Researchers reveal genetic factors for rapid craniofacial development in marsupials

Researchers have discovered genetic elements that lead to the rapid development of marsupial facial features.

The study on fat-tailed dunnarts, native to Australia, is published today in eLife. The editors describe it as an important work with compelling data, including a new assembly of Dunnart’s genome, which they say provides an “invaluable reference” for future studies of mammalian evolution.

Marsupials and placental mammals differ greatly in their modes of reproduction and growth. While marsupials are born very underdeveloped after a short gestation period and complete their development inside the maternal pouch, mammalian placental fetuses develop entirely inside the uterus. Compared to placental mammals, marsupials exhibit accelerated orofacial (mouth and face) development relative to their central nervous system, reflecting functional demands after birth.

Cis-acting regulatory elements (regions of DNA that regulate the expression of neighboring genes) have been proposed to play an important role in differences in mammalian facial development. But no study so far has attempted to compare the overall landscape of genetic regulation between marsupials and placentals at the same developmental stage.

“Such studies can provide functional insights into how regulatory elements in the genome control mammalian craniofacial development and, therefore, the evolutionary changes that have resulted in divergent growth patterns in marsupials and placentals,” says first author Laura Cook, who undertook this work as a doctoral student. candidate at the School of BioSciences, University of Melbourne, Australia, and is now a postdoctoral researcher at Lawrence Berkeley National Laboratory, USA

“Having previously described accelerated orofacial development in the fat-tailed dunnart, a tiny marsupial with a gestation of only 13 days, we wanted to see how the regulation of genes driving early facial development in marsupials differs from that of placental mammals like mice.”

To do this, Cook and the team used two sequencing techniques – ChIP sequencing (ChIP-seq) and RNA sequencing (RNA-seq) – on craniofacial tissues from young pouches of newborn Dunnarts. Tissues were collected from the frontal region of the face and nose (frontonasal tissue), from the mandibular (relating to the lower jaw) and maxillary (relating to the upper jaw, upper lip and cheeks) prominences.

Applying sequencing methods to this tissue allowed the team to perform detailed characterization of chromatin marks (chemical changes on DNA that regulate gene expression) during dunnarts’ early craniofacial development. They then examined the similarities and differences between two chromatin modifications associated with cis-regulatory elements (H3K4me3 and H3K27ac) between dunnart and mouse, and incorporated comparisons of gene expression between species.

For comparisons, they used publicly available craniofacial ChIP-seq data for H3K4me3 and H3K27ac generated by the mouse ENCODE consortium, spanning multiple developmental time points.

Their analyzes revealed that genes involved in regulating facial development are largely conserved in mice and Dunnart, but their cis-regulatory elements vary considerably. In particular, they discovered Dunnart-specific regulatory elements near highly expressed genes that are either weakly or not at all expressed in mice. These genes are linked to three main developmental processes: skin/epidermis development, muscle development and contraction, and sensory system development.

“The recurrence of genes linked to the development of the dunnarts’ sensory system highlights a unique aspect of early pouch life in marsupials: the challenge of reaching it,” says co-author Irene Gallego Romero, associate professor at the St Vincent’s Institute of Medical Research, Melbourne, Australia. “Newborn marsupials need their sensory systems, particularly their sense of smell, to be highly developed – and quickly – so that they can follow the signals that guide them to their mother’s pouch where they will complete their development.”

Andrew Pask, professor of genetics and developmental biology at the School of BioSciences at the University of Melbourne, adds: “Together, the data from our experiments suggest that accelerated craniofacial development in dunnarts may be driven by enhancer activity that evolved specifically to support their postnatal survival. activators in driving different growth strategies between species.

A notable limitation of the study is that it does not include several postnatal stages of the dunnart, due to the limited availability of pouched young. The authors say they now hope to extend their work to more advanced stages of development in future studies to provide additional information. “We also plan to apply single-cell and multimodal technologies to Dunnart tissues in future studies to investigate specific regulatory differences between their central nervous system and orofacial development,” concludes Pask.