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SUMMARYThe isocortex and hippocampal formation are two major structures in the mammalian brain that play critical roles in perception, cognition, emotion and learning. Both structures contain multiple regions, for many of which the cellular composition is still poorly understood. In this study, we used two complementary single-cell RNA-sequencing approaches, SMART-Seq and 10x, to profile ∼1.2 million cells covering all regions in the adult mouse isocortex and hippocampal formation, and derived a cell type taxonomy comprising 379 transcriptomic types. The completeness of coverage enabled us to define gene expression variations across the entire spatial landscape without significant gaps. We found that cell types are organized in a hierarchical manner and exhibit varying degrees of discrete or continuous relatedness with each other. Such molecular relationships correlate strongly with the spatial distribution patterns of the cell types, which can be region-specific, or shared across multiple regions, or part of one or more gradients along with other cell types. Glutamatergic neuron types have much greater diversity than GABAergic neuron types, both molecularly and spatially, and they define regional identities as well as inter-region relationships. For example, we found that glutamatergic cell types between the isocortex and hippocampal formation are highly distinct from each other yet possess shared molecular signatures and corresponding layer specificities, indicating their homologous relationships. Overall, our study establishes a molecular architecture of the mammalian isocortex and hippocampal formation for the first time, and begins to shed light on its underlying relationship with the development, evolution, connectivity and function of these two brain structures.

The efficiency of gene targeting can vary drastically. Even utilizing CRISPR/Cas9 does not ensure rapid, successful gene targeting. InDrosophila, we previously established Golic+ to augment gene-targeting productivity simply through fly pushing. This transgene-based system elicits gene targeting in germ cells. It further implements lethality selection to enrich for progeny with accurate gene targeting. However, limitations still remain. Here we deliver an improved Golic+ technique that we name Enhanced Golic+ (E-Golic+). E-Golic+ incorporates genetic modifications to eliminate false positives while simultaneously boosting efficiency. Strikingly, male germ cells are exceptionally susceptible to gene targeting using E-Golic+. With male founders, we easily achieve 100% recovery of correct gene targeting. Given the superior efficiency/specificity and relatively effortless scalability, E-Golic+ promises to triumph in any challenging and otherwise unattainable gene targeting projects inDrosophila.

SummaryWiring a complex brain requires enormous cell specificity. This specificity is laid out via a developmental process where neural stem cells produce countless diverse neurons. To help elucidate this process and resolve the considerable dynamic specificity, we need to observe the development of multiple neuronal lineages.Drosophilacentral brain lineages are predetermined, comprised of a fixed set of neurons born in pairs in a specific order. To reveal specific roles of lineage identity, Notch-dependent sister fate specification, and temporal patterning in morphological diversification, we mapped approximately one quarter of theDrosophilacentral brain lineages. While we found large aggregate differences, we also discovered similar patterns of morphological specification and diversification. Lineage identity plus Notch state govern primary neuronal trajectories, whereas temporal fates diversify terminal elaborations in target-specific manners. In addition, we identified ‘related’ lineages of analogous neuron types produced in similar temporal patterns. Two stem cells even yield identical series of dopaminergic neuron types, but with completely disparate sister neurons. These phenomena suggest that large changes in morphological diversity can be the consequence of relatively small differences in lineage fating. Taken together, this large-scale lineage mapping study reveals that relatively simple rules drive incredible neuronal complexity.

SummaryDrosophilatype II neuroblasts produce numerous neurons and glia due to transiently amplifying, intermediate neural progenitors (INP). Consecutively born INPs produce morphologically distinct progeny, presumably due to temporal patterning in type II neuroblasts. We therefore profiled type II neuroblasts’ transcriptome across time. Our results reveal opposing temporal gradients of Imp and Syp RNA-binding proteins (descending and ascending, respectively). Maintaining Imp expression throughout brain development expands the number of neurons/glia with early temporal fate at the expense of cells with late fate. Conversely, precocious upregulation of Syp reduces the number of cells with early fate. Further, we reveal that the transcription factor, Seven-up initiates progression of the Imp/Syp gradients. Interestingly, genetic manipulations that fix Imp or Syp levels still yield progeny with a small range of early fates. We propose that the Seven-up-initiated Imp/Syp gradients create coarse temporal windows within type II neuroblasts to pattern INPs, which subsequently undergo fine-tuned subtemporal patterning.

Reversal learning has been widely used to probe the implementation of cognitive flexibility in the brain. Previous studies in monkeys identified an essential role of the orbitofrontal cortex (OFC) in reversal learning. However, the underlying circuits and molecular mechanisms are poorly understood. Here, we use the T-maze to investigate the neural mechanism of olfactory reversal learning in Drosophila. By adding a reversal training cycle to the classical learning protocol, we show that wild-type flies are able to reverse their choice according to the alteration of conditioned stimulus (CS)-unconditioned stimulus (US) contingency. The reversal protocol induced a specific suppression of the initial memory, an effect distinct from memory decay or extinction. GABA down-regulation in the anterior paired lateral (APL) neurons, which innervate the mushroom bodies (MBs), eliminates this suppression effect and impairs normal reversal. These findings reveal that inhibitory regulation from the GABAergic APL neurons facilitates olfactory reversal learning by suppressing initial memory in Drosophila.