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. 2024 Dec 30;15:10787. doi: 10.1038/s41467-024-54924-5

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a CADs for SALL4 system and DsRed system. PO, permanently open. CO, close to open. OC, open to close. Take the DsRed system as a reference is shown. b The histogram shows the number of peaks for CO, OC, and PO subgroups of the SALL4 system and DsRed system. SALL4, SALL4 system. DsRed, DsRed system. c Venn diagrams show the overlapping number and factor-specific number of CO1-4, OC1-4, and PO peaks between the SALL4 system and the DsRed system. SALL4, SALL4 system. DsRed, DsRed system. d Motif analysis of the SALL4-specific enrichment peaks at D0, D4, D7, and D10 during iPSCs induction, the peaks for each day in the DsRed system as a background was removed from the peaks at D0, D4, D7, and D10 in SALL4 system. Statistical analysis was performed using Karlin/Altschul statistics, and the -Log10(p-value) for the motif is shown. SALL4, SALL4 system. e Representative Genomic loci and genes for SALL4-specific close-to-open (SALL4-CO) peaks, SALL4-specific open-to-close (SALL4-OC) and SALL4-binding peaks (Cut&Tag data). f The iPSCs induction efficiency using SALL4 overepressing with representative SALL4-occupied gene Esrrb, Rsk1, and ATAC-seq motif-enriched gene Nkx6.1. The reprogramming efficiency induced by Sall4 when knocking down Tfap2c or Esrrb(right). Data are mean ± SD. Statistical analysis was performed using a two-tailed, unpaired t test; n = 6 well from 3 independent experiments. Sall4 + DsRed versus Sall4 + Nkx6.1, ****p = 0.0000162; Sall4 + DsRed versus Sall4 + Esrrb, ***p = 0.0001515; Sall4 + DsRed versus Sall4 + Rsk1, **p = 0.0019697; Sall4 + shTfap2c-1 versus Sall4 + shLuc, ***p = 0.0001119; Sall4 + shTfap2c-2 versus Sall4 + shLuc, ****p = 0.0000343; Sall4 + shEsrrb-1 versus Sall4 + shLuc, ***p = 0.0001059; Sall4 + shEsrrb-2 versus Sall4 + shLuc, ***p = 0.0002597. shLuc, shLuciferase.