A dynamic and expandable Digital 3D-Atlas MAKER for monitoring the temporal changes in tissue growth during hindbrain morphogenesis
- Universitat Pompeu Fabra, Spain
- European Molecular Biology Laboratory, Spain
Abstract
Reconstruction of prototypic three-dimensional (3D) atlases at the scale of whole tissues or organs requires specific methods to be developed. We have established a digital 3D-atlas maker (DAMAKER) and built a digital 3D-atlas to monitor the changes in the growth of the neuronal differentiation domain in the zebrafish hindbrain upon time. DAMAKER integrates spatial and temporal data of cell populations, neuronal differentiation and brain morphogenesis, through in vivo imaging techniques paired with image analyses and segmentation tools. First, we generated a 3D-reference from several imaged hindbrains and segmented them using a trainable tool; these were aligned using rigid registration, revealing distribution of neuronal differentiation growth patterns along the axes. Second, we quantified the dynamic growth of the neuronal differentiation domain by in vivo neuronal birthdating experiments. We generated digital neuronal birthdating 3D-maps and revealed that the temporal order of neuronal differentiation prefigured the spatial distribution of neurons in the tissue, with an inner-outer differentiation gradient. Last, we applied it to specific differentiated neuronal populations such as glutamatergic and GABAergic neurons, as proof-of-concept that the digital birthdating 3D-maps could be used as a proxy to infer neuronal birthdate. As this protocol uses open-access tools and algorithms, it can be shared for standardized, accessible, tissue-wide cell population atlas construction.
Data availability
All data generated or analysed during this study are included in the manuscript or in the supplementary files.All code is available in https://github.com/cristinapujades/Blanc-et-al.-2022.
Article and author information
Author details
Funding
Agencia Estatal de Investigación (PGC2018-095663-B-I00)
- Cristina Pujades
Agencia Estatal de Investigación (PGC2018-101643-B-I00)
- Frederic Udina
Agencia Estatal de Investigación (CEX2018-000792-M)
- Matthias Blanc
- Cristina Pujades
Institució Catalana de Recerca i Estudis Avançats
- Cristina Pujades
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: Zebrafish (Dario rerio) were treated according to the Spanish/European regulations for the handling of animals in research. All protocols were approved by the Institutional Animal Care and Use Ethic Committee (Comitè Etica en Experimentació Animal, PRBB) and the Generalitat of Catalonia (Departament de Territori i Sostenibilitat), and they were implemented according to European regulations. The Project Licenses covering the proposed work (Ref 10642, Ref 10477, GC) pay particular attention to the 3Rs (Replacement, Reduction, Refinement).
Copyright
© 2022, Blanc 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.
Metrics
-
- 964
- views
-
- 186
- downloads
-
- 0
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
A dynamic and expandable Digital 3D-Atlas MAKER for monitoring the temporal changes in tissue growth during hindbrain morphogenesis
eLife 11:e78300.
https://doi.org/10.7554/eLife.78300
Further reading
-
- Developmental Biology
During the first lineage segregation, mammalian embryos generate the inner cell mass (ICM) and trophectoderm (TE). ICM gives rise to the epiblast (EPI) that forms all cell types of the body, an ability referred to as pluripotency. The molecular mechanisms that induce pluripotency in embryos remain incompletely elucidated. Using knockout (KO) mouse models in conjunction with low-input ATAC-seq and RNA-seq, we found that Oct4 and Sox2 gradually come into play in the early ICM, coinciding with the initiation of Sox2 expression. Oct4 and Sox2 activate the pluripotency-related genes through the putative OCT-SOX enhancers in the early ICM. Furthermore, we observed a substantial reorganization of chromatin landscape and transcriptome from the morula to the early ICM stages, which was partially driven by Oct4 and Sox2, highlighting their pivotal role in promoting the developmental trajectory toward the ICM. Our study provides new insights into the establishment of the pluripotency network in mouse preimplantation embryos.
-
- Developmental Biology
- Neuroscience
The ligand Netrin mediates axon guidance through a combination of haptotaxis over short distances and chemotaxis over longer distances.
