1. Developmental Biology
  2. Genetics and Genomics

PRMT1-SFPQ regulates intron retention to control matrix gene expression during craniofacial development

  1. Julia Raulino Lima
  2. Nicha Ungvijanpunya
  3. Qing Chen
  4. Hoang Quoc Hai Pham
  5. Tal Rosen
  6. Greg Park
  7. Mohammadreza Vantankhah
  8. Steven Yen
  9. Yang Chai
  10. Amy E Merrill
  11. Zhaoyang Liu
  12. Jian-Fu Chen
  13. Yanzhong Yang
  14. Weiqun Peng  Is a corresponding author
  15. Jian Xu  Is a corresponding author
  1. Center for Craniofacial Molecular Biology, Department of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, United States
  2. Department of Orthodontics, Faculty of Dentistry, Chulalongkorn University, Thailand
  3. Department of Physics, The George Washington University, United States
  4. Department of Cancer Genetics and Epigenetics, City of Hope, United States
  5. Children’s Hospital Los Angeles, United States
https://doi.org/10.7554/eLife.101386.3
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Cite this article
  1. Julia Raulino Lima
  2. Nicha Ungvijanpunya
  3. Qing Chen
  4. Hoang Quoc Hai Pham
  5. Tal Rosen
  6. Greg Park
  7. Mohammadreza Vantankhah
  8. Steven Yen
  9. Yang Chai
  10. Amy E Merrill
  11. Zhaoyang Liu
  12. Jian-Fu Chen
  13. Yanzhong Yang
  14. Weiqun Peng
  15. Jian Xu
(2026)
PRMT1-SFPQ regulates intron retention to control matrix gene expression during craniofacial development
eLife 13:RP101386.
https://doi.org/10.7554/eLife.101386.3
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10 figures, 1 table and 5 additional files

Figures

Figure 1
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CNCC-specific deletion of Prmt1 elevates intron retention in the embryonic mandibular process.

(A) Expression levels of PRMT1–9 mRNAs in primary isolated cranial neural crest cells (CNCCs) from Wnt1-Cre; Rosa26LSLtdTomato mouse embryo heads at E13.5 and E15.5. TPM, transcript per million. (B) Diagram illustrating the isolation of CNCCs from embryonic mandibles, followed by poly(A)+mRNA isolation and sequencing (n = 4 in control and Prmt1 CKO group). (C) Prmt1 deletion in CNCC caused changes in alternative splicing (AS). Changes in AS events were analyzed by rMATS using RNA sequencing data and significant changes in each type of AS were shown in a stacked bar chart. SE, skipped exon. IR, intron retention. MXE, mutually exclusive exons. A5SS, alternative 5′ splice site. A3SS, alternative 3′ splice site. (D, E) Intron retention was prevalent in CNCCs and altered by Prmt1 deletion. Track view of genes demonstrating intronic and exonic expression with blue boxes indicating exons and blue lines indicating introns. Intron retention was elevated by Prmt1 deletion in Pex12, Mmp23, and Ecm1 (D) and reduced in Tbx1 (E). (F) Quantification of intron expression in Pex12, Mmp23, Ecm1, and Tbx1 by the percentage of intron-retaining mRNAs in each gene, calculated from IRI analysis based on RNA-seq data. *p < 0.05 Prmt1 CKO vs. Control. Control: Wnt1-Cre; Rosa26LSLtdTomato. Prmt1 CKO: Wnt1-Cre; Prmt1fl/fl; Rosa26LSLtdTomato.

Figure 1—source data 1

CNCCs labeled by Tdtomato in mouse embryo.

Sagittal sections of Wnt-Cre; Rosa26LSLtdTomato. whole mouse embryo at E13.5 showing the CNCCs (red, labeled by Tdtomato) and nuclei (blue, labeled by DAPI). The boxed fields showed higher magnification of the craniofacial structures including the mesenchyme, where CNCCs are located, and epithelium, labeled by the asterisks. Scale bars = 1.0 mm, 500 μm, and 100 μm, respectively.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig1-data1-v1.pdf
Figure 1—source data 2

GO analysis of genes with differentially regulated intron retention in Prmt1 CKO mandibles.

Excel file attached.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig1-data2-v1.xlsx
Figure 1—source data 3

Prmt1 deletion in CNCCs did not cause a global change in intron retention.

