PreprintCited by 2Developmental Biology and Gene RegulationGenomics and Chromatin DynamicsCraniofacial Disorders and Treatments

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Neural crest induction requires SALL4-mediated BAF recruitment to lineage specific enhancers

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Preprint — published as 10.1242/dev.205248 · Paper page

Abstract

Neural crest induction begins early during neural plate formation, requiring precise transcriptional control to activate lineage-specific enhancers. Here, we demonstrate that SALL4, a transcription factor associated with syndromes featuring craniofacial anomalies, plays a critical role in early cranial neural crest (CNCC) specification. Using SALL4 -het-KO human iPSCs to model clinical haploinsufficiency, we show that SALL4 directly recruits BAF to CNCC-lineage specific enhancers at the neuroectodermal stage, specifically when neural crest gene expression is induced at the neural plate border. Without functional SALL4, BAF is not loaded at chromatin, leaving CNCC enhancers inaccessible. Consequently, the cells cannot undergo proper CNCC induction and specification due to persistent enhancer repression, despite normal neuroectodermal and neural plate progression. Moreover, by performing SALL4 isoform-specific depletion, we demonstrate that the SALL4A is the isoform essential for CNCC induction and specification, and that SALL4B cannot compensate for SALL4A loss in this developmental process. In summary, our findings reveal SALL4 as essential regulator of BAF-dependent enhancer activation during early stages of neural crest development, providing molecular insights into SALL4-associated craniofacial anomalies.

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Figures

Fig. 1. SALL4A interacts with the BAF complex through DP+F2. (A) Immunoblot of nuclear extract (5% input), co-immunoprecipitations (co-IP) of ARID1B and IgG (negative control) from SALL4-WT cells at day 5. (B) AlphaFold structure model showing the predicted interactions between SALL4A (red), DPF2 (dark blue) and other BAF components, including SMARCA4, SMARCB1 and ACTL6A. (C) SALL4A protein sequence and visual representation of output model of SALL4A (model 0). C2H2 zinc-fingers (ZFs) annotations are highlighted in dark purple and numbered. Interactions between SALL4A and DPF2 through the ZFs 4, 5 and 6 (ZFC3) and 7 (ZFC4) are highlighted in light purple. Made with BioRender.com. (D) Zoomed view of SALL4 (pink) and DPF2 (purple) interacting surfaces. Highlighted are the functional domains involved in the predicted interaction. In red, contacts predicted by AlphaFold (Jumper et al., 2021). (E) Expression (transcripts per million; TPMs) of the four members of the DPF protein family in iPSCs (day 0; n=2). Differences between conditions were assessed using unpaired Student's t-test. (F) Expression of the four members of the DPF protein at day 5 (n=3). Differences between conditions were assessed using unpaired student's t-test. Data are mean±s.e.m. Individual biological replicates are displayed as circles.
Fig. 1. SALL4A interacts with the BAF complex through DP+F2. (A) Immunoblot of nuclear extract (5% input), co-immunoprecipitations (co-IP) of ARID1B and IgG (negative control) from SALL4-WT cells at day 5. (B) AlphaFold structure model showing the predicted interactions between SALL4A (red), DPF2 (dark blue) and other BAF components, including SMARCA4, SMARCB1 and ACTL6A. (C) SALL4A protein sequence and visual representation of output model of SALL4A (model 0). C2H2 zinc-fingers (ZFs) annotations are highlighted in dark purple and numbered. Interactions between SALL4A and DPF2 through the ZFs 4, 5 and 6 (ZFC3) and 7 (ZFC4) are highlighted in light purple. Made with BioRender.com. (D) Zoomed view of SALL4 (pink) and DPF2 (purple) interacting