Cited by 1RNA modifications and cancerRetinal Development and DisordersEpigenetics and DNA Methylation

METTL3 uncouples chromatin accessibility from transcription during retinal development

Open access
Xu, Jing, Huang, Yuanhao, Han, Zhaowei, Li, Qiang, Liu, Jie, Rao, Rajesh C.·2025·Stem Cell Reports

Abstract

METTL3 is a key regulator of RNA metabolism, yet its genomic and epitranscriptomic roles in tissue development are largely unexplored. Using embryonic stem cell-derived 3D retinal organoids to model retinal progenitor cell (RPC) differentiation, we integrated transcriptome-wide m6A profiling (GLORI), protein-DNA (chromatin immunoprecipitation sequencing [ChIP-seq] and CUT&RUN) and chromatin accessibility (ATAC-seq) mapping, and targeted m6A engineering (dCas13b-FTO) to dissect METTL3 function. Loss of METTL3 nuclear m6A activity disrupted Rx+ retinal anlage formation in vitro, with dCas13b-FTO epitranscriptome engineering revealing that m6A at the Six3 3'UTR governs its stability. Surprisingly, while METTL3 loss altered histone modifications and chromatin accessibility, its direct chromatin targets showed little transcriptional correlation. A degron-based METTL3 degradation strategy, paired with protein-RNA interaction profiling, exposed rapid regulatory shifts in RPCs, revealing a METTL3-Ythdf1 protein-RNA axis. Our multi-omics approach establishes METTL3-dependent m6A as a critical epitranscriptomic layer in retinal development, unveiling a genomic paradigm in which chromatin accessibility diverges from transcriptional output.

AI snapshot

Written from the paper’s full text.

TL;DR

In mESC-derived retinal organoids, nuclear METTL3 catalytic activity is required for Rx+ retinal progenitor cell differentiation, largely through m6A-mediated RNA stability rather than direct chromatin regulation. Acute METTL3 loss changes transcription and m6A without altering chromatin accessibility, revealing uncoupling of chromatin accessibility from transcription and a METTL3-Ythdf1 protein-RNA axis.

Key findings

  • Mettl3KO mESCs failed to form Rx+ RPCs; Dox-inducible HA-METTL3WT rescued differentiation, whereas catalytic mutants APPA, W475A, and N477A did not. Nuclear METTL3WT-GRBD with Dex rescued Rx:GFP+ RPC differentiation, but cytosolic METTL3 without Dex/Dox did not.
  • Nanopore m6A mapping in day 6 RPCs identified n = 26,729 m6A sites, mainly at 3′UTR (56.33%) and CDS (~40%), with ~4% at 5′UTR. GLORI in day 4 organoids found 28,689 WT and 11,881 Mettl3KO high-confidence m6A sites, yielding 27,832 METTL3-dependent m6A sites with the DRACH motif.
  • ChIP-seq identified 314 high-stringency METTL3-specific binding peaks annotated to 222 genes, and CUT&RUN identified 126 METTL3-specific peaks; these chromatin targets showed no transcriptional correlation and no correlation with H3K4me3 or H3K27me3 changes. Acute dTAG-13 (125 nM) degradation caused transcriptional changes at 8 and 24 h but no chromatin accessibility changes by ATAC-seq; 40 RNAs were METTL3-bound and significantly up-regulated at both 8 and 24 h.
  • dCas13b-FTO removal of m6A at Six3 3′UTR sites A1745, A1777, and A1798 increased Six3 mRNA, while removal at CDS site A789 had no effect. METTL3-eCLIP identified 2,584 high-stringency METTL3 target RNAs; Ythdf1 RNA was bound by METTL3, m6A-modified, and rapidly up-regulated after METTL3 degradation, and Ythdf1/2/3 triple-knockout RPCs phenocopied Mettl3KO, rescued by Dox-induced YTHDF2.

Methods

  • Mouse ESC-derived Rx:GFP retinal organoids were used to model mESC-to-RPC differentiation, with CRISPR-Cas9 Mettl3 knockout, Dox-inducible HA-METTL3WT rescue, catalytic mutants, GRBD-Dex nuclear translocation, and dTAG-13 degron-based acute METTL3 degradation.
  • Multi-omics included GLORI for absolute m6A quantification, RNA-seq, ChIP-seq, CUT&RUN, ATAC-seq, METTL3-eCLIP, SELECT for locus-specific m6A detection, and dCas13b-FTO m6A engineering.
  • RNA stability assays used actinomycin D treatment at 0, 2, 4, 6, and 8 h followed by mRNA-seq; several experiments report n = 3 independent experiments.