Whole genome IRI value distribution in the control (Cont, pink) and Prmt1 CKO mutant (Mut, blue) embryos was plotted. There is no significant difference between control and mutate intron retention distribution.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig1-data3-v1.pdf
Figure 2
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CNCC-specific Prmt1 deletion reduced matrix gene expression in the developing mandibles.

(A) Volcano plot illustrating upregulation of 160 and downregulation of 303 genes in the mandibular primordium of Prmt1-deficient embryos at E13.5, compared to control mandibles. (B) Heatmap showing differential gene expression between control and Prmt1-deficient mandibles. (C) GO analysis of pathway enrichment in downregulated genes demonstrating glycosaminoglycan (GAG) degradation and extracellular matrix (ECM) organization as the top pathways. (D) Ingenuity Pathway Analysis suggesting connective tissue, bone, and cartilage development as affected biological processes based on downregulated genes. (E) GO analysis of pathway enrichment in upregulated genes demonstrating adult behavior and cytokine-mediated signaling and p53 signal transduction as top pathways. Control: Wnt1-Cre; Rosa26LSLtdTomato (n = 4). Prmt1 CKO: Wnt1-Cre; Prmt1fl/fl; Rosa26LSLtdTomato (n = 4).

Figure 3
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PRMT1 regulates intron retention in ECM and GAG degradation genes.

(A–C) Intron retention increased in the majority of ECM gene transcripts that were downregulated in Prmt1-deficient embryos, as illustrated by a scatter plot based on intron retention index (IRI). The red line delineates unchanged levels of intron retention. Genes with the top differential IR were represented by red dots and labeled. ECM gene transcripts Adamts16 and Cthrc1 demonstrating higher intron retention in Prmt1-deleted embryos were illustrated by track view in B and quantified for intronic (left) and exonic (right) expression as shown in C. (D) Higher intron retention and lower mRNA abundance of ECM genes were validated in additional embryo samples by RT-PCR. Primers that span the intronic or intron–exon junction region were used to assess intronic expression. Primers that span the exonic region were used to examine exonic expression that indicated mRNA abundance. Reduced expression of LOXL1 and FBLN5 was examined at the protein level by immunostaining (E, G) and quantified (F, H). Ee and Ef illustrated the plane of section and the region of analysis for E and G. (I–K) Intron retention increased in the majority of GAG degradation gene transcripts that were downregulated in Prmt1 deficiency, as indicated by a scatter plot based on IRI. The red line defines where intron retention is unchanged. Genes were represented by black dots and labeled in red. GAG degradation genes St6galnac3 and Galnt11 demonstrating higher intron retention in Prmt1-deleted embryos were illustrated by track view (J) and quantified for intronic (left) and exonic (right) expression (K). *p < 0.05 Prmt1 CKO vs. Control. Control: Wnt1-Cre; Rosa26LSLtdTomato. Prmt1 CKO: Wnt1-Cre; Prmt1fl/fl; Rosa26LSLtdTomato. Scale bar: (E, G) 100 µm.

Figure 4
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IR-triggered NMD functions as a basal and stress-responsive mechanism for mRNA decay in CNCCs.

(Aa, Ab) Treatment with the NMD inhibitor NMDI14 (NMDI) led to accumulation of intron-retaining (intron) transcripts of Gpx1, Adamts2, and Alpl in CNCCs from Control (Prmt1 Het) and Prmt1 CKO embryos, analyzed by RT-PCR. Gpx1 serves as a positive control to validate NMD inhibition by NMDI14. (Ba–Bf) NMDI14 caused accumulation of intron-retaining (intron) and total mRNAs (exon) of Adamts2, Alpl, Eln, Matn2, Loxl1, and Bgn in CNCCs. CNCCs were isolated from E13.5 Wnt1-Cre; Rosa26LSLtdTomato and analyzed by RT-PCR. Primers that span the intronic or intron–exon junction region were used to assess intronic expression. Primers that span the exonic region were used to examine exonic expression that indicated mRNA abundance. (Ca, Cd) Intron retention of matrix transcripts Adamts2 and Fbln5 was detected in four independent control embryos by RNA-seq, as illustrated by track views. (Cb–Cf) NMDI14 treatment caused accumulation of intron-retaining Adamts2 and Fbln5 transcripts. CNCCs isolated from E13.5 Wnt1-Cre; Rosa26LSLtdTomato embryos were treated by DMSO or NMDI14 (NMDI), followed by mRNA extraction and assessment with semi-quantitative PCR. Primers (indicated by the red arrows) were designed to span regions (red line) of intron 19 of Adamts2 or intron 7 of Fbln5. *p < 0.05 NMDI vs. DMSO of the same group.