surfaces. Highlighted are the functional domains involved in the predicted interaction. In red, contacts predicted by AlphaFold (Jumper et al., 2021). (E) Expression (transcripts per million; TPMs) of the four members of the DPF protein family in iPSCs (day 0; n=2). Differences between conditions were assessed using unpaired Student's t-test. (F) Expression of the four members of the DPF protein at day 5 (n=3). Differences between conditions were assessed using unpaired student's t-test. Data are mean±s.e.m. Individual biological replicates are displayed as circles.CC BY · PubMed Central
Fig. 2. Generation of a SALL4-haploinsufficient hiPSC line. (A) Visual representation of the CRISPR/Cas9 approach used for SALL4-het-KO. The star represents the exact location of the deletion. Sanger sequencing confirming the 11-bp deletion in one allele of SALL4 is displayed (clone F1). Created in BioRender by Demurtas, M., 2025. https://BioRender.com/ufbzgfa. This figure was sublicensed under CC BY 4.0 terms. (B) Immunoblot for SALL4 in SALL4-WT and SALL4-het-KO (clone F1) iPSC lines. (C) Densitometry analysis of SALL4A and SALL4B expression in WT and SALL4-het-KO iPSC lines from immunoblot assay. (D) RNA expression (transcripts per million; TPMs) for SALL4A and SALL4B in WT and SALL4-het-KO iPSCs (n=2). (E) Bar plots displaying expression TPMs of all SALL paralogues in SALL4-WT and SALL4-het-KO iPSCs (n=2). Individual biological replicates are displayed as circles. (F) Immunoblot for SALL1 in SALL4-WT and SALL4-het-KO (clone F1) iPSC lines. (G) Growth curve comparing SALL4-WT with SALL4-het-KO iPSC lines. N=2 biologically independent experiments. Statistical significance was assessed using unpaired Student's t-test. Data are mean±s.e.m.
Fig. 2. Generation of a SALL4-haploinsufficient hiPSC line. (A) Visual representation of the CRISPR/Cas9 approach used for SALL4-het-KO. The star represents the exact location of the deletion. Sanger sequencing confirming the 11-bp deletion in one allele of SALL4 is displayed (clone F1). Created in BioRender by Demurtas, M., 2025. https://BioRender.com/ufbzgfa. This figure was sublicensed under CC BY 4.0 terms. (B) Immunoblot for SALL4 in SALL4-WT and SALL4-het-KO (clone F1) iPSC lines. (C) Densitometry analysis of SALL4A and SALL4B expression in WT and SALL4-het-KO iPSC lines from immunoblot assay. (D) RNA expression (transcripts per million; TPMs) for SALL4A and SALL4B in WT and SALL4-het-KO iPSCs (n=2). (E) Bar plots displaying expression TPMs of all SALL paralogues in SALL4-WT and SALL4-het-KO iPSCs (n=2). Individual biological replicates are displayed as circles. (F) Immunoblot for SALL1 in SALL4-WT and SALL4-het-KO (clone F1) iPSC lines. (G) Growth curve comparing SALL4-WT with SALL4-het-KO iPSC lines. N=2 biologically independent experiments. Statistical significance was assessed using unpaired Student's t-test. Data are mean±s.e.m.CC BY · PubMed Central
Fig. 3. Stem cell identity is unaffected by SALL4 loss. (A) (Left) Immunofluorescence labelling quantifying the expression of the canonical pluripotency markers OCT4 and NANOG in SALL4-WT and SALL4-het-KO (clone F1) iPSCs. Scale bars: 100 µm. (Right) Corrected total cell fluorescence values were used to quantify and compare marker expression (OCT4, n=34; NANOG, n=37). Box plots show median values (middle bars) and first to third interquartile ranges (boxes); whiskers indicate minimum and maximum values; dots represent each fragmented nucleus considered. (B) Flow cytometry quantifying the expression of surface markers for pluripotency (TRA-60-1-R and SSEA-4). (C) Volcano plot of genes differentially expressed in SALL4-het-KO relative to SALL4-WT in iPSCs (day 0). Blue dots (n=50) represent downregulated genes with Padj<0.05 and log2FoldChange<−1.5. Purple dots (n=63) represent upregulated genes with Padj<0.05 and log2FoldChange>1.5.
