bioRxiv

Spatial patterning of transcriptional and regulatory programs in the primate subcortex

Shu Dan, Meghan A. Turner, Mike DeBerardine, Lakme Caceres, Victor E. Nieto-Caballero, Jessica Schembri, Kirsten Levandowski, Christopher Cardenas, Ning Wang, Chang Li, Soumyadeep Basu, Hongyu Zheng, Xinhao Liu, Thomas Höllt, Jessica Feliciano, Qiangge Zhang, Reilly Nakamoto, Delissa A. McMillen, Naomi Martin, Nasmil Valera Cuevas, Paul Olsen, Josh Nagra, Jazmin Campos, Marshall M. VanNess, Jack Waters, Shea Ransford, Zoe Juneau, Sam Hastings, Stuard Barta, Augustin Ruiz, Jeanelle Ariza, Benjamin J. Raphael, Hongkui Zeng, Ed S. Lein, Boudewijn P. F. Lelieveldt, Guoping Feng, Brian Long, and Fenna M. Krienen

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Mammalian brain cell identity is shaped by intrinsic factors and external context. We present a spatially resolved transcriptomic and gene regulatory atlas of cell types found across all subcortical brain regions in a primate - the marmoset monkey. Dense sampling and cross-species integrations revealed spatially precise neuronal assemblies, including in complex structures such as hypothalamus. We find chromatin accessibility and transcriptional identity are spatially tuned within and across subcortical structures. Spatial gradients within subfields of the hippocampal formation are predominantly orchestrated by graded transcription factors coupled with graded enhancers. The primate-expanded population of GABAergic neurons in the thalamus shares transcriptional and regulatory syntax with neurons in superior colliculus, reflecting an evolutionary adaptation compared with rodents. We show that unexpected transcriptional convergence, such as between striatal GABAergic medium spiny neurons and telencephalic glutamatergic neurons, can arise when distinct gene regulatory networks impinge on the same downstream genes.

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@journal{bib:dan:2026,
    author       = { Dan, Shu and Turner, Meghan A. and DeBerardine, Mike and Caceres, Lakme and Nieto-Caballero, Victor E. and Schembri, Jessica and Levandowski, Kirsten and Cardenas, Christopher and Wang, Ning and Li, Chang and Basu, Soumyadeep and Zheng, Hongyu and Liu, Xinhao and Höllt, Thomas and Feliciano, Jessica and Zhang, Qiangge and Nakamoto, Reilly and McMillen, Delissa A. and Martin, Naomi and Valera Cuevas, Nasmil and Olsen, Paul and Nagra, Josh and Campos, Jazmin and VanNess, Marshall M.  and Waters, Jack and Ransford, Shea and Juneau, Zoe and Hastings, Sam and Barta, Stuard and Ruiz, Augustin and Ariza, Jeanelle and Raphael, Benjamin J. and Zeng, Hongkui and Lein, Ed S. and Lelieveldt, Boudewijn P. F. and Feng, Guoping and Long, Brian and Krienen, Fenna M. },    
    title        = { Spatial patterning of transcriptional and regulatory programs in the primate subcortex },
    journal      = { bioRxiv },
    year         = { 2026 },
    doi          = { 10.1101/2025.11.22.689869 },
    url          = { https://publications.graphics.tudelft.nl/papers/842 },
}