Figure 4—source data 1

Number of premature termination codons (PTCs) in the retained introns of ECM and GAG degradation transcripts of Prmt1 CKO group.

Excel file attached.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig4-data1-v1.xlsx
Figure 4—source data 2

PDF file containing original gel blot for Figure 4C, indicating the relevant genes and bands.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig4-data2-v1.zip
Figure 4—source data 3

Original files for gel blot analysis displayed in Figure 4C.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig4-data3-v1.zip
Figure 5
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PRMT1 methylates SFPQ, EWSR1, and TRA2B in CNCCs.

(A) Expression levels of splicing factors SFPQ, SRSF1, EWSR1, TAF15, TRA2B, HnRNPA1, WDR70, and G3BP1 in primary isolated CNCCs from Wnt1-Cre; Rosa26LSLtdTomato mouse embryonic heads at E13.5 and E15.5. TPM, transcript per million. (B, C) Subcellular localization of splicing factors in CNCCs by immunostaining using sagittal sections of the mandibular process from wild-type mouse embryos, which revealed nuclear expression of SFPQ (a–d), EWSR1 (e–h), and TAF15 (i–l); even distribution of TRA2B between nucleus and cytosolic compartment (m–p), and cytoplasmic expression of SRSF1 (q–t) and G3BP1 (u–x). The subcellular distribution was quantified in C and presented as nuclear to cytosolic signal ratio (Nuc/Cyto Ratio). SFPQ methylation diminished in the mandibular (D, E) and maxillary (F, G) processes of Prmt1 deficient embryos at E13.5. (H–K) Reduction of EWSR1 and TRA2B methylation was observed in the mandibular processes of Prmt1 deficient embryos at E13.5. Methylation was detected by proximity ligation assay (PLA). Green puncta indicated methyl-SFPQ, TRA2B, or EWSR1. Nuclei were counterstained with DAPI (blue). Representative images are shown for Control (Da–Dc; Fa–Fc; Ha–Hc; Ja–Jc) and Prmt1 CKO (Dd–Df; Fd–Ff; Hd–Hf; Jd–Jf). Higher magnification views in (Dc, Df, Fc, Ff, Hc, Hf, Jc, Jf) illustrate methyl-SFPQ, TRA2B, and EWSR1 (green puncta) in the nuclei, as indicated by white arrows. (E, G, I, and K) showed quantification of PLA puncta normalized to cell number in four biological replicates, presented as mean ± SEM. *p < 0.05 Prmt1 CKO vs. Control. Control: Wnt1-Cre; Rosa26LSLtdTomato. Prmt1 CKO: Wnt1-Cre; Prmt1fl/fl; Rosa26LSLtdTomato. Scale bar = 100 µm in B, D, F, H, and J except in enlarged panels, where scale bar = 25 µm (Bd, Bh, Bl, Bp, Bt, Bx, Dc, Df, Fc, Ff, Hc, Hf, Jc, Jf).

Figure 5—source data 1

SFPQ, EWSR1, TAF15, and TRA2B methylation in control and Prmt1 CKO embryos.

(A) SFPQ methylation signal remained robust in the epithelial region of craniofacial structures in both control (Aa, Ab) and CNCC-specific Prmt1 deletion (Ac, Ad) embryos. (B) EWSR1 methylation signal was robust in the abdominal region of control (Ba, Bb) and Prmt1 CKO (Bc, Bd) embryos. (C) TRA2B methylation signal was robust in the abdominal region of control (Ca, Cb) and Prmt1 CKO (Cc, Cd) embryos. Control: Wnt1-Cre; Rosa26LSLtdTomato. Prmt1 CKO: Wnt1-Cre; Prmt1fl/fl; Rosa26LSLtdTomato. Scale bars = 25 µm in A, B, C.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig5-data1-v1.pdf
Figure 6
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PRMT1 depletion reduces SFPQ protein levels via proteasomal degradation.