Fig. 3. Stem cell identity is unaffected by SALL4 loss. (A) (Left) Immunofluorescence labelling quantifying the expression of the canonical pluripotency markers OCT4 and NANOG in SALL4-WT and SALL4-het-KO (clone F1) iPSCs. Scale bars: 100 µm. (Right) Corrected total cell fluorescence values were used to quantify and compare marker expression (OCT4, n=34; NANOG, n=37). Box plots show median values (middle bars) and first to third interquartile ranges (boxes); whiskers indicate minimum and maximum values; dots represent each fragmented nucleus considered. (B) Flow cytometry quantifying the expression of surface markers for pluripotency (TRA-60-1-R and SSEA-4). (C) Volcano plot of genes differentially expressed in SALL4-het-KO relative to SALL4-WT in iPSCs (day 0). Blue dots (n=50) represent downregulated genes with Padj<0.05 and log2FoldChange<−1.5. Purple dots (n=63) represent upregulated genes with Padj<0.05 and log2FoldChange>1.5.CC BY · PubMed Central
Fig. 4. SALL4 relocates to CNCC enhancers to induce chromatin accessibility. (A) (Bottom) Schematic representation of the iPSC-to-CNCC differentiation protocol. The experimental timeline shows in vitro differentiation of iPSCs into CNCCs via a neuroectodermal-like stage. (Top) Immunofluorescence labelling quantifying the expression of the canonical stage-specific markers (iPSCs: OCT4; neuroectoderm: PAX6; CNCCs: SOX9) showing ratio of cells successfully undergoing stage-specific specifications during CNCC generation. Scale bars: 100 µm. (B) Diagram showing the number of regions bound by SALL4 uniquely at day 0 (‘day-0-specific’, n=6114), at day 5 (‘day-5-specific’, n=17,137) and regions that maintain SALL4 binding at both time points (shared, n=15,570). (C) Heatmaps showing the distribution of SALL4 binding at day 0 and day 5 across day-0-specific (left) and day-5-specific (right) binding regions. CUT&RUN signal intensity was plotted across ±2 kb regions centred on peak summits. Rows represent individual peaks ranked by signal intensity. (D) Genomic distribution of SALL4 binding sites relative to the nearest transcription start site (TSS). Peaks are categorised by distance into six bins: <1 kb, 1-3 kb, 3-5 kb, 5-10 kb, 10-100 kb and >100 kb. Peaks located at >1 kb from the nearest TSS were classified as putative enhancers. Percentages of peaks for each bin are represented by bars to the left (downstream) or right (upstream) of the TSS. (E) Gene ontology analysis of downregulated nearest genes to day-5-specific SALL4-bound regions as determined using WebGestalt (Liao et al., 2019) over-representation pathway analysis, using affinity propagation as parameter for redundancy removal (FDR<0.05). (F) Table of motifs enriched in day-5-specific SALL4-bound regions as determined using HOMER (Heinz et al., 2010).
Fig. 4. SALL4 relocates to CNCC enhancers to induce chromatin accessibility. (A) (Bottom) Schematic representation of the iPSC-to-CNCC differentiation protocol. The experimental timeline shows in vitro differentiation of iPSCs into CNCCs via a neuroectodermal-like stage. (Top) Immunofluorescence labelling quantifying the expression of the canonical stage-specific markers (iPSCs: OCT4; neuroectoderm: PAX6; CNCCs: SOX9) showing ratio of cells successfully undergoing stage-specific specifications during CNCC generation. Scale bars: 100 µm. (B) Diagram showing the number of regions bound by SALL4 uniquely at day 0 (‘day-0-specific’, n=6114), at day 5 (‘day-5-specific’, n=17,137) and regions that maintain SALL4 binding at both time points (shared, n=15,570). (C) Heatmaps showing the distribution of SALL4 binding at day 0 and day 5 across day-0-specific (left) and day-5-specific (right) binding regions. CUT&RUN signal intensity was plotted across ±2 kb regions centred on peak summits. Rows represent individual peaks ranked by signal intensity. (D) Genomic distribution of SALL4 binding sites relative to the nearest transcription start site (TSS). Peaks are categorised by distance into six bins: <1 kb, 1-3 kb, 3-5 kb, 5-10 kb, 10-100 kb and >100 kb. Peaks located at >1 kb from the nearest TSS were classified as putative enhancers. Percentages of peaks for each bin are represented by bars to the left (downstream) or right (upstream) of the TSS. (E) Gene ontology analysis of downregulated nearest genes to day-5-specific SALL4-bound regions as determined using WebGestalt (Liao et al., 2019) over-representation pathway analysis, using affinity propagation as parameter for redundancy removal (FDR<0.05). (F) Table of motifs enriched in day-5-specific SALL4-bound regions as determined using HOMER (Heinz et al., 2010).CC BY · PubMed Central
