Massive multiplexing of spatially resolved single neuron projections with axonal BARseq.

Neurons in the cortex are heterogeneous, sending diverse axonal projections to multiple brain regions. Unraveling the logic of these projections requires single-neuron resolution. Although a growing number of techniques have enabled high-throughput reconstruction, these techniques are typically limited to dozens or at most hundreds of neurons per brain, requiring that statistical analyses combine data from different specimens.

A genetic, genomic, and computational resource for exploring neural circuit function.

The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.

Illuminating spatial A-to-I RNA editing signatures within the brain.

Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a ubiquitous mechanism that generates transcriptomic diversity. This process is particularly important for proper neuronal function; however, little is known about how RNA editing is dynamically regulated between the many functionally distinct neuronal populations of the brain. Here, we present a spatial RNA editing map in the brain and show that different neuronal populations possess distinct RNA editing signatures.

Nuclear Transcriptomes of the Seven Neuronal Cell Types That Constitute the Mushroom Bodies.

The insect mushroom body (MB) is a conserved brain structure that plays key roles in a diverse array of behaviors. The MB is the primary invertebrate model of neural circuits related to memory formation and storage, and its development, morphology, wiring, and function has been extensively studied. MBs consist of intrinsic Kenyon Cells that are divided into three major neuron classes (γ, α'/β' and α/β) and 7 cell subtypes (γd, γm, α'/β'ap, α'/β'm, α/βp, α/βs and α/βc) based on their birth order, morphology, and connectivity.

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.

Neuronal diversity is essential for mammalian brain function but poses a challenge to molecular profiling. To address the need for tools that facilitate cell-type-specific epigenomic studies, we developed the first affinity purification approach to isolate nuclei from genetically defined cell types in a mammal. We combine this technique with next-generation sequencing to show that three subtypes of neocortical neurons have highly distinctive epigenomic landscapes.

High-performance probes for light and electron microscopy.

We describe an engineered family of highly antigenic molecules based on GFP-like fluorescent proteins. These molecules contain numerous copies of peptide epitopes and simultaneously bind IgG antibodies at each location. These 'spaghetti monster' fluorescent proteins (smFPs) distributed well in neurons, notably into small dendrites, spines and axons.

Cell type-specific genomics of Drosophila neurons.

Many tools are available to analyse genomes but are often challenging to use in a cell type-specific context. We have developed a method similar to the isolation of nuclei tagged in a specific cell type (INTACT) technique [Deal,R.B.

Chipping away at brain function: mining for insights with microarrays.

The impact of microarray studies on neurobiology has been limited because, with the exception of a few outstanding papers, most reports provide little more than lists of genes, often leaving the reader at a loss to understand which and how many of the identified transcripts will be true positives with significant biological impact. However, some recent papers have offered considerable biological insight by providing independent in vivo confirmation of the roles of candidate genes, offering a glimpse of the potential power of microarrays in neurobiological research.