SFPQ protein level was significantly reduced in the mandibular (A, B) and maxillary (C, D) processes of Prmt1 deficient embryos. SFPQ protein was detected by immunostaining and quantified in B and D. SFPQ protein levels declined dramatically in the Prmt1 deficient embryonic head, as detected by western blotting (E) and quantified with ImageJ (F). (G) PRMT1 deletion did not alter SFPQ mRNA levels in CNCC. (H–K) SFPQ protein accumulated in Prmt1-deficient CNCCs upon MG132 treatment, and the accumulated SFPQ protein remained un-methylated. CNCCs isolated from Prmt1 CKO embryos and littermate controls (Prmt1 heterozygous) were treated with MG132. SFPQ protein was detected by immunostaining in H and quantified in I. SFPQ methylation was detected by PLA in J and quantified in K.* p < 0.05 Prmt1 CKO Control. Control, Wnt1-Cre; Rosa26LSLtdTomato. Prmt1 CKO, Wnt1-Cre; Prmt1fl/fl; Rosa26LSLtdTomato. Scale bar = 100 µm in A and C. Scale bar = 25 µm in H and J.

Figure 6—source data 1

SFPQ, EWSR1, TAF15, and TRA2B protein expression and subcellular localization in control and Prmt1 CKO embryos.

EWSR1, TAF15, and TRA2B protein expression and subcellular localization were not altered in the mandibular processes of Prmt1 deficient embryos. The level of EWSR1 (A), TAF15 (C), and TRA2B (E) protein was detected by immunostaining in the embryonic mandible of control and Prmt1 deficient embryos. The protein expression level was quantified in B, D, and F. Subcellular localization was quantified in G–I. Control: Wnt1-Cre; Rosa26LSLtdTomato. Prmt1 CKO: Wnt1-Cre; Prmt1fl/fl; Rosa26LSLtdTomato. Scale bars = 100 μm in Aa–e, Ca–e, Ea–e. Scale bars = 25 μm in Ac, Af, Cc, Cf, Ec, Ef.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig6-data1-v1.pdf
Figure 6—source data 2

PDF file containing original western blots for Figure 6E, indicating the relevant bands and treatments.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig6-data2-v1.zip
Figure 6—source data 3

Original files for western blot analysis displayed in Figure 6E.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig6-data3-v1.zip
Figure 7
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PRMT1-SFPQ pathway regulates matrix genes in CNCCs.

(A) SFPQ knockdown caused around 50% reduction in Sfpq expression in CNCCs. CNCCs were transfected with two independent siRNAs targeting SFPQ, or control siRNA, followed by poly(A)+ mRNA extraction and RNA sequencing. *p < 0.01 siSFPQ vs. siControl. (B) The two independent siRNAs targeting SFPQ caused similar transcriptomic and intronic changes, shown by scatter plot of DEG (Ba) and IRI (Bb). DEG, differentially expressed genes. IRI, intron retention index. (C) SFPQ depletion altered intron retention in CNCCs. Changes of IR events in genes showing increased (Up, yellow color) or decreased (Down, orange color) IR were illustrated by stacked bar graphs. Pie chart demonstrated differentially regulated genes, with shaded areas among downregulated genes (orange) highlighting their overlap with IR elevated genes (red). (D) GO analysis of genes with elevated IR following SFPQ depletion. (E, F) Heatmap and GO analysis of SFPQ-regulated genes in CNCC. (G, H) Pol II CUT&Tag analysis in ST2 cells transfected with control or SFPQ siRNAs showing Pol II recruitment in downregulated and upregulated genes (G), promoter regions (Ha), and gene body (Hb). p-value was indicated at the top. siControl, control siRNA. siSFPQ#1 and siSFPQ#2, two independent SFPQ siRNAs.

Figure 7—source data 1

CNCC marker expression in siRNA transfected CNCCs compared to fresh isolated CNCCs from mouse embryos.

Bar chart depicting the CNCC’s marker expression in three different conditions. Each condition is presented as mean ± SEM.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig7-data1-v1.pdf
Figure 8
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SFPQ regulates intron retention of Wnt signaling and neuronal genes in CNCCs.