Limitations

  • Stated: further investigation of the METTL3-Ythdf1 interaction during mESC-to-RPC differentiation is needed; functions of METTL3-direct m6A catalytic targets and the basis for rapid transcriptional changes without major chromatin accessibility changes require deeper study. The authors also state they cannot rule out an indirect effect of METTL3 on chromatin modification and suggest future work on METTL3-associated chromatin modifiers and m6A-modified RNA-chromatin contacts.
  • Evident: the study relies on in vitro mESC-derived retinal organoid models, with no in vivo validation reported in this paper.

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

Integrity signals

Registry

Crossref · 10.1016/j.stemcr.2025.102690

Cites

44 of 44 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

23 of 45 cited sources checked · 14 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    Zfp292 showed the highest reduction in m6A in both SIX3+ RPCs with Mettl3 deletion and CHX10+ RPCs with Mettl14 loss.

    “Zfp292, which inhibits cell cycle progression, showed the highest reduction in m6A in both SIX3+ RPCs with Mettl3 deletion and CHX10+ RPCs with Mettl14 loss.”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites Xin et al., 2022 source

      The Results section, “Overexpression of m6A-tagged RPC genes in late RPCs disturbs late-stage retinogenesis” (page unavailable), identifies Zfp292 among transcripts with reduced m6A modification in Mettl3-CKO retinas. It does not establish that Zfp292 had the highest reduction, or report that result specifically in SIX3+ RPCs or in CHX10+ RPCs with Mettl14 loss. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites Li et al., 2023

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Premisecitation

    In mice, Mettl3 loss leads to abnormalities in RPC-to-Müller glia transition in late retinogenesis due to increased half-life and reduced m6A of RPC transcripts.

    “In mice, Mettl3 loss leads to abnormalities in RPC-to-Müller glia transition in late retinogenesis due to increased half-life and reduced m6A of RPC transcripts (Xin et al., 2022).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Xin et al., 2022 source
  • Findingown data

    METTL3 protein is present in both cytosol and nucleus of Rx:GFP+ RPCs at day 6.

    “METTL3 protein is present in both cytosol and nucleus of Rx:GFP+ RPCs at day 6.”
    Quote in the paperSubstantial claim
  • Findingown data

    Loss of METTL3 nuclear m6A activity disrupts Rx+ retinal anlage formation in vitro.

    “Loss of METTL3 nuclear m6A activity disrupted Rx+ retinal anlage formation in vitro”
    Quote in the paperSubstantial claim
    • Rests on an assumption: mESC-derived retinal organoids faithfully model the mESC-to-RPC differentiation and retinal anlage formation.
  • Findingown data

    The distribution of m6A sites in day 6 RPCs is mainly at 3′UTR (56.33%) and CDS (~40%), with only about 4% at 5′UTR.

    “The distribution of m6A sites (n = 26,729) within transcripts was mainly at 3′UTR (56.33%) and CDS (∼40%), with only about 4% of m6A sites detected localize at 5′UTR (Figure S1A)”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim. 35
  • May combine two claims. 27
  • The quote only partly states this claim. 1
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Similar findings were reported for Mettl14 inactivation and triple deletion of m6A readers Ythdf1, Ythdf2, and Ythdf3.

    “Similar findings were reported for Mettl14 inactivation and triple deletion of m6A readers Ythdf1, Ythdf2, and Ythdf3 (Niu et al., 2022; Li et al., 2023).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Niu et al., 2022 source
    • cites Li et al., 2023

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

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

    Premisecitation

    METTL3 and METTL14 associate in an m6A methyltransferase complex to modify RNA, which regulates RNA metabolism, including stability.

    “RNA methyltransferases (“writers”) such as METTL3 and METTL14 associate in an N6-methyladenosine (m6A) methyltransferase complex to modify RNA, which regulates RNA metabolism, including stability (Liu et al., 2014).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Liu et al., 2014 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Overexpression of Zfp292 phenocopied the effects of Mettl3 and Mettl14 inactivation in late RPCs.

