Optogenetic inhibition of the electrical activity of neurons enables the causal assessment of their contributions to brain functions. Red light penetrates deeper into tissue than other visible wavelengths. We present a red-shifted cruxhalorhodopsin, Jaws, derived from Haloarcula (Halobacterium) salinarum (strain Shark) and engineered to result in red light–induced photocurrents three times those of earlier silencers. Jaws exhibits robust inhibition of sensory-evoked neural activity in the cortex and results in strong light responses when used in retinas of retinitis pigmentosa model mice. We also demonstrate that Jaws can noninvasively mediate transcranial optical inhibition of neurons deep in the brains of awake mice. The noninvasive optogenetic inhibition opened up by Jaws enables a variety of important neuroscience experiments and offers a powerful general-use chloride pump for basic and applied neuroscience.
Summary Diverse subsets of cortical interneurons play vital roles in higher-order brain functions. To investigate how this diversity is generated, we used single cell RNA-seq to profile the transcriptomes of murine cells collected along a developmental timecourse. Heterogeneity within mitotic progenitors in the ganglionic eminences is driven by a highly conserved maturation trajectory, alongside eminence-specific transcription factor expression that seeds the emergence of later diversity. Upon becoming postmitotic, progenitors diverge and differentiate into transcriptionally distinct states, including an interneuron precursor state. By integrating datasets across developmental timepoints, we identified shared sources of transcriptomic heterogeneity between adult interneurons and their precursors, revealing the embryonic emergence of interneuron cardinal subtypes. Our analysis revealed that the ASD-associated transcription factor Mef2c delineates early Pvalb-precursors, and is essential for their development. These findings shed new light on the molecular diversification of early inhibitory precursors, and identify gene modules that may influence the specification of human subtypes.
Diverse subsets of cortical interneurons play a particularly important role in the stability of the neural circuits underlying cognitive and higher order brain functions, yet our understanding of how this diversity is generated is far from complete. We applied massively parallel single-cell RNA-seq to profile a developmental time course of interneuron development, measuring the transcriptomes of over 60,000 progenitors during their maturation in the ganglionic eminences and embryonic migration into the cortex. While diversity within mitotic progenitors is largely driven by cell cycle and differentiation state, we observed sparse eminence-specific transcription factor expression, which seeds the emergence of later cell diversity. Upon becoming postmitotic, cells from all eminences pass through one of three precursor states, one of which represents a cortical interneuron ground state. By integrating datasets across developmental timepoints, we identified transcriptomic heterogeneity in interneuron precursors representing the emergence of four cardinal classes (Pvalb, Sst, Id2 and Vip), which further separate into subtypes at different timepoints during development. Our analysis revealed that the ASD-associated transcription factor Mef2c discriminates early Pvalb-precursors in E13.5 cells, and removal of Mef2c confirms its essential role for Pvalb interneuron development. These findings shed new light on the molecular diversification of early inhibitory precursors, and suggest gene modules that may link developmental specification with the etiology of neuropsychiatric disorders.
During neurogenesis, mitotic progenitor cells lining the ventricles of the embryonic mouse brain undergo their final rounds of cell division, giving rise to a wide spectrum of postmitotic neurons and glia1,2. The link between developmental lineage and cell-type diversity remains an open question. Here we used massively parallel tagging of progenitors to track clonal relationships and transcriptomic signatures during mouse forebrain development. We quantified clonal divergence and convergence across all major cell classes postnatally, and found diverse types of GABAergic neuron that share a common lineage. Divergence of GABAergic clones occurred during embryogenesis upon cell-cycle exit, suggesting that differentiation into subtypes is initiated as a lineage-dependent process at the progenitor cell level.
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