Fig. 5. Chromatin accessibility at the CNCC enhancers is SALL4 dependent. (A) Venn diagram showing chromatin accessibility in SALL4-WT (ATAC-seq peaks, n=58,375) and SALL4-het-KO (n=60,186). It also depicts the number of regions uniquely accessible in SALL4-WT (‘Sites losing accessibility in KO’, n=1649), in SALL4-het-KO (‘Sites gaining accessibility in KO’, n=3460) and regions that remain accessible in both conditions (‘Sites maintaining accessibility in WT and KO’, n=60,186). (B) Heatmaps showing ATAC-seq signals at day 0 (left) and day 5 (right), at day-5-specific SALL4 CUT&RUN peaks. Signal intensity was plotted across ±2 kb regions centred on peak summits. Rows represent individual peaks ranked by signal intensity. (C) Average profiles showing ATAC-seq signal at day-5-specific SALL4 CUT&RUN peaks (n=17,137) in SALL4-WT and SALL4-het-KO cells in two distinct biological replicates. (D,E) Tables of motifs enriched in regions gaining or maintaining accessibility (D) or regions losing accessibility (E) at day 5 in SALL4-het-KO regions as determined using HOMER (Heinz et al., 2010).
Fig. 5. Chromatin accessibility at the CNCC enhancers is SALL4 dependent. (A) Venn diagram showing chromatin accessibility in SALL4-WT (ATAC-seq peaks, n=58,375) and SALL4-het-KO (n=60,186). It also depicts the number of regions uniquely accessible in SALL4-WT (‘Sites losing accessibility in KO’, n=1649), in SALL4-het-KO (‘Sites gaining accessibility in KO’, n=3460) and regions that remain accessible in both conditions (‘Sites maintaining accessibility in WT and KO’, n=60,186). (B) Heatmaps showing ATAC-seq signals at day 0 (left) and day 5 (right), at day-5-specific SALL4 CUT&RUN peaks. Signal intensity was plotted across ±2 kb regions centred on peak summits. Rows represent individual peaks ranked by signal intensity. (C) Average profiles showing ATAC-seq signal at day-5-specific SALL4 CUT&RUN peaks (n=17,137) in SALL4-WT and SALL4-het-KO cells in two distinct biological replicates. (D,E) Tables of motifs enriched in regions gaining or maintaining accessibility (D) or regions losing accessibility (E) at day 5 in SALL4-het-KO regions as determined using HOMER (Heinz et al., 2010).CC BY · PubMed Central
Fig. 6. SALL4 recruits BAF to CNCC enhancers. (A) Heatmap showing BRG1 ChIP-seq signal at the genomic sites bound by SALL4 in WT cells at day 5 (n=17,137). Signal intensity was plotted across ±2 kb regions centred on peak summits. Rows represent individual peaks ranked by signal intensity. (B) Venn diagram showing peaks bound by SALL4 uniquely at day 5 and that lose accessibility in SALL4-het-KO. (C) Heatmap and average profiles show BRG1 ChIP-seq signal at day 5 at the BRG1 peaks lost in SALL4-het-KO (clone F1; n=13,505). Signal intensity was plotted across ±2 kb regions centred on peak summits. Rows represent individual peaks ranked by signal intensity. (D) Heatmap and average profiles show SALL4 CUT&RUN signal at the genomic sites that lose BRG1 in SALL4-het-KO cells at day 0 and day 5 (n=13,505). (E) Heatmaps and average profile show ATAC-seq signal at the genomic sites that lose BRG1 in SALL4-het-KO cells (clone F1; n=13,505). Signal intensity was plotted across ±2 kb regions centred on peak summits. Rows represent individual peaks ranked by signal intensity. (F) Two representative examples of enhancers bound by SALL4 at day 5 that lose BRG1 co-occupancy and chromatin accessibility in the SALL4-het-KO (clone F1) cells. Both correspond to ChIP-seq peaks annotated as enhancer regions, as reported in GeneHancer (left) and VISTA Enhancer Browser (right).