    “Overexpression of Zfp292 phenocopied the effects of Mettl3 and Mettl14 inactivation in late RPCs (Xin et al., 2022; Li et al., 2023).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Xin et al., 2022 source

      The Results section reports that Zfp292 overexpression delayed cell-cycle exit and increased Müller glial fate in late RPCs, effects that overlap with those reported for Mettl3 deficiency. But the Discussion explicitly says overexpression did not faithfully recapitulate the Mettl3-knockout cell-population phenotype, and the passages found do not establish the claimed comparison with Mettl14 inactivation. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites Li et al., 2023

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

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

    Premisecitation

    METTL3 is observed predominantly in nuclear speckles.

    “METTL3 is observed predominantly in nuclear speckles, although m6A methyltransferase activity has been detected in both nuclear and cytoplasmic fractions, including in RPCs (Lin et al., 2016).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Lin et al., 2016 source
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductcitation

    Histone clusters served as a quality control for eCLIP assay and have been previously reported target RNAs for METTL3.

    “We identified histone clusters, which served as a quality control for eCLIP assay, which have been previously reported target RNAs for METTL3 (Figure S4A) (Van Nostrand et al., 2016).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Van Nostrand et al., 2016 source

      In Results, ‘Input normalization improves CLIP signal-to-noise’ (page not provided), the paper uses SLBP binding to histone RNAs to distinguish true eCLIP signal from false-positive signal, supporting their use as an assay check. The cited paper does not identify histone RNAs as previously reported METTL3 targets; that part of the claim is unsupported by our copy. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim.

    Premisecitation

    m6A modifications reduce RNA stability.

    “Classically, m6A modifications are thought to reduce RNA stability; thus loss of m6A leads to increased expression of corresponding RNA (Wang et al., 2014).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Wang et al., 2014 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    m6A methyltransferase activity has been detected in both nuclear and cytoplasmic fractions, including in RPCs.

    “METTL3 is observed predominantly in nuclear speckles, although m6A methyltransferase activity has been detected in both nuclear and cytoplasmic fractions, including in RPCs (Lin et al., 2016).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Lin et al., 2016 source

      The Introduction (page not provided) says that m6A methyltransferase activity has been detected in both nuclear and cytoplasmic extracts. It does not say that this activity was detected in RPCs; searching the indexed copy for “RPCs” found no supporting passage. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim.

    Premisecitation

    Loss of m6A leads to increased expression of corresponding RNA.

    “Classically, m6A modifications are thought to reduce RNA stability; thus loss of m6A leads to increased expression of corresponding RNA (Wang et al., 2014).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Wang et al., 2014 source
  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    The YTHDF family consists of YTHDF1, 2, and 3, and these three m6A readers have overlapping roles in mESCs.

    “The YTHDF family consists of YTHDF1, 2, and 3, and these three m6A readers have overlapping roles in mESCs (Lasman et al., 2020).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Lasman et al., 2020 source
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    m6A depletion via 3′UTR mutations of insulin mRNA or indirectly by mutating Mettl3 decreased insulin protein production, leading to aberrant homeostasis and diabetic-like phenotype.

    “Interestingly, m6A depletion via 3′UTR mutations of insulin mRNA or indirectly by mutating Mettl3 decreased insulin protein production, leading to aberrant homeostasis and diabetic-like phenotype (Wilinski and Dus 2023).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Wilinski and Dus 2023 source
  • May combine two claims.

    Premisecitation

    A functional nuclear localization signal (NLS) on METTL3 has been reported, and NLS mutant of METTL3 retains in cytoplasm.

    “A functional nuclear localization signal (NLS) on METTL3 has been reported, and NLS mutant of METTL3 retains in cytoplasm (Schöller et al., 2018).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Schöller et al., 2018 source
  • Classified as probably not a substantial claim.

    Study design and conductcitation

    The dTAG system (Nabet et al., 2018) was adapted to induce FKBP12F36V-METTL3 acute degradation.

    “The dTAG system (Nabet et al., 2018) was adapted to induce FKBP12F36V-METTL3 acute degradation.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Nabet et al., 2018 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Several reports identified specific crosstalk between m6A RNA modifications and histone modifications, including H3K36me3, H3K9me2, H3K9me3, and K3K27Ac.

    “Indeed, several reports identified specific crosstalk between m6A RNA modifications and histone modifications, including H3K36me3 (Huang et al., 2019), H3K9me2 (Li et al., 2020a), H3K9me3 (Liu et al., 2021a; 2021b), and K3K27Ac (Huang et al., 2025).”
    Quote in the paperNot a substantial claim1 of 3 sources checked
    • cites Huang et al., 2019 source
    • cites Li et al., 2020a

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Liu et al., 2021a

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Classified as probably not a substantial claim.

    Premisecitation

    m6A modifications in the 3′UTR are recognized by YTHDF2 to regulate mRNA degradation.

    “m6A modifications in the 3′UTR are recognized by YTHDF2 to regulate mRNA degradation (Wang et al., 2014), while synergistic interactions between YTHDF1 and YTHDF3 allow recognition of m6A in the 3′UTR to facilitate translation (Wang and Roundtree, 2015; Shi et al., 2017).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Wang et al., 2014 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Synergistic interactions between YTHDF1 and YTHDF3 allow recognition of m6A in the 3′UTR to facilitate translation.

    “m6A modifications in the 3′UTR are recognized by YTHDF2 to regulate mRNA degradation (Wang et al., 2014), while synergistic interactions between YTHDF1 and YTHDF3 allow recognition of m6A in the 3′UTR to facilitate translation (Wang and Roundtree, 2015; Shi et al., 2017).”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites Wang and Roundtree, 2015 source

      The Results sections “YTHDF1 Binds m6A inside Cells” and “YTHDF1 Modulates the Translation Dynamics of m6A-Modified mRNA” show that YTHDF1 recognizes m6A and promotes translation. The Discussion places YTHDF1-binding sites near the stop codon and in the 3′ UTR. The cited paper does not establish a synergistic interaction between YTHDF1 and YTHDF3; its discussion of cooperation concerns YTHDF1 and YTHDF2. Page numbers were not available in our copy. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites Shi et al., 2017 source

      The ‘YTHDF3 facilitates translation’ section reports that YTHDF3 amplified YTHDF1’s translation-promoting effect in a 3′-UTR tethering assay. But that assay replaced the proteins’ m6A-binding domains with artificial tethering domains, so it does not directly show that their interaction recognizes m6A in the 3′UTR. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim.

    Study design and conductcitation

    For Dex inducible WT or APPA Mettl3 plasmid, GRBD insert from pPyCAG-cGR-IP plasmid (RIKEN, #RDB10440) was subcloned to constitutive PiggyBac plasmid to generate GRBD-FLAG-METTL3WT or GRBD-FLAG-METTL3APPA fusion protein (Murakami et al., 2016).

    “For Dex inducible WT or APPA Mettl3 plasmid, GRBD insert from pPyCAG-cGR-IP plasmid (RIKEN, #RDB10440) was subcloned to constitutive PiggyBac plasmid to generate GRBD-FLAG-METTL3WT or GRBD-FLAG-METTL3APPA fusion protein (Murakami et al., 2016).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Murakami et al., 2016 source

      The Methods section on the PiggyBac Tet-on system describes doxycycline-inducible constructs for genes including Nanog, not the claimed dexamethasone-inducible METTL3 constructs. Searches for GRBD, pPyCAG-cGR-IP, METTL3 and APPA found no passage describing the specified insert, subcloning step or fusion proteins in our copy. (LLM, conf=0.75)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    YTHDF1/2/3 are redundant in their roles to promote degradation of m6A-modified RNAs.

    “YTHDF1/2/3 are redundant in their roles to promote degradation of m6A-modified RNAs (Zaccara and Jaffrey 2020, 2024; Niu et al., 2022).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Zaccara and Jaffrey 2020, 2024

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Niu et al., 2022 source

      The Discussion (page not available in our copy) says YTHDF1/2/3 regulate degradation and translation of target mRNAs, and reports that they function redundantly in retinal neurogenesis. It does not establish that the three readers are redundant specifically in promoting degradation of m6A-modified RNAs. (LLM, conf=0.85)

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

    Premisecitation

    A recent report demonstrated crosstalk between m6A RNA methylation and 5mC DNA methylation by METTL14-mediated recruitment of DNMT1 to chromatin, and the balance between these two marks controls key differentiation genes in mESCs.

    “A recent report demonstrated crosstalk between m6A RNA methylation and 5mC DNA methylation by METTL14-mediated recruitment of DNMT1 to chromatin, and the balance between these two marks controls key differentiation genes in mESCs (Quarto et al., 2025).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Quarto et al., 2025 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Some m6A-modified chromatin-associated RNAs can bind directly to DNA to regulate chromatin state and downstream transcription.

    “Some m6A-modified chromatin-associated RNAs can bind directly to DNA to regulate chromatin state and downstream transcription (Liu et al., 2020).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Liu et al., 2020 source

      The paper's Abstract reports that m6A-modified chromosome-associated regulatory RNAs affect chromatin state and downstream transcription. It does not establish the claim that these RNAs bind directly to DNA; the passages on chromatin-associated RNAs and recruited proteins do not demonstrate direct RNA–DNA binding. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim.

    Study design and conductcitation

    METTL3-eCLIP was performed as described previously (Van Nostrand et al., 2016).

    “METTL3-eCLIP was performed as described previously (Van Nostrand et al., 2016).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Van Nostrand et al., 2016 source
  • May combine two claims.

    Findingown data

    METTL3 binds RPC chromatin and regulates bivalent histone modifications and chromatin accessibility, but these events do not alter transcription.

    “We observe that METTL3 binds RPC chromatin and regulates bivalent histone modifications and chromatin accessibility, but these events do not alter transcription.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Mettl3 loss impairs induction of EFTF genes Lhx2, Six3, and Rax but not loss of pluripotency or induction of Sox2/Otx2/Pax6 neuroectodermal genes.

    “In both wild-type (WT) and Mettl3KO organoids, we observed comparable loss of pluripotency gene Nanog as well as similar induction of Sox2+/Otx2+/Pax6+ neuroectodermal genes. In contrast, the induction of EFTF genes Lhx2, Six3, and Rax was remarkably impaired”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Neither nuclear METTL3APPA nor cytosolic METTL3APPA rescues RPC differentiation defects.

    “Neither nucleic METTL3APPA (+Dex) nor cytosolic METTL3APPA (-Dex; -Dox) could rescue the defects (Figures 1F and S1F).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Down-regulated genes in Mettl3 KO vs WT RPCs are less enriched with H3K4me3 and harbor H3K27me3 marks.

    “we found that the down-regulated genes in Mettl3 knockout (KO) vs. WT RPCs were indeed less enriched with H3K4me3 modifications, but these sites harbored H3K27me3 marks (Figure 2B).”
    Quote in the paperSubstantial claim
  • The quote only partly states this claim.

    Findingown data

    m6A modifications are enriched at the 3′UTR in WT and Mettl3KO organoids.

    “We analyzed distribution of m6A modifications across RNA domains, including enrichment at the 3′UTR (Figure 3C)”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Bulk RNA-seq showed DEGs in Mettl3KO organoids were rescued by nucleus-translocated METTL3 (+Dex), but not cytosolic METTL3 (-Dex).

    “Bulk RNA-seq showed differentially expressed genes in Mettl3KO organoids were rescued by nucleus-translocated METTL3 (+Dex), but not cytosolic METTL3 (-Dex).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Cytosol-to-nuclear METTL3 translocation induced by Dex rescued Rx:GFP+ expression in Mettl3KO RPCs, but cytosolic METTL3 did not.

    “Cytosol-to-nuclear METTL3 translocation was induced by adding Dex (10 μM), which rescued the Rx:GFP+ expression in Mettl3KO RPCs, but cytosolic METTL3 (without Dex, without Dox) did not.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    The most enriched GO pathway among METTL3-bound RNAs is RNA binding (p = 2.60e−44), followed by ribonucleoprotein complex and mRNA processing.

    “Gene Ontology (GO) term pathway analysis of the 2584 METTL3-bound RNAs showed that the most enriched pathway is RNA binding (p = 2.60e−44) and followed by ribonucleoprotein complex and mRNA processing (Figure 4B).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Acute degradation of endogenous METTL3 by dTAG-13 is near-complete as quickly as 2 h post-treatment or as low as 62.5 nM.

