Cell fate decision by a morphogen-transcription factor-chromatin modifier axis
Bulk RNA-sequences show the differences upon primitive endoderm cell related gene expression between JGES induced somatic cell reprogramming with or without BMP4 treatment, and between WT-SALL4 or delN12-SALL4 induced transdifferentiation from E13.5 mouse embryonic fibroblasts, primitive endoderm cell related gene are from our single cell RNA sequence data So as to estimate the chromatin remodeling differences between SALL4-WT and SALL4-delN12 during single factor induced PrE formation, we performed Tn5 dependent ATAC-sequence to compare the open and close chromatin of the two group. In order to identify the bingding differences of SALL4 and H3K27ac level  diversity between SALL4-WT and SALL4-delN12 on PrE related genes, wo performed CUTandTAG experiments. Single cell analysis provides clarity unattainable with bulk approaches. Here we apply single cell RNA-seq to a newly established mouse somatic cell reprogramming system with or without BMP4 treatment at Day 7, this reprogramming system are induced by four transcriptional factors Jdp2-Glis1-Esrrb-Sall4 or JGES and cultured in iCD3. We first show that cells could be clustered into four group, primitive endoderm cell like cells, pluripotent cells, endothelial cells, and intermediate state cells which are hard to be clarified, after BMP4 treatment, a placenta-like state arise, the percentage of endothelial cells and primitive endoderm cell like cells increase and pluripotent cells decrease sharply. Our results not only show the ability of JGES and BMP4 in different cell lineage induction but also provide a model to explore mechanisms of first and second cell lineage decision during early embryogenesis. Overall design: We analyzed the transcriptome expression of mixture cells generated during mouse somatic cell reprogramming and transdifferentiation We analyzed the transcriptome expression of mixture cells generated during mouse somatic cell reprogramming with or without BMP4 treatment ATAC-seq data shows the chromatin accessibility differences between SALL4-WT and SALL4-delN12 single factor indeuced PrE formation, four time points were checked, Day1, Day5, Day9 and Day11 CUT&Tag analysis was performed in PrE formation at day 6 to map SALL4 and H3K27ac  binding sites.