Cited by 77Single-cell and spatial transcriptomicsDevelopmental Biology and Gene RegulationGene Regulatory Network Analysis

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, Marioni, John C., Guibentif, Carolina, Göttgens, Berthold·2021·Genome Biology

Published version of a preprint

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.

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  • Ninety-six multiple rate kinetics (MURK) genes possess coordinated step-change in transcription and hence violate the assumptions behind scVelo.

    “Ninety-six multiple rate kinetics (MURK) genes previously shown to possess coordinated step-change in transcription and hence violate the assumptions behind scVelo were removed82.”

    From Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution (2023) · cites this paper as [82]

    The Results section, “Analysis of unspliced reads reveals complex expression kinetics,” links MURK genes’ increased transcription rates to incorrect scVelo velocity predictions, and the Discussion says removing them can improve predictions. But the Methods section, “MURK gene identification,” reports 89 mouse genes and 97 human genes, not 96; the Discussion also notes that MURK genes can occur where scVelo predictions are correct. (LLM, conf=0.90)

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Authors
Barile, M., Imaz-Rosshandler, I., Inzani, I., Ghazanfar, S., Nichols, J., Marioni, J. C., Guibentif, C., & Göttgens, B.
Affiliations
  • Wellcome/MRC Cambridge Stem Cell Institute (GB)
  • University of Cambridge (GB)
  • European Bioinformatics Institute (GB)
Corresponding author
  • Guibentif, Carolina
  • Göttgens, Berthold
Venue
Genome Biology
Published
2021-07-05
Volume
22
Issue
1
Pages
197-197
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
OpenAlex
W3182034091
Cited by
77
References
60
Citations by year
2026: 20 · 2025: 12 · 2024: 8 · 2023: 21 · 2022: 11 · 2021: 5
FWCI
3.51
Type
journal article
Language
en
Open access
Locations
  • Genome biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Apollo (University of Cambridge) (submittedVersion)
  • Apollo
  • Apollo (cc-by)
Funders
  • Wellcome Trust (105031/D/14/Z, 097922/Z/11/Z, 206328/Z/17/Z)
  • Vetenskapsrådet (2017-06278)
  • Royal Society (NIF\R1\181950)
  • Blood Cancer UK (18002)
  • Medical Research Council (MR/M008975/1, MR/S036113/1)
  • British Heart Foundation (FS/18/56/35177)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Keywords
RNA velocity, erythropoiesis, erythroid maturation, gene expression kinetics, differentiation trajectories, GATA-1, PU.1, megakaryocyte progenitors, epiblast, gastrulation, single-cell RNA sequencing
MeSH terms
Proto-Oncogene Protein Spi-1, Animals, Cell Differentiation, Embryo, Mammalian, Erythropoiesis, Fetus, Gastrula, Humans, Kinetics, Liver, Proto-Oncogene Proteins, Transcriptional Activation, Trans-Activators, Gene Expression Regulation, Developmental, Organogenesis, Erythroid Cells, GATA1 Transcription Factor, Mice, Single-Cell Analysis, Datasets as Topic

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