.G. (2009). G2Cdb: the Genes to Cognition database. Nucleic Acids Res. 37 (Database issue), D846–D851. · DOI
  9. Darnell, J.C., Fraser, C.E., Mostovetsky, O., Stefani, G., Jones, T.A., Eddy, S.R., and Darnell, R.B. (2005a). Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes. Genes Dev. 19, 903–918. · DOI · Paper page
  10. Darnell, J.C., Fraser, C.E., Mostovetsky, O., and Darnell, R.B. (2009). Discrimination of common and unique RNA-binding activities among Fragile X mental retardation protein paralogs. Hum. Mol. Genet. 18, 3164–3177. · DOI
  11. Darnell, R.B. (2010). HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip Rev RNA 1, 266–286. · DOI · Paper page
  12. Heiman, M., Schaefer, A., Gong, S., Peterson, J.D., Day, M., Ramsey, K.E., Suárez-Fariñas, M., Schwarz, C., Stephan, D.A., Surmeier, D.J., et al. (2008). A translational profiling approach for the molecular characterization of CNS cell types. Cell 135, 738–748. · DOI · Paper page
  13. Mathews, M., Sonenberg, N., and Hershey, J.W.B. (2007). Translational Control in Biology and Medicine (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press).
  14. Zang, J.B., Nosyreva, E.D., Spencer, C.M., Volk, L.J., Musunuru, K., Zhong, R., Stone, E.F., Yuva-Paylor, L.A., Huber, K.M., Paylor, R., et al. (2009). A mouse model of the human Fragile X syndrome I304N mutation. PLoS Genet. 5, e1000758. · DOI · Paper page

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Authors
Darnell, J. C., Van Driesche, S. J., Zhang, C., Hung, K. Y. S., Mele, A., Fraser, C. E., Stone, E. F., Chen, C., Fak, J. J., Chi, S. W., Licatalosi, D. D., Richter, J. D., & Darnell, R. B.
Affiliations
  • Rockefeller University (US)
  • University of Massachusetts Chan Medical School (US)
  • Howard Hughes Medical Institute (US)
Corresponding author
  • Darnell, Jennifer C.
  • Darnell, Robert B.
ORCID
Venue
Cell
Publisher
Elsevier BV
Published
2011-07
Volume
146
Issue
2
Pages
247-261
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2011.06.013
PMC
PMC3232425
OpenAlex
W2052326665
Semantic Scholar
938ef69c910e44431f6c9295bcd1a3a11aa04807
Cited by
2,072
References
102
Citations by year
2026: 78 · 2025: 100 · 2024: 127 · 2023: 118 · 2022: 136 · 2021: 148 · 2020: 182 · 2019: 159 · 2018: 168 · 2017: 159 · 2016: 151 · 2015: 144 · 2014: 158 · 2013: 125 · 2012: 97
FWCI
79.81
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
Funders
  • Howard Hughes Medical Institute
  • Georgia Clinical and Translational Science Alliance
  • National Institute on Aging (R01AG030323, AG30323)
  • National Institute of General Medical Sciences (GM95713, K99GM095713, GM46779, R01GM046779)
  • National Institute of Neurological Disorders and Stroke (R01NS040955, NS34389, NS40955)
  • National Center for Research Resources (UL1RR024143)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD40647, R01HD040647, HD37267)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords
FMRP, fragile X syndrome, autism spectrum disorder, ribosome translocation, polysomes, synaptic proteins, RNA-binding proteins, HITS-CLIP, translational regulation
MeSH terms
Animals, Autistic Disorder, Brain, Fragile X Syndrome, Humans, Polyribosomes, Ribosomes, Synapses, Protein Biosynthesis, RNA-Binding Proteins, Sequence Analysis, RNA, Mice, Knockout, Mice, Fragile X Mental Retardation Protein, Fragile X Messenger Ribonucleoprotein 1

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