Fig. 6. SALL4 recruits BAF to CNCC enhancers. (A) Heatmap showing BRG1 ChIP-seq signal at the genomic sites bound by SALL4 in WT cells at day 5 (n=17,137). Signal intensity was plotted across ±2 kb regions centred on peak summits. Rows represent individual peaks ranked by signal intensity. (B) Venn diagram showing peaks bound by SALL4 uniquely at day 5 and that lose accessibility in SALL4-het-KO. (C) Heatmap and average profiles show BRG1 ChIP-seq signal at day 5 at the BRG1 peaks lost in SALL4-het-KO (clone F1; n=13,505). Signal intensity was plotted across ±2 kb regions centred on peak summits. Rows represent individual peaks ranked by signal intensity. (D) Heatmap and average profiles show SALL4 CUT&RUN signal at the genomic sites that lose BRG1 in SALL4-het-KO cells at day 0 and day 5 (n=13,505). (E) Heatmaps and average profile show ATAC-seq signal at the genomic sites that lose BRG1 in SALL4-het-KO cells (clone F1; n=13,505). Signal intensity was plotted across ±2 kb regions centred on peak summits. Rows represent individual peaks ranked by signal intensity. (F) Two representative examples of enhancers bound by SALL4 at day 5 that lose BRG1 co-occupancy and chromatin accessibility in the SALL4-het-KO (clone F1) cells. Both correspond to ChIP-seq peaks annotated as enhancer regions, as reported in GeneHancer (left) and VISTA Enhancer Browser (right).CC BY · PubMed Central
Fig. 7. CNCC induction and specification are impaired in SALL4-het-KO. (A) Relative mRNA expression of canonical CNCC markers in SALL4-WT and SALL4-het-KO cells at day 14 (n=2). Statistical significance was assessed using unpaired Student's t-test. 18S rRNA was used to normalise. Data are mean±s.e.m. (B) Flow cytometry for the CNCC surface marker CD99 in SALL4-WT and SALL4-het-KO (clone F1) CNCCs at day 14. (C) Volcano plot of genes differentially expressed in SALL4-het-KO relative to SALL4-WT in CNCCs (day 14). Blue dots (n=659) represent downregulated genes with Padj<0.05 and log2FoldChange<−1.5. Purple dots (n=447) represent upregulated genes with Padj<0.05 and log2FoldChange>1.5. (D,E) GO term enrichment for downregulated (D) and upregulated (E) genes in SALL4-het-KO cells (FDR<0.05). (F) Heatmap displaying the expression of canonical epithelial-to-mesenchymal transition (EMT) markers in SALL4-WT and SALL4-het-KO cells (day 14).
Fig. 7. CNCC induction and specification are impaired in SALL4-het-KO. (A) Relative mRNA expression of canonical CNCC markers in SALL4-WT and SALL4-het-KO cells at day 14 (n=2). Statistical significance was assessed using unpaired Student's t-test. 18S rRNA was used to normalise. Data are mean±s.e.m. (B) Flow cytometry for the CNCC surface marker CD99 in SALL4-WT and SALL4-het-KO (clone F1) CNCCs at day 14. (C) Volcano plot of genes differentially expressed in SALL4-het-KO relative to SALL4-WT in CNCCs (day 14). Blue dots (n=659) represent downregulated genes with Padj<0.05 and log2FoldChange<−1.5. Purple dots (n=447) represent upregulated genes with Padj<0.05 and log2FoldChange>1.5. (D,E) GO term enrichment for downregulated (D) and upregulated (E) genes in SALL4-het-KO cells (FDR<0.05). (F) Heatmap displaying the expression of canonical epithelial-to-mesenchymal transition (EMT) markers in SALL4-WT and SALL4-het-KO cells (day 14).CC BY · PubMed Central
Fig. 8. SALL4A is the only SALL4 isoform necessary for CNCC specification. (A) Schematic of pomalidomide-mediated ubiquitin ligation. Ub, ubiquitin; POM, pomalidomide. CRBN, DDB1, Cul4 and Rbx1 are subunits of CRL4/CRBN E3 ubiquitin ligase. Created in BioRender by Demurtas, M., 2025. https://BioRender.com/oij5pkv. This figure was sublicensed under CC BY 4.0 terms. (B) Schematic representation of pomalidomide treatment during iPSC-to-CNCC differentiation protocol. (C) Time-course immunoblot for SALL4 in SALL4-WT at day 5 and day 14 after daily treatment with DMSO (control) or 5 µM pomalidomide (5 µM POM). (D) Relative mRNA expression of canonical CNCC markers (SOX9, TFAP2A and NR2F1) in SALL4-WT at day 14 treated with 5 µM pomalidomide or DMSO (control) daily for 14 days. Individual biological replicates (n=2) are displayed as circles. Statistical significance was assessed using unpaired Student's t-test. Data are mean±s.e.m. (E) Immunofluorescence labelling quantifying the expression of the canonical CNCC markers SOX9 and TFAP2A in SALL4-WT treated with 5 µM pomalidomide or DMSO (control) daily for 14 days. (F) Immunofluorescence labelling quantifying the expression of the canonical EMT markers EPCAM and VIM in SALL4-WT treated with 5 μM pomalidomide or DMSO (control) daily for 14 days. Scale bars: 100 µm.
