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Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here, we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases, we provide an extensive resource for further investigation of mouse neuronal cell types.

SummarySynaptic scaling is a form of homeostatic plasticity driven by transcription-dependent changes in AMPA-type glutamate receptor (AMPAR) trafficking. To uncover the pathways involved, we performed a cell-type-specific screen for transcripts persistently altered during scaling, which identified the μ subunit (μ3A) of the adaptor protein complex AP-3A. Synaptic scaling increased μ3A (but not other AP-3 subunits) in pyramidal neurons and redistributed dendritic μ3A and AMPAR to recycling endosomes (REs). Knockdown of μ3A prevented synaptic scaling and this redistribution, while overexpression (OE) of full-length μ3A or a truncated μ3A that cannot interact with the AP-3A complex was sufficient to drive AMPAR to REs. Finally, OE of μ3A acted synergistically with GRIP1 to recruit AMPAR to the dendritic membrane. These data suggest that excess μ3A acts independently of the AP-3A complex to reroute AMPAR to RE, generating a reservoir of receptors essential for the regulated recruitment to the synaptic membrane during scaling up.

The mammalian nervous system is constructed of many neuronal cell types, but the principles underlying this diversity are poorly understood. To begin to assess brain-wide transcriptional diversity, we sequenced the transcriptomes of the largest collection of genetically and/or anatomically identified neuronal classes from throughout the central nervous system. Using improved expression metrics that distinguish information content from signal-to-noise-ratio, we found that homeobox transcription factors contain the highest information about cell types and have the lowest noise. Non-transcription factors that contribute the most to neuronal diversity tend to be long, due to large introns, and are enriched in genes specifically involved in neuronal function. Genome accessibility measurements reveal that long genes have more candidate regulatory elements arrayed in more distinct patterns. These candidate regulatory elements frequently overlap interspersed repeats and the pattern of repeats is predictive of gene expression. Elongation of neuronal genes by insertions of mobile elements and the resulting new regulatory sites may be an evolutionary force enhancing nervous system complexity.

The broadly-distributed, non-topographic projections to and from the olfactory cortex may suggest a flat, non-hierarchical organization in odor information processing. Layer 2 principal neurons in the anterior piriform cortex (APC) can be divided into 2 subtypes: semilunar (SL) and superficial pyramidal (SP) cells. Although it is known that SL and SP cells receive differential inputs from the olfactory bulb (OB), little is known about their projections to other olfactory regions. Here, we examined axonal projections of SL and SP cells using a combination of mouse genetics and retrograde labeling. Retrograde tracing from the OB or posterior piriform cortex (PPC) showed that the APC projects to these brain regions mainly through layer 2b cells, and dual-labeling revealed many cells extending collaterals to both target regions. Furthermore, a transgenic mouse line specifically labeling SL cells showed that they send profuse axonal projections to olfactory cortical areas, but not to the OB. These findings support a model in which information flow from SL to SP cells and back to the OB is mediated by a hierarchical feedback circuit, whereas both SL and SP cells broadcast information to higher olfactory areas in a parallel manner.

The dopamine systems of the brain powerfully influence movement and motivation. We demonstrate that striatonigral fibers originating in striosomes form highly unusual bouquet-like arborizations that target bundles of ventrally extending dopamine-containing dendrites and clusters of their parent nigral cell bodies. Retrograde tracing showed that these clustered cell bodies in turn project to the striatum as part of the classic nigrostriatal pathway. Thus, these striosome–dendron formations, here termed “striosome–dendron bouquets,” likely represent subsystems with the nigro–striato–nigral loop that are affected in human disorders including Parkinson’s disease. Within the bouquets, expansion microscopy resolved many individual striosomal fibers tightly intertwined with the dopamine-containing dendrites and also with afferents labeled by glutamatergic, GABAergic, and cholinergic markers and markers for astrocytic cells and fibers and connexin 43 puncta. We suggest that the striosome–dendron bouquets form specialized integrative units within the dopamine-containing nigral system. Given evidence that striosomes receive input from cortical regions related to the control of mood and motivation and that they link functionally to reinforcement and decision-making, the striosome–dendron bouquets could be critical to dopamine-related function in health and disease.