    “near-complete degradation of FKBP12F36V-HA-METTL3 as quickly as 2 h post-dTAG-13, or as low as 62.5 nM of dTAG-13, was observed (Figure S4B).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Mettl3-dependent H3K4me3 marks are depleted of H3K4me3 and enriched with H3K27me3 in Mettl3KO RPCs.

    “We observed Mettl3-dependent H3K4me3 marks that were not only depleted of this modification in Mettl3KO RPCs but enriched with the repressive H3K27me3 modification at these sites (Figure 2A).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Lhx2 carries m6A modifications both at 5′UTR and 3′UTR, Six3 at 3′UTR, and Rax at 5′UTR.

    “Lhx2 carries m6A modifications both at 5′UTR and at 3′UTR, Six3 with m6A at 3′UTR and Rax at 5′UTR (Figure S3B).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    WT and Mettl3KO organoids harbor 28,689 and 11,881 high-confidence m6A sites, respectively.

    “we found that WT and Mettl3KO organoids harbor 28,689 and 11,881 high-confidence m6A sites, respectively.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Following acute METTL3 degradation, there were changes in transcription and m6A modifications.

    “While we saw changes in transcription and m6A modifications, we did not observe major alterations to chromatin accessibility, indicating an uncoupling between the epigenome and epitranscriptome in this context.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    WDR5 controls EFTF activity and cell fate during retinogenesis.

    “we found that WDR5, a histone methyltransferase co-factor, controls EFTF activity and cell fate during retinogenesis (Li et al. 2020b, 2021).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Li et al. 2020b, 2021

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Premisecitation

    In zebrafish, Mettl3 knockdown leads to microphthalmia due to delayed RPC differentiation and increased cell death.

    “In zebrafish, Mettl3 knockdown leads to microphthalmia due to delayed retinal progenitor cell (RPC) differentiation and increased cell death (Huang et al., 2021).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Huang et al., 2021 source
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    METTL3 non-canonically regulates chromatin accessibility in mESCs via m6A-dependent interaction with histone-modifying enzymes and chromatin-regulatory RNAs, and in fibroblasts through m6A-independent association with enhancers.

    “METTL3 non-canonically regulates chromatin accessibility in mESCs via an m6A-dependent interaction with histone-modifying enzymes and chromatin-regulatory RNAs, as well as the senescence-associated secretary phenotype in fibroblasts through m6A-independent association with enhancers (Liu et al. 2020, 2021a; Xu et al., 2021).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Liu et al. 2020, 2021a

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Xu et al., 2021

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Classified as probably not a substantial claim.

    Premisecitation

    METTL3-dependent m6A modifications have been implicated in regulation of chromatin accessibility.

    “Since METTL3-dependent m6A modifications have been implicated in regulation of chromatin accessibility (Deng et al., 2022)”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Deng et al., 2022 source
  • May combine two claims.

    Interpretationown data

    METTL3 regulates histone modifications, but its direct targets on chromatin do not contribute to gene regulation during mESC-to-RPC differentiation.

    “METTL3 regulates histone modifications, but its direct targets on chromatin do not contribute to gene regulation during mESC-to-RPC differentiation”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Bivalent chromatin dynamics accompanies early mESC lineage commitment.

    “Moreover, bivalent chromatin dynamics accompanies early mESC lineage commitment (Ruthenburg et al., 2007; Schwartz and Pirrotta 2007; Liu et al., 2016).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Ruthenburg et al., 2007 source
    • cites Schwartz and Pirrotta 2007 source
    • cites Liu et al., 2016 source
  • May combine two claims.

    Interpretationown data

    METTL3 associates with specific H3K4me3 modifications in Mettl3-dependent DEGs, likely related to activation of specific genes during mESC-to-RPC differentiation.

    “Our data indicate that METTL3 associates with specific H3K4me3 modifications in Mettl3-dependent DEGs, likely related to activation of specific genes during the mESC-to-RPC differentiation program.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    METTL3 regulates the mESC-to-RPC and RPC-to-retina transcriptional programs.