SFPQ depletion in CNCCs elevated intron retention and decreased mRNA abundance of Wnt signaling components (A) and neuronal genes (B). The levels of mRNA abundance (left) and intron retention (right) were illustrated by a two-sided bar graph. TPM, transcripts per million. *p < 0.01 siSFPQ vs. siControl. siControl, control siRNA. siSFPQ#1 and siSFPQ#2, two independent SFPQ siRNAs.

Figure 9
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SFPQ depletion reduces long gene expression via intron retention triggered NMD.

(A) SFPQ depletion promoted intron retention and reduced mRNA abundance of Col4a2, St6galnac3, and Ptk7 in ST2 cells. Bar chart showing RT-PCR analysis of intronic and exonic expression. (B, C) NMD inhibitor NMDI14 caused the accumulation of retained introns and total mRNAs of Col4a2, St6galnac3, and Ptk7 in ST2 cells. Bar chart showing RT-PCR analysis of intronic (B) and exonic expression (C) in DMSO or NMDI-treated cells. NMDI14-mediated inhibition of NMD was validated using Gpx1 as a positive control. *p < 0.05 siSFPQ vs. siControl. #p < 0.05 NMDI vs. DMSO treatment of the same group. (D) SFPQ binding peaks were mapped to retained intron 1 but not spliced intron 6 of Ptk7. Peak distribution from published Sfpq CLIP-seq data using E13.5 brain (top) and track view of RNA-seq data using siControl or siSFPQ-transfected CNCCs (bottom) for Ptk7, with the retained Ptk7 intron 1 (red box) and spliced intron 6 (green box) highlighted. (E) SFPQ binding peaks were significantly enriched in retained intron regions within CNCCs. Violin plot displaying the density of SFPQ binding peaks in introns with elevated retention compared to introns with reduced retention or no change. p-value was calculated using Mann–Whitney U test and indicated at the top. (F) SFPQ binding peaks were preferentially enriched in genes with higher intron retention when compared to genes with no IR change. p = 0.07 using Fisher’s exact test. (G) SFPQ-regulated genes were significantly longer than average. Violin plot displaying the distribution of length for genes showing increased intron retention (IR Up), decreased intron retention (IR Down), or unchanged intron retention (No Change). Median length of the IR Up group was highlighted with solid blue line. Median length of the IR Down and No Change groups was highlighted with dotted blue line. p-value was calculated using Mann–Whitney U test and indicated at the top.

Figure 9—source data 1

Number of premature termination codons (PTCs) in the retained introns of matrix transcripts of Sfpq knockdown group.

Excel file attached.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig9-data1-v1.xlsx
Figure 10
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SFPQ, EWSR1, TAF15, and TRA2B regulate distinct transcriptional and splicing programs.

(A) Genes with increased IR events in SFPQ-depleted CNCCs demonstrated 8.28% (64 out of 773) overlap with Prmt1-deficient CNCCs. (B, E) Matrix genes Col4a2, Adam12, Ntn1, App, St6Galnac3, Galnt10, and Asph were regulated by both Prmt1 deletion and SFPQ depletion. Bar graph showing elevated IR (B, C) and reduced mRNA abundance (D, E) in CNCCs. TPM, transcripts per million. *p < 0.05 siSFPQ vs. siControl. *p < 0.05 Prmt1 CKO vs. Control. Control: Wnt1-Cre; Rosa26LSLtdTomato. Prmt1 CKO: Wnt1-Cre; Prmt1fl/fl; Rosa26LSLtdTomato. (F–S) ST2 cells were transfected with control or SFPQ, EWSR1, TAF15, TRA2B siRNAs and mature mRNA was extracted for sequencing. GSEA demonstrated enrichment of ECM genes among downregulated genes upon depletion of SFPQ, EWSR1, TRA2B, and TAF15 (F–I). Pie charts showed the percentage of genes with increased (dark gray) or decreased IRI (light gray) upon SFPQ, EWSR1, TAF15, and TRA2B deletion (J–M). rMATS analysis showed widespread and significant splicing changes following depletion of SFPQ, EWSR1, TAF15, and TRA2B (N). Postn mRNA expression was decreased in all four depletion groups (O). Exon skipping events of Postn were noted in all four depletion groups, illustrated by Sashimi plots (P) and quantified by bar graphs based on rMATS analysis (Q–S). *p < 0.05 siRNAs vs. siControl. siControl, control siRNA. siSFPQ#1 and siSFPQ#2, two independent SFPQ siRNAs.

