4.7 Article

Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions

Journal

BMC GENOMICS
Volume 23, Issue 1, Pages -

Publisher

BMC
DOI: 10.1186/s12864-022-08953-3

Keywords

Pluripotency; BMP; Activin; Smads; Neural; Epidermal; Mesendoderm; Neural default model; Xenopus

Funding

  1. Simons Foundation/SFARI [597491-RWC]
  2. National Science Foundation [1764421]
  3. NIH [R01GM116538]
  4. Direct For Mathematical & Physical Scien
  5. Division Of Mathematical Sciences [1764421] Funding Source: National Science Foundation

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This study investigates the process of pluripotent cells transitioning to lineage-restricted states using transcriptomics, providing valuable time series data for understanding developmental decision making.
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.

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