    “Here, we show that METTL3, the main m6A writer, regulates the mESC-to-RPC and RPC-to-retina transcriptional programs through mechanisms independent of chromatin accessibility and its ability to directly engage chromatin.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: METTL3 is the main m6A writer.
  • May combine two claims.

    Interpretationown data

    METTL3 chromatin targets are not functional: not associated with changes in bivalent histone modifications or transcript expression in RPCs.

    “we conclude that METTL3 chromatin binding in RPCs is uncommon and that METTL3 chromatin targets are not functional: they are not associated with changes in bivalent histone modifications or transcript expression in RPCs.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    Targeted acute METTL3 loss in RPCs leads to impaired retinal development in vitro and in vivo.

    “Targeted acute METTL3 loss in RPCs leads to impaired retinal development in vitro and in vivo”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    More than 95% transduction efficacy was seen on day 6 Rx:GFP+ RPCs following day 0 infection.

    “More than 95% transduction efficacy was seen on day 6 Rx:GFP+ RPCs following day 0 (mESC) infection (Figure 3F).”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Two independent Mettl3 guide RNAs were used to generate independent Mettl3 KO ES clones.

    “For CRISPR-Cas9-mediated Mettl3 knockout, two independent Mettl3 guide RNAs (GTGCTTATTGATAATTCGTCTGG and TGTGAAGCTGGTTAAAGCTCAGG) were used to generate independent Mettl3 KO ES clones.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Both the dose-dependent assay and time-course assay of dTAG-13 treatment using the knockin Rx:GFP mESC cell line were performed to determine the ideal dose and time point of dTAG-13 treatment to achieve acute METTL3 degradation.

    “Both the dose-dependent assay and time-course assay of dTAG-13 treatment using the knockin Rx:GFP mESC cell line were performed to determine the ideal dose and time point of dTAG-13 treatment to achieve acute METTL3 degradation.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Study design and conductnone given

    The knockin stable colonies were screened by genotyping and western blot with both HA antibody and METTL3 antibody.

    “The knockin stable colonies were screened by genotyping and western blot with both HA antibody and METTL3 antibody.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Study design and conductcitation

    The detection of m6A at targeted sites was based on the SELECT method previously developed by Xiao et al. (2018).

    “The detection of m6A at targeted sites was based on SELECT method previously developed by Xiao et al., (2018).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Xiao et al., (2018) source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    CUT&RUN was performed as previously described (Li et al., 2020b; Li et al. 2020b; Li et al. 2021).

    “2×106 cells were subjected to CUT&RUN per antibody as previously described (Li et al., 2020b; Li et al. 2020b; Li et al. 2021).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Li et al., 2020b

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Li et al. 2021

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

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

    Study design and conductcitation

    ChIP-seq was performed using a slightly modified version of ChIP Assay Kit (Millipore)-based protocol as described previously (Li et al. 2020b, 2021).

    “ChIP-seq was performed using a slightly modified version of ChIP Assay Kit (Millipore)-based protocol as described previously (Li et al. 2020b, 2021).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Li et al. 2020b, 2021

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

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

    Study design and conductnone given

    Two biological replicates were conducted for each experiment.

    “Two biological replicates were conducted for each experiment.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductcitation

    Rx:GFP ESC maintenance, induced retinal neuroectoderm differentiation, and plasmid electroporation were performed as described previously (Eiraku et al., 2011; Li et al. 2020b, 2021).

    “Rx:GFP ESC maintenance, induced retinal neuroectoderm differentiation, and plasmid electroporation were performed as described previously (Eiraku et al., 2011; Li et al. 2020b, 2021).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Eiraku et al., 2011 source
    • cites Li et al. 2020b, 2021

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    WT or mutant Mettl3 inserts (APPA, W475A and N477A) were subcloned to Dox-inducible or constitutive PiggyBac plasmids as described previously (Xu et al., 2021).

    “WT or mutant Mettl3 inserts (APPA, W475A and N477A) were subcloned to Dox-inducible or constitutive PiggyBac plasmids as described previously (Xu et al., 2021).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Xu et al., 2021

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    GLORI was performed as reported previously (Liu et al., 2023), slightly modified.

    “GLORI was performed as reported previously (Liu et al., 2023), slightly modified, as follows:”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Liu et al., 2023 source
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationown data

    We cannot rule out an indirect effect of METTL3 on chromatin modification.

    “While we did not find many METTL3-binding sites on chromatin, and that METTL3 chromatin targets did not show differential transcription, we cannot rule out an indirect effect of METTL3 on chromatin modification, given that we observed METTL3-dependent changes in histone modifications.”
    Quote in the paperNot a substantial claim
55 of 55
  • The paper relies on this without support.

    The role of METTL3 and m6A modifications in retinal development is incompletely understood.

    “Despite the relative abundance of m6A RNA methylation, our understanding of the role of Mettl3 and the function of m6A modifications in retinal development is incomplete.”
  • The paper relies on this without support.

    No prior study has explored the direct RNA targets of METTL3, its chromatin targets, or whether epitranscriptomics-epigenetics crosstalk occurs during retinal development.

    “To date, no study has explored the direct RNA targets of METTL3, nor its chromatin targets and whether epitranscriptomics-epigenetics crosstalk occurs during retinal development.”
  • The paper relies on this without support.

    The molecular events of early retinal development cannot be easily studied in vivo due to lack of isolable tissue for NGS-based analyses.

    “The related molecular events cannot be easily studied in vivo due to the dearth of isolable tissue that limit NGS-based analyses.”
  • The paper relies on this without support.

    mESC-derived retinal organoids faithfully model the mESC-to-RPC differentiation and retinal anlage formation.

    “Using embryonic stem cell-derived 3D retinal organoids to model retinal progenitor cell (RPC) differentiation”
  • The paper relies on this without support.

    METTL3 is the primary RNA methyltransferase that catalyzes m6A deposition.

    “METTL3 is the primary RNA methyltransferase that catalyzes m6A deposition.”
  • The paper relies on this without support.

    METTL3 is the main m6A writer.

    “Here, we show that METTL3, the main m6A writer, regulates the mESC-to-RPC and RPC-to-retina transcriptional programs through mechanisms independent of chromatin accessibility and its ability to directly engage chromatin.”
6 of 6

Self-check

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

Each contradiction between two passages listed here was confirmed by an independent check.

  • METTL3 CUT&RUN comparison groups disagree

    Minor

    The Results describe the CUT&RUN comparison as knockout without Dox versus rescued knockout with Dox. The Figure 2 legend instead identifies the groups as WT and Mettl3KO organoids.

  • Figure 3 assigns opposite Six3 results to panels I and J

    Minor

    The legend first includes panels I and J among results in which targeting the Six3 3′UTR increased transcript level, then says those panels show that targeting the CDS had no effect.

  • GLORI replicate counts disagree

    Minor

    The Results state that GLORI was performed in duplicate for each group, whereas the Figure 3 legend reports three independent experiments for the GLORI analyses.

3 of 3

Cites

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Cited by

Sorted by citations

Authors
Xu, J., Huang, Y., Han, Z., Li, Q., Liu, J., & Rao, R. C.
Affiliations
University of Michigan (US)
Corresponding author
Rao, Rajesh C.
Venue
Stem Cell Reports
Publisher
Elsevier BV
Published
2025-11
Volume
20
Issue
11
Pages
102690
ISSN
2213-6711 (ISSN-L)
OpenAlex
W4415478789
Cited by
1
References
43
Citations by year
2026: 1
FWCI
0.25
Type
journal article
Language
en
Open access
Locations
  • Stem Cell Reports (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
Funders
  • National Eye Institute (R01EY030989)
  • National Human Genome Research Institute (R35HG011279)
  • Foundation for the National Institutes of Health
  • March Hoops to BEAT Blindness
  • Research to Prevent Blindness
  • University of Michigan A Alfred Taubman Medical Research Institute
  • Beatrice and Reymont Paul Foundation
  • National Institute of General Medical Sciences
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Retinal Development and Disorders
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
METTL3, m6A RNA methylation, epitranscriptomics, retinal development, retinal progenitor cells, chromatin accessibility, transcription, mRNA stability, YTHDF1, RNA-protein interactions, retinal organoids, histone modifications
MeSH terms
Animals, Cell Differentiation, Chromatin, Methyltransferases, Retina, Transcription, Genetic, Gene Expression Regulation, Developmental, Mice

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 2026-10-23.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-23.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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