Figure 10—source data 1

Transcriptional landscape altered by the knockdown of EWSR1, TAF15, and TRA2B.

ST2 cells were transfected with control siRNA or siRNAs targeting EWSR1, TAF15, or TRA2B, followed by mRNA isolation, sequencing, and bioinformatic analysis for GO analysis of upregulated (6A, 6C, 6E) and downregulated (6B, 6D, 6F) genes.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig10-data1-v1.pdf
Figure 10—source data 2

SFPQ motifs in the vicinity of differential alternative splicing events of CNCCs.

rMAPS2 output pages depicting the spatial distribution of SFPQ motifs for mutually exclusive exons (MXE) (A), exon skipping (SE) (B), intron retention (RI) (C), alternative 5′ splice site (A5SS) (D), and alternative 3′ splice site (A3SS) (E) events. The results demonstrate high motif scores paired with low p-values for SFPQ, underscoring its significant role in alternative splicing regulation. The red line represents the enriched motif for enhanced exons, the blue line represents the enriched motif for silenced exons, and the black line represents the motif density for background (nonregulated) exons. Solid lines represent the peak quality Motif score (peak height) as scaled on the left. The dotted lines represent the negative log10 (p-value) as scaled on the right. The green box indicates the cassette exon.

https://cdn.elifesciences.org/articles/101386/elife-101386-fig10-data2-v1.pdf

Tables

Key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Gene (M. musculus)Prmt1GenBankNC_000080.7N/A
Strain, strain background (M. musculus)Prmt1fl/+Yu et al., 2009N/AN/A
Strain, strain background (M. musculus)Wnt1-CreJackson Laboratory009107N/A
Strain, strain background (M. musculus)R26RtdTomatoJackson Laboratory007914N/A
Cell line (M. musculus)ST2Cell Engineering DivisionRCB0224N/A
Transfected construct (M. musculus)siRNA to SFPQQIAGENSI0578384816 µl
Transfected construct (M. musculus)siRNA to SFPQQIAGENSI057838766 µl
Biological sample (M. musculus)Primary CNCCThis paperN/AN/A
Biological sample (M. musculus)Mouse embryosThis paperN/AN/A
AntibodyGoat polyclonal anti-rabbit Alexa Fluor 488InvitrogenA110701/500
AntibodyRabbit monoclonal mix anti-AsymmetricCell Signaling135221/100
AntibodyGoat polyclonal anti-SFPQEverest BiotechEB095231/100
AntibodyRabbit polyclonal anti-SFPQCell Signaling23020S1/100
AntibodyPRMT1 antibodyCell Signaling Technology24491/100
AntibodySFPQ antibodyEverest BiotechEB095231/100
AntibodySFPQ antibodyCell Signaling Technology230201/100
AntibodyAsymmetric di-methyl arginine antibody (ADMA)Cell Signaling Technology135221/100
AntibodyTRA2B antibodyGeneTexGTX1147521/100
AntibodyTAF15 antibodyThermo Fisher Scientific8TA-2B101/100
AntibodyG3BP1 antibodyThermo Fisher ScientificMA5-574061/100
AntibodySRSF1 antibodyThermo Fisher ScientificMA5635181/100
AntibodyEWSR1 antibodyAbcamab1332881/100
AntibodyGAPDH antibodyCell Signaling Technology971661/5000
Commercial assay or kitDuolink in Situ kitMillipore SigmaDUO92101-1KTN/A
Chemical compound, drugNMDI14MedChemExpressHY-11137450 µg/ml
Chemical compound, drugLipofectamine RNAiMAXThermo Fisher137785009 µl
Chemical compound, drug Antigen Unmasking SolutionsVector LaboratoriesH-3300–250N/A
Software, algorithmFigures-Illustrator CC 2017.1.1Adobehttp://www.adobe.com/cn/N/A
Software, algorithm Image Analysis-CellProfiler2Kamentsky et al., 2011https://cellprofiler.orgN/A
Software, algorithmRstudioR Foundation for Statistical Computinghttp://www.rstudio.com/N/A
Software, algorithmAcquisition- analysis-Keyence BZ-X800KEYENCEhttps://www.keyence.comN/A
Software, algorithmAcquisition- analysis-Leica DMI 3000BLeicahttp://www.leica-microsystems.comN/A
Software, algorithmFastQC v0.11.8Babraham Institutehttps://www.bioinformatics.babraham.ac.uk/projects/fastqc/N/A
Software, algorithmTrim GaloreBabraham Institutehttps://www.bioinformatics.babraham.ac.uk/projects/trim_galore/N/A
Software, algorithmhisat2 (v2.1.0)Kim et al., 2019PMID:31375807 PMCID:PMC7605509N/A
Software, algorithmsamtools (v1.7)Li et al., 2009PMID:19505943 PMCID:PMC2723002N/A
Software, algorithmhtseq-count (v1.99.2)Anders et al., 2015PMID:25260700 PMCID:PMC4287950N/A
Software, algorithmIRToolsPeng, 2018https://github.com/WeiqunPengLab/IRTools/N/A
Software, algorithmEdgeRRobinson et al., 2010PMID:19910308
PMCID:PMC2796818		N/A
Software, algorithmDAVIDSherman et al., 2022https://david.ncifcrf.gov/tools.jspN/A
Software, algorithmMetascapeZhou et al., 2019https://metascape.org/gp/index.html#/main/step1N/A
Software, algorithmrMATS
version 4.0 (turbo)
Xinglabhttps://github.com/Xinglab/rmats-turbo
RRID:SCR_023485		N/A
Software, algorithmrMAPS2rMAPS2https://rmaps.cecsresearch.org/N/A
Chemical compound, drugHuman/Mouse/Rat BMP-2Gibco12002C250UGN/A
Chemical compound, drugMG-132MedChem ExpressHY-13259N/A
Chemical compound, drugDMSOSigma-AldrichD4540N/A
Commercial assay or kitPeroxidase AffiniPure Goat Anti-Mouse IgG, light chain specificJackson ImmunoResearch115-035-174N/A
Commercial assay or kitMaxima H Minus cDNA Synthesis Master MixThermo Fisher ScientificM1681N/A
Commercial assay or kitPowerUp SYBR Green Master Mix for qPCRApplied BiosystemsA25742N/A
Chemical compound, drugFormalinMillipore SigmaHT501128N/A
Chemical compound, drugRIPA Lysis and Extraction BufferThermo Fisher Scientific89900N/A
Commercial assay or kitPierce ECL Western Blotting SubstrateThermo Fisher Scientific32106N/A
Commercial assay or kitDynaMag-2 MagnetInvitrogen12321DN/A
Commercial assay or kitNEBNext Poly(A) mRNA Magnetic Isolation ModuleNew England BiolabsE7490LN/A

