@article {70191,
	title = {Multimodal cell lineage reconstruction in the hindbrain reveals a link between progenitor origin and activity patterning},
	journal = {bioRxiv},
	year = {2025},
	month = {2025 Nov 14},
	abstract = {<p>The vertebrate brain develops through a precisely orchestrated sequence of events, where neural progenitors generate neuronal diversity. However, the importance of stem cell origin in the acquisition of functional characteristics and the assembly into circuits are largely unknown. Here, by multimodal cell lineage reconstruction we reveal a link between progenitor origin and excitatory and inhibitory activity in the hindbrain. By combining progenitor intersectional fate mapping with newly developed computational tools and CRISPR/Cas9-based loss-of-function experiments, we discovered the differential temporal contribution of distinct progenitor pools {\textendash}defined by proneural gene expression{\textendash} to both glutamatergic and GABAergic neurons. Whereas neurog1-progenitors contribute to both lineages in early embryonic stages, later, other progenitor pools either also assume this role or take over. Using calcium imaging in combination with genetic perturbations, we unveiled that spatiotemporally defined stem cell origin determines specific neuronal activity features. Overall, we provide in vivo evidence for a link between cell ontogeny and functionality in the vertebrate hindbrain.For more information or any specific tool, you can contact us.</p>
},
	doi = {10.1101/2025.11.14.688499},
	url = {https://www.biorxiv.org/content/early/2025/11/14/2025.11.14.688499},
	author = {Blanc, Matthias and Meister, Lydvina and Lemon, William C. and Fiuza, Ulla-Maj and Keller, Philipp J. and Espinosa-Medina, Isabel and Pujades, Cristina}
}
@article {65114,
	title = {Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians.},
	journal = {Developmental Biology},
	volume = {448},
	year = {2019},
	month = {2019 Apr 15},
	pages = {71-87},
	abstract = {<p>Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages. Here, we explored the evolution of transcriptional control between P. mammillata and C. robusta. We combined genome-wide mapping of open chromatin regions in both species with a comparative analysis of the regulatory sequences of a test set of 10 pairs of orthologous early regulatory genes with conserved expression patterns. We find that ascidian chromatin accessibility landscapes obey similar rules as in other metazoa. Open-chromatin regions are short, highly conserved within each genus and cluster around regulatory genes. The dynamics of chromatin accessibility and closest-gene expression are strongly correlated during early embryogenesis. Open-chromatin regions are highly enriched in cis-regulatory elements: 73\% of 49 open chromatin regions around our test genes behaved as either distal enhancers or proximal enhancer/promoters following electroporation in Phallusia eggs. Analysis of this datasets suggests a pervasive use in ascidians of "shadow" enhancers with partially overlapping activities. Cross-species electroporations point to a deep conservation of both the trans-regulatory logic between these distantly-related ascidians and the cis-regulatory activities of individual enhancers. Finally, we found that the relative order and approximate distance to the transcription start site of open chromatin regions can be conserved between Ciona and Phallusia species despite extensive sequence divergence, a property that can be used to identify orthologous enhancers, whose regulatory activity can partially diverge.</p>
},
	issn = {1095-564X},
	doi = {10.1016/j.ydbio.2019.01.003},
	author = {Madgwick, Alicia and Magri, Marta Silvia and Dantec, Christelle and Gailly, Damien and Fiuza, Ulla-Maj and Guignard, Leo and Hettinger, Sabrina and Gomez-Skarmeta, Jose Luis and Lemaire, Patrick}
}
