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BMC Genomics 2022 Oct 23;231:723. doi: 10.1186/s12864-022-08953-3.
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Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions.

Johnson K , Freedman S , Braun R , LaBonne C .

BACKGROUND: During embryogenesis, the developmental potential of initially pluripotent cells becomes progressively restricted as they transit to lineage restricted states. The pluripotent cells of Xenopus blastula-stage embryos are an ideal system in which to study cell state transitions during developmental decision-making, as gene expression dynamics can be followed at high temporal resolution. RESULTS: Here we use transcriptomics to interrogate the process by which pluripotent cells transit to four different lineage-restricted states: neural progenitors, epidermis, endoderm and ventral mesoderm, providing quantitative insights into the dynamics of Waddington's landscape. Our findings provide novel insights into why the neural progenitor state is the default lineage state for pluripotent cells and uncover novel components of lineage-specific gene regulation. These data reveal an unexpected overlap in the transcriptional responses to BMP4/7 and Activin signaling and provide mechanistic insight into how the timing of signaling inputs such as BMP are temporally controlled to ensure correct lineage decisions. CONCLUSIONS: Together these analyses provide quantitative insights into the logic and dynamics of developmental decision making in early embryos. They also provide valuable lineage-specific time series data following the acquisition of specific lineage states during development.

PubMed ID: 36273135
PMC ID: PMC9588240
Article link: BMC Genomics

Species referenced: Xenopus laevis
Genes referenced: a2m bix1.1 bmp2 bmp4 bmp7.1 dand5 dlx3 eomes evx1 foxi1 foxi2 grhl1 grn gsc gtpbp2 id3 krt12.4 mix1 msx1 otx1 otx2 post pou5f3.3 pygm smad1 smad2 sox11 sox17a sox17b.1 sox2 sox3 tgfb1 vegt ventx2 ventx2.2 wnt8a zic1
Morpholinos: dand5 MO1

GEO Series: GSE198598: NCBI

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