Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors
- University of Washington, United States
Abstract
Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens of cell types. The heterogeneity of tissues and temporally-sensitive fate decisions involved has made it difficult to articulate the gene regulatory programs enabling regeneration of individual cell types. To better understand how a regenerative program is fulfilled by neural progenitor cells (NPCs) of the spinal cord, we analyzed pax6-expressing NPCs isolated from regenerating Xenopus tropicalis tails. By intersecting chromatin accessibility data with single-cell transcriptomics, we find that NPCs place an early priority on neuronal differentiation. Late in regeneration, the priority returns to proliferation. Our analyses identify Pbx3 and Meis1 as critical regulators of tail regeneration and axon organization. Overall, we use transcriptional regulatory dynamics to present a new model for cell fate decisions and their regulators in NPCs during regeneration.
Data availability
Sequencing data has been deposited in GEO under accession code GSE146837 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146837)
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RNA-Seq of Xenopus tail regenerationNCBI Gene Expression Omnibus, GSE88975.
Article and author information
Author details
Andrea Elizabeth Wills
Funding
National Institute of Neurological Disorders and Stroke (R01NS099124)
- Andrea Elizabeth Wills
National Institute of General Medical Sciences (T32GM007270)
- Anneke Dixie Kakebeen
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols (#4374) of the University of Washington, an AALAC-accredited institution. All surgeries were carried out under MS222 or Benzocaine anesthesia, and every effort was made to minimize suffering.
Reviewing Editor
- Marianne E Bronner, California Institute of Technology, United States
Publication history
- Received: October 11, 2019
- Accepted: April 25, 2020
- Accepted Manuscript published: April 27, 2020 (version 1)
- Version of Record published: May 26, 2020 (version 2)
Copyright
© 2020, Kakebeen et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors
eLife 9:e52648.
https://doi.org/10.7554/eLife.52648
Further reading
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- Stem Cells and Regenerative Medicine
- Developmental Biology
During development of the human cerebral cortex, multipotent neural progenitors generate excitatory neurons and glial cells. Investigations of the transcriptome and epigenome have revealed important gene regulatory networks underlying this crucial developmental event. However, the posttranscriptional control of gene expression and protein abundance during human corticogenesis remains poorly understood. We addressed this issue by using human telencephalic brain organoids grown using a dual reporter cell line to isolate neural progenitors and neurons and performed cell class and developmental stage-specific transcriptome and proteome analysis. Integrating the two datasets revealed modules of gene expression during human corticogenesis. Investigation of one such module uncovered mTOR-mediated regulation of translation of the 5’TOP element-enriched translation machinery in early progenitor cells. We show that in early progenitors partial inhibition of the translation of ribosomal genes prevents precocious translation of differentiation markers. Overall, our multiomics approach proposes novel posttranscriptional regulatory mechanisms crucial for the fidelity of cortical development.
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- Developmental Biology
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How does wiring specificity of neural maps emerge during development? Formation of the adult Drosophila olfactory glomerular map begins with patterning of projection neuron (PN) dendrites at the early pupal stage. To better understand the origin of wiring specificity of this map, we created genetic tools to systematically characterize dendrite patterning across development at PN type-specific resolution. We find that PNs use lineage and birth order combinatorially to build the initial dendritic map. Specifically, birth order directs dendrite targeting in rotating and binary manners for PNs of the anterodorsal and lateral lineages, respectively. Two-photon- and adaptive optical lattice light-sheet microscope-based time-lapse imaging reveals that PN dendrites initiate active targeting with direction-dependent branch stabilization on the timescale of seconds. Moreover, PNs that are used in both the larval and adult olfactory circuits prune their larval-specific dendrites and re-extend new dendrites simultaneously to facilitate timely olfactory map organization. Our work highlights the power and necessity of type-specific neuronal access and time-lapse imaging in identifying wiring mechanisms that underlie complex patterns of functional neural maps.
