Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors

Abstract
Data availability
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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)

The following data sets were generated

(2020) Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors
NCBI Gene Expression Omnibus, GSE146830.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146830
(2019) Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors
NCBI Gene Expression Omnibus, GSE146836.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146836
(2020) Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors
NCBI Gene Expression Omnibus, GSE146837.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146837

The following previously published data sets were used

1. Chang J
2. Baker J
3. Wills A
(2017) RNA-Seq of Xenopus tail regeneration
NCBI Gene Expression Omnibus, GSE88975.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE88975

Article and author information

Author details

Anneke Dixie Kakebeen

Biochemistry, University of Washington, Seattle, United States

Competing interests
The authors declare that no competing interests exist.
Alex D Chitsazan

Biochemistry, University of Washington, Seattle, United States

Competing interests
The authors declare that no competing interests exist.
Madison Corinne Williams

Biochemistry, University of Washington, Seattle, United States

Competing interests
The authors declare that no competing interests exist.
Lauren M Saunders

Department of Genome Sciences, University of Washington, Seattle, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4377-4252
Andrea Elizabeth Wills

Biochemistry, University of Washington, Seattle, United States

For correspondence
aewills@uw.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3647-8105

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.

Copyright

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.