Periodic Reporting for period 4 - EVOCELFATE (Evolution of cell fate specification modes in spiral cleavage)
Reporting period: 2023-08-01 to 2024-07-31
Spiral cleavage is a conserved mode of development ancestral to one of the largest groups of animals–Spiralia. During spiral cleavage, embryos can specify their cell fates (i.e. the progenitor cell of posterodorsal structures) in two ways, either conditionally –via cell interactions– or autonomously –via segregation of molecules deposited in the oocyte by the mother. This variation occurs naturally, even between closely related species, and has been related to the precocious formation of adult characters in larvae of autonomous spiral-cleaving species. How spiralian lineages repeatedly shifted between these two cell fate specification modes is largely unexplored because the mechanisms controlling spiral cleavage are still poorly characterised.
This project tests the hypothesis that maternal chromatin and transcriptional regulators differentially incorporated in oocytes with autonomous spiral cleavage explain the evolution of this mode of cell fate specification. Through a comparative and phylogenetic-guided approach, we will combine bioinformatics, live imaging, and molecular and experimental techniques to (i) Comprehensively identify differentially supplied maternal factors among spiral cleaving oocytes with distinct cell fate specification modes using comparative RNA-seq and proteomics; (ii) Uncover the developmental mechanisms driving conditional spiral cleavage, which is the ancestral embryonic mode; and (iii) Investigate how maternal chromatin and transcriptional regulators define early cell fates, and whether these factors account for the repeated evolution of autonomous specification modes.
Our results have revealed that conserved molecular mechanisms control conditional spiral cleavage and that the transition to autonomous development involved the diversification of the gene regulatory networks controlling axial patterning. Interestingly, autonomous and conditional development also correlate with different life cycles in spiralians. Our findings have shown that temporal changes in the developmental programmes forming the animal trunk might explain how direct and indirect development and different larval types evolve, with conditional spiral cleavers showing a delayed activation of trunk formation compared with autonomous spiral cleavers.
This project tests the hypothesis that maternal chromatin and transcriptional regulators differentially incorporated in oocytes with autonomous spiral cleavage explain the evolution of this mode of cell fate specification. Through a comparative and phylogenetic-guided approach, we will combine bioinformatics, live imaging, and molecular and experimental techniques to (i) Comprehensively identify differentially supplied maternal factors among spiral cleaving oocytes with distinct cell fate specification modes using comparative RNA-seq and proteomics; (ii) Uncover the developmental mechanisms driving conditional spiral cleavage, which is the ancestral embryonic mode; and (iii) Investigate how maternal chromatin and transcriptional regulators define early cell fates, and whether these factors account for the repeated evolution of autonomous specification modes.
Our results have revealed that conserved molecular mechanisms control conditional spiral cleavage and that the transition to autonomous development involved the diversification of the gene regulatory networks controlling axial patterning. Interestingly, autonomous and conditional development also correlate with different life cycles in spiralians. Our findings have shown that temporal changes in the developmental programmes forming the animal trunk might explain how direct and indirect development and different larval types evolve, with conditional spiral cleavers showing a delayed activation of trunk formation compared with autonomous spiral cleavers.
At the end of this project, our team has made progress in all three proposed objectives, producing transformative results and unprecedented datasets that advance the field of EvoDevo and the study of spiral cleavage. We have generated transcriptomic and proteomic data for oocytes of annelids and molluscs with distinct modes of spiral cleavage. We have investigated how differences in maternal determinants might account for changes in the timing of specification of the progenitor cells. Additionally, we have characterised the gene regulatory networks controlling conditional spiral cleavage and body patterning in the annelid Owenia fusiformis, a new model species for developmental biology, identifying the genes and signalling pathways involved in the specification of the embryonic organiser and demonstrating that conserved molecular mechanisms control conditional spiral cleavage. This better characterisation of conditional cleavage has also allowed us to conclude that autonomous specification evolved through losing an FGF-ERK1/2-mediated embryonic organiser. Furthermore, we have established cutting-edge approaches for epigenomic profiling in annelid embryos to investigate the impact of chromatin accessibility, DNA methylation, and histone post-translational modifications on cell-fate specification dynamics and distinct life cycle strategies. This has allowed us to demonstrate that temporal changes in the developmental programmes controlling trunk formation correlate with the evolution of direct and indirect development. Altogether, this project has contributed to the career development of five early-career researchers (three PhD students and two postdocs; two females and three males), resulting in 11 peer-reviewed research manuscripts, including publications in high-profile journals like Nature and Nature Communications, and over 40 dissemination and exploitation activities.
Our work has generated unprecedented datasets for studying spiral cleavage in annelid embryos and spiralians in general. Our data in Owenia fusiformis has transformed current views on spiral cleavage, demonstrating that conserved, ancient molecular mechanisms control spiral cleavage. In Mollusca and Annelida, however, these mechanisms have diverged independently multiple times in parallel with the evolution of an autonomous mode of spiral cleavage. This project has also pioneered and established epigenomic profiling methods in spiralian embryos, which, combined with new high-quality genomic data that my lab, are generating new views on how spiral cleavage is controlled, from changes in genome sequence and genome regulation to distinct dynamics of gene expression and cell behaviour. In particular, we have demonstrated that temporal changes in the activation of genes involved in trunk development, such as the Hox genes, explain transitions in life cycle strategies and larval types in annelids and other animals. Together, this ERC has established new research species, created unprecedented datasets and optimised novel approaches for the study of spiral cleavage, opening new research opportunities to investigate the mechanisms that control early animal embryogenesis and result in phenotypic change.