Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation
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 cover...
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| Format: | Article |
| Language: | English |
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BMC
2021-07-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-021-02414-y |
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| author | Melania Barile Ivan Imaz-Rosshandler Isabella Inzani Shila Ghazanfar Jennifer Nichols John C. Marioni Carolina Guibentif Berthold Göttgens |
| author_facet | Melania Barile Ivan Imaz-Rosshandler Isabella Inzani Shila Ghazanfar Jennifer Nichols John C. Marioni Carolina Guibentif Berthold Göttgens |
| author_sort | Melania Barile |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-17T05:50:37Z |
| format | Article |
| id | doaj.art-612c8ca067714602822b1e9460b4c3c2 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-17T05:50:37Z |
| publishDate | 2021-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-612c8ca067714602822b1e9460b4c3c22022-12-21T22:01:11ZengBMCGenome Biology1474-760X2021-07-0122112210.1186/s13059-021-02414-yCoordinated changes in gene expression kinetics underlie both mouse and human erythroid maturationMelania Barile0Ivan Imaz-Rosshandler1Isabella Inzani2Shila Ghazanfar3Jennifer Nichols4John C. Marioni5Carolina Guibentif6Berthold Göttgens7Department of Haematology, University of CambridgeDepartment of Haematology, University of CambridgeUniversity of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases UnitCancer Research UK Cambridge Institute, University of CambridgeWellcome-Medical Research Council Cambridge Stem Cell Institute, University of CambridgeCancer Research UK Cambridge Institute, University of CambridgeDepartment of Haematology, University of CambridgeDepartment of Haematology, University of CambridgeAbstract 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.https://doi.org/10.1186/s13059-021-02414-yRNA velocityGastrulationErythropoiesisGata1 |
| spellingShingle | Melania Barile Ivan Imaz-Rosshandler Isabella Inzani Shila Ghazanfar Jennifer Nichols John C. Marioni Carolina Guibentif Berthold Göttgens Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation Genome Biology RNA velocity Gastrulation Erythropoiesis Gata1 |
| title | Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation |
| title_full | Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation |
| title_fullStr | Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation |
| title_full_unstemmed | Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation |
| title_short | Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation |
| title_sort | coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation |
| topic | RNA velocity Gastrulation Erythropoiesis Gata1 |
| url | https://doi.org/10.1186/s13059-021-02414-y |
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