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

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Barile, Melania 
Imaz-Rosshandler, Ivan 
Inzani, Isabella 
Ghazanfar, Shila 
Nichols, Jennifer 

BACKGROUND: Single-cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single-cell RNA-Seq permits prediction of future expression states. Here we apply this RNA velocity concept to an extended timecourse dataset covering mouse gastrulation and early organogenesis. RESULTS: Intriguingly, RNA velocity correctly identifies epiblast cells as the starting point, but several trajectory predictions at later stages are inconsistent with both real-time ordering and existing knowledge. The most striking discrepancy concerns red blood cell maturation, with velocity-inferred trajectories opposing the true differentiation path. Investigating the underlying causes reveals a group of genes with a coordinated step-change in transcription, thus violating the assumptions behind current velocity analysis suites, which do not accommodate time-dependent changes in expression dynamics. Using scRNA-Seq analysis of chimeric mouse embryos lacking the major erythroid regulator Gata1, we show that genes with the step-changes in expression dynamics during erythroid differentiation fail to be upregulated in the mutant cells, thus underscoring the coordination of modulating transcription rate along a differentiation trajectory. In addition to the expected block in erythroid maturation, the Gata1-chimera dataset reveals induction of PU.1 and expansion of megakaryocyte progenitors. Finally, we show that erythropoiesis in human fetal liver is similarly characterized by a coordinated step-change in gene expression. CONCLUSIONS: By identifying a limitation of the current velocity framework coupled with in vivo analysis of mutant cells, we reveal a coordinated step-change in gene expression kinetics during erythropoiesis, with likely implications for many other differentiation processes.

Erythropoiesis, Gastrulation, Gata1, RNA velocity, Animals, Cell Differentiation, Datasets as Topic, Embryo, Mammalian, Erythroid Cells, Erythropoiesis, Fetus, GATA1 Transcription Factor, Gastrula, Gene Expression Regulation, Developmental, Humans, Kinetics, Liver, Mice, Organogenesis, Proto-Oncogene Proteins, Single-Cell Analysis, Trans-Activators, Transcriptional Activation
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Genome Biol
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Springer Science and Business Media LLC
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Wellcome Trust (105031/D/14/Z)
Wellcome Trust (206328/Z/17/Z)
Wellcome Trust (097922/Z/11/Z)
Medical Research Council (MR/M008975/1)
Medical Research Council (MR/S036113/1)
Medical Research Council (MC_PC_17230)
National Institute of Diabetes and Digestive and Kidney Diseases (R24DK106766)
Bloodwise (18002)