There is a continuing need for driver strains to enable cell-type-specific manipulation in the nervous system. Each cell type expresses a unique set of genes, and recapitulating expression of marker genes by BAC transgenesis or knock-in has generated useful transgenic mouse lines. However, since genes are often expressed in many cell types, many of these lines have relatively broad expression patterns. We report an alternative transgenic approach capturing distal enhancers for more focused expression. We identified an enhancer trap probe often producing restricted reporter expression and developed efficient enhancer trap screening with the PiggyBac transposon. We established more than 200 lines and found many lines that label small subsets of neurons in brain substructures, including known and novel cell types. Images and other information about each line are available online (enhancertrap.bio.brandeis.edu). DOI: http://dx.doi.org/10.7554/eLife.13503.001, eLife digest Scientists can track and even alter the activity of different kinds of neurons, as well as the connections between neurons, by manipulating their genes. However, most genes are active in many different kinds of cells in many different places in the brain, making it difficult to track or target only a particular neuron or brain area. Enhancers are sections of DNA that can regulate the activity of nearby genes so that they are only active in very specific cell types, and an “enhancer trap” is a genetic approach that essentially hijacks enhancers to express artificial genes in those same cell types. The technique relies on inserting a genetic marker, which can be easily tracked, into random locations in the genome. If this marker then interacts with an enhancer, it is activated and the effect of the enhancer on gene expression can be assessed. This method has been used in fruit flies and fish to identify enhancers that specifically restrict gene expression to a small subset of cells. Now, Shima et al. show that enhancer traps can be used successfully in mammals too. The experiments produced over 200 different strains of mice, many with the fluorescent marker only in specific brain areas or in specific kinds of brain cells. Some of the types of brain cells uncovered by these experiments are new, and the labelling of specific brain cells and brain areas in different strains makes these mice a useful resource for future work. Furthermore, it will be relatively straightforward to produce many more strains of these mice, because it would simply involve crossbreeding mice. It is likely that some of these to-be-discovered strains will be useful tools for research as well. DOI: http://dx.doi.org/10.7554/eLife.13503.002

Acetoacetyl-CoA thiolase (AT) is an enzyme that catalyses the CoA-dependent thiolytic cleavage of acetoacetyl-CoA to yield 2 molecules of acetyl-CoA, or the reverse condensation reaction. A full-length cDNA clone pBSGT-3, which has homology to known thiolases, was isolated from Dictyostelium cDNA library. Expression of the protein encoded in pBSGT-3 in Escherichia coli, its thiolase enzyme activity, and the amino acid sequence homology search revealed that pBSGT-3 encodes an AT. The recombinant AT (r-thiolase) was expressed in an active form in an E. coli expression system, and purified to homogeneity by selective ammonium sulfate fractionation and two steps of column chromatography. The purified enzyme exhibited a specific activity of 4.70 mU/mg protein. Its N-terminal sequence was (NH2)-Arg-Met-Tyr-Thr-Thr-Ala-Lys-Asn-Leu-Glu-, which corresponds to the sequence from positions 15 to 24 of the amino acid sequence deduced from pBSGT-3 clone. The r-thiolase in the inclusion body expressed highly in E. coli was the precursor form, which is slightly larger than the purified r-thiolase. When incubated with the cell-free extract of Dictyostelium cells, the precursor was converted to the same size to the purified r-thiolase, suggesting that the presequence at the N-terminus is removed by a Dictyostelium processing peptidase.

Despite its comparatively simple trilaminar architecture, the primary olfactory (piriform) cortex of mammals is capable of performing sophisticated sensory processing, an ability that is thought to depend critically on its extensive associational (intracortical) excitatory circuits. Here, we used a novel transgenic mouse model and optogenetics to measure the connectivity of associational circuits that originate in semilunar (SL) cells in layer 2a of the anterior piriform cortex (aPC). We generated a mouse line (48L) in which channelrhodopsin-2 (ChR) could be selectively expressed in a subset of SL cells. Light-evoked excitatory postsynaptic currents (EPSCs) could be evoked in superficial pyramidal cells (17.4% of n = 86 neurons) and deep pyramidal cells (33.3%, n = 9) in the aPC, but never in ChR- SL cells (0%, n = 34). Thus, SL cells monosynaptically excite pyramidal cells, but not other SL cells. Light-evoked EPSCs were also selectively elicited in 3 classes of GABAergic interneurons in layer 3 of the aPC. Our results show that SL cells are specialized for providing feedforward excitation of specific classes of neurons in the aPC, confirming that SL cells comprise a functionally distinctive input layer.

Background: Cofilin, a key regulator of actin filament dynamics, is inactivated by phosphorylation at Ser-3 by LIM-kinases and is reactivated by dephosphorylation by a family of protein phosphatases, termed Slingshot (SSH). Results: We have identