Journal Article

An atlas of rabbit development as a model for single-cell comparative genomics

Ahnfelt-Rønne, Jonas, Benito-Gutiérrez, Èlia, Göttgens, Berthold, Keitley, Daniel, Calero-Nieto, Fernando J., Theeuwes, Bart, Andreassen, Thomas Kjærgaard, Imaz-Rosshandler, Ivan, Marioni, John C., Guibentif, Carolina, Pijuan-Sala, Blanca, Nichols, Jennifer, Ton, Mai-Linh Nu

2023

Overview

Traditionally, the mouse has been the favoured vertebrate model for biomedical research, due to its experimental and genetic tractability. However, non-rodent embryological studies highlight that many aspects of early mouse development, such as its egg-cylinder gastrulation and method of implantation, diverge from other mammals, thus complicating inferences about human development. Like the human embryo, rabbits develop as a flat-bilaminar disc. Here we constructed a morphological and molecular atlas of rabbit development. We report transcriptional and chromatin accessibility profiles for over 180,000 single cells and high-resolution histology sections from embryos spanning gastrulation, implantation, amniogenesis and early organogenesis. Using a neighbourhood comparison pipeline, we compare the transcriptional landscape of rabbit and mouse at the scale of the entire organism. We characterize the gene regulatory programmes underlying trophoblast differentiation and identify signalling interactions involving the yolk sac mesothelium during haematopoiesis. We demonstrate how the combination of both rabbit and mouse atlases can be leveraged to extract new biological insights from sparse macaque and human data. The datasets and computational pipelines reported here set a framework for a broader cross-species approach to decipher early mammalian development, and are readily adaptable to deploy single-cell comparative genomics more broadly across biomedical research. Ton, Keitley et al. provide a morphological and molecular atlas of rabbit development. Comparative studies reveal that combining rabbit and mouse atlases can serve as a model for dissecting early primate development.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 14/63 / 38/91 / 631/114/2114 / 631/136/2086 / Animals / Biomedical and Life Sciences / Biomedical research / Cancer Research / Cell and Molecular Biology / Cell Biology / Cell Differentiation / Cell- och molekylärbiologi / Chromatin / Comparative studies / Developmental Biology / differentiation / Embryo Implantation - genetics / Embryo, Mammalian / Embryonic Development - genetics / Embryos / endoderm / expression / Gastrulation / Gastrulation - genetics / Genomics / Hemopoiesis / Histology / Humans / Implantation / layer / leads / Life Sciences / lineage / Mammals / Medical research / Mesothelium / Mice / Morphology / mouse embryo / Organogenesis / Organogenesis - genetics / Rabbits / Resource / Stem Cells / transcription factor / trophectoderm / Vertebrates / Yolk sac