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Transcriptomic analysis of the developing neocortex of the Australian marsupial fat-tailed dunnart (Sminthopsis crassicaudata)

ABSTRACT: Transcriptomic analysis of the developing neocortex of the Australian marsupial fat-tailed dunnart (Sminthopsis crassicaudata)

PROVIDER: PRJNA676111 | ENA |

REPOSITORIES: ENA

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Transcriptomic analysis of the developing neocortex of the Australian marsupial fat-tailed dunnart (Sminthopsis crassicaudata)

Project description:The six-layered neocortex is exclusively present in mammals and mediates sensory-motor and higher-order functions. Key differences in this structure and its connections exist between the main mammalian groups: eutherians and marsupials, however, the molecular changes that underlie these known morphological differences remain unknown. This question is particularly difficult to address because small and transient changes in gene expression during development may be crucial to brain formation, which would not be detectable in adult transcriptomic analyses. To address this question of the developmental origin of changes in the evolution of the mammalian neocortex, we performed transcriptomic analysis on the marsupial fat-tailed dunnart (Sminthopsis crassicaudata) at postnatal ages P12 and P20 corresponding to the generation of infragranular (layers 5/6) and supragranular (layers 2/3) neurons, respectively. We assembled a de novo transcriptome of the neocortex of fat-tailed dunnarts using RNA-seq data from all samples, then differential gene expression analysis performed across the two ages. Additional cross-species analysis was performed against existing mouse neocortical datasets in the NCBI Sequence Read Archive at equivalent developmental ages embryonic (E) day 12.5 (SRR1509162, SRR1509163, SRR1509164) and E16 (SRR5755669, SRR5755670, SRR5755671, SRR5755672). We identified 12,632 protein-coding transcripts orthologous to mouse RNA reference sequences (Refseq) in the dunnart neocortical transciptome. The results also revealed divergences in gene sets known to be enriched in different neuronal populations, revealing a more advanced stage of maturation in the marsupial neocortex at the period of infragranular birth compared to the eutherian mouse.

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Project description:Australian marsupial phylogeny with denovo assembly of target exons captured sequences.

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Profiling epigenomic modifications, H3K4me3 and H3K27ac, during craniofacial development in a marsupial model, the fat-tailed dunnart (Sminthopsis crassicaudata; Dasyuridae)

Project description:Marsupials display accelerated development of the craniofacial region relative to the differentiation of the CNS when compared to placental mammals. This heterochrony is thought to be due to the functional demands on the oral region for suckling post-birth while in a highly altricial state after a very short gestation period. While cis-regulatory regions are thought to play a significant role in morphological evolution of the mammalian face, the genetic mechanisms involved in craniofacial heterochrony in marsupials remain unclear. To assess this question, we generated ChIP-seq data for H3K4me3 and H3K27ac from fat-tailed dunnart (Sminthopsis crassicaudata; Dasyuridae) craniofacial tissue collected from pouch young on the day of birth and characterised the cis-regulatory landscape during craniofacial development. Using data from the mouse ENCODE consortium we explored the similarities and differences in active regulatory pathways between the dunnart and mouse during early craniofacial development. We found that dunnart promoter- and enhancer- associated peaks overlap to some extent with all the stages (E10.5 – E15.5) in the mouse. However, dunnart genes with peaks were significantly enriched for genes that exhibit linear increases in expression from E10.5 to E15.5 in mice, suggesting a greater similarity with late development. In turn, genes displaying this temporal expression pattern were enriched for Gene Ontology terms related to ossification and skeletal development, processes that underlie development of the cranial muscles and bones of the face. This study provides useful insights into genomic regions associated with cis-regulatory elements regulating craniofacial development in marsupials and their potential role in craniofacial heterochrony

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