Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation
Year: 2021
Type: article
Abstract: 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.
Source: Genome biology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $4,890
Funders: Wellcome Trust, European Molecular Biology Laboratory, Cancer Research UK, British Heart Foundation, Royal Society, Vetenskapsrådet, Blood Cancer UK, National Institutes of Health, Medical Research Council, Cambridge Institute for Medical Research, University of Cambridge, Cancer Research UK Cambridge Institute, University of Cambridge, National Institute of Diabetes and Digestive and Kidney Diseases
Awards: G1305121252, Defining the Haematopoietic System through Integrated Multi-Scale Analysis, Joint Wellcome and MRC Centre, ‘Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute’, Establishment of the Cambridge Single Cell Analysis Clinical Core Facility [SCACCF], From Mesoderm to Blood: a Transcriptional Roadmap at Single-Cell Resolution, Tracing early mammalian lineage decisions by single cell genomics., G3187034290, Tracing early mammalian lineage decisions by single cell genomics., G55385154, G6116745146, G6364503916, G654986153, G6633812446, G7306926374, A protein-transcriptome atlas of haematopoiesis across the human life span, Cambridge Stem Cell Institute., G8242440306, VISION: ValIdated Systematic IntegratiON of epigenomic data
OpenAlex ID: W3182034091