Fig. 8. SALL4A is the only SALL4 isoform necessary for CNCC specification. (A) Schematic of pomalidomide-mediated ubiquitin ligation. Ub, ubiquitin; POM, pomalidomide. CRBN, DDB1, Cul4 and Rbx1 are subunits of CRL4/CRBN E3 ubiquitin ligase. Created in BioRender by Demurtas, M., 2025. https://BioRender.com/oij5pkv. This figure was sublicensed under CC BY 4.0 terms. (B) Schematic representation of pomalidomide treatment during iPSC-to-CNCC differentiation protocol. (C) Time-course immunoblot for SALL4 in SALL4-WT at day 5 and day 14 after daily treatment with DMSO (control) or 5 µM pomalidomide (5 µM POM). (D) Relative mRNA expression of canonical CNCC markers (SOX9, TFAP2A and NR2F1) in SALL4-WT at day 14 treated with 5 µM pomalidomide or DMSO (control) daily for 14 days. Individual biological replicates (n=2) are displayed as circles. Statistical significance was assessed using unpaired Student's t-test. Data are mean±s.e.m. (E) Immunofluorescence labelling quantifying the expression of the canonical CNCC markers SOX9 and TFAP2A in SALL4-WT treated with 5 µM pomalidomide or DMSO (control) daily for 14 days. (F) Immunofluorescence labelling quantifying the expression of the canonical EMT markers EPCAM and VIM in SALL4-WT treated with 5 μM pomalidomide or DMSO (control) daily for 14 days. Scale bars: 100 µm.CC BY · PubMed Central

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Metadata

Authors
Demurtas, M., Barnada, S. M., van Domselaar, E., Mitchell, Z. H., Deelen, L., & Trizzino, M.
Affiliations
  • Imperial College London (GB)
  • Thomas Jefferson University (US)
Corresponding author
Trizzino, Marco
Venue
Development
Publisher
openRxiv
Published
2025-06-10
Volume
152
Issue
24
ISSN
0950-1991 (ISSN-L)
OpenAlex
W4416785166
Cited by
2
References
1
Citations by year
2026: 1 · 2025: 1
FWCI
0.60
Type
journal article
Language
en
Open access
Locations
  • Development (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • Spiral (Imperial College London) (submittedVersion, cc-by)
Funders
  • Wellcome Trust (104931/Z/14/Z)
  • G. Harold and Leila Y. Mathers Foundation
  • Imperial College London
  • Biotechnology and Biological Sciences Research Council (BB/L015129/1, BB/Y000854/1)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Health Sciences › Medicine › Surgery › Craniofacial Disorders and Treatments
Keywords
SALL4, BAF chromatin remodeling complex, neural crest induction, enhancer activation, enhancer repression, haploinsufficiency, neural plate border, craniofacial anomalies, transcriptional regulation, induced pluripotent stem cells
MeSH terms
Animals, DNA-Binding Proteins, Enhancer Elements, Genetic, Humans, Neural Crest, Transcription Factors, Gene Expression Regulation, Developmental, Cell Lineage, Neural Plate, Induced Pluripotent Stem Cells

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