Additional files

Supplementary file 1

Differential alternative splicing events caused by SFPQ, EWSR1, TAF15, and TRA2B knockdown in ST2 cells.

Excel file attached.

https://cdn.elifesciences.org/articles/101386/elife-101386-supp1-v1.xlsx
Supplementary file 2

Candidate splicing regulators identified by motif analysis with significantly differential binding in splicing events altered by PRMT1 (p < 0.00001).

Excel file attached.

https://cdn.elifesciences.org/articles/101386/elife-101386-supp2-v1.xlsx
Supplementary file 3

GO analysis for genes with differential alternative splicing events.

Excel file attached.

https://cdn.elifesciences.org/articles/101386/elife-101386-supp3-v1.xlsx
Supplementary file 4

List of primers.

Excel file attached.

https://cdn.elifesciences.org/articles/101386/elife-101386-supp4-v1.xlsx
MDAR checklist
https://cdn.elifesciences.org/articles/101386/elife-101386-mdarchecklist1-v1.docx

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  1. Julia Raulino Lima
  2. Nicha Ungvijanpunya
  3. Qing Chen
  4. Hoang Quoc Hai Pham
  5. Tal Rosen
  6. Greg Park
  7. Mohammadreza Vantankhah
  8. Steven Yen
  9. Yang Chai
  10. Amy E Merrill
  11. Zhaoyang Liu
  12. Jian-Fu Chen
  13. Yanzhong Yang
  14. Weiqun Peng
  15. Jian Xu
(2026)
PRMT1-SFPQ regulates intron retention to control matrix gene expression during craniofacial development
eLife 13:RP101386.
https://doi.org/10.7554/eLife.101386.3