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The cellular and molecular landscape of hypothalamic patterning and differentiation

By Dong Won Kim, Parris Whitney Washington, Zoe Qianyi Wang, Sonia Hao Lin, Changyu Sun, Basma Taleb Ismail, Hong Wang, Lizhi Jiang, Seth Blackshaw

Posted 05 Jun 2019
bioRxiv DOI: 10.1101/657148

The hypothalamus is a central regulator of many innate behaviors essential for survival, but the molecular mechanisms controlling hypothalamic patterning and cell fate specification are poorly understood. To identify genes that control hypothalamic development, we have used single-cell RNA sequencing (scRNA-Seq) to profile mouse hypothalamic gene expression across 12 developmental time points between embryonic day 10 and postnatal day 45. This identified genes that delineated clear developmental trajectories for all major hypothalamic cell types, and readily distinguished major regional subdivisions of the developing hypothalamus. By using our developmental dataset, we were able to rapidly annotate previously unidentified clusters from existing scRNA-Seq datasets collected during development, and to identify the developmental origins of major neuronal populations of the ventromedial hypothalamus. We further show that our approach can rapidly and comprehensively characterize mutants that have altered hypothalamic patterning, identifying Nkx2.1 as a negative regulator of prethalamic identity. These data serve as a resource for further studies of hypothalamic development, physiology and dysfunction.

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