Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation.

Area of Science:

• Biomedical research
• Developmental biology
• Genomics

Background:

• Single-cell RNA sequencing (scRNA-Seq) enables prediction of future cell expression states using unspliced pre-mRNA.
• RNA velocity applies this concept to infer cell differentiation trajectories.

Purpose of the Study:

• To apply RNA velocity to a mouse gastrulation and organogenesis dataset.
• To investigate discrepancies between RNA velocity predictions and known differentiation paths, particularly in red blood cell maturation.

Main Methods:

• Analysis of an extended timecourse scRNA-Seq dataset from mouse gastrulation and early organogenesis.
• Investigated genes with coordinated step-change in transcription dynamics.
• Utilized scRNA-Seq analysis of chimeric mouse embryos lacking the Gata1 regulator.

Main Results:

• RNA velocity predictions showed inconsistencies with established differentiation paths, notably in red blood cell maturation.
• Identified genes with coordinated step-changes in transcription, violating assumptions of current velocity analysis.
• Gata1-deficient chimeric embryos demonstrated impaired upregulation of these genes during erythroid differentiation.
• Observed PU.1 induction and megakaryocyte progenitor expansion in Gata1-chimera embryos.
• Erythropoiesis in human fetal liver also exhibited coordinated gene expression step-changes.

Conclusions:

• Current RNA velocity frameworks have limitations in modeling differentiation processes with coordinated gene expression kinetics.
• A coordinated step-change in gene expression kinetics characterizes erythropoiesis, with implications for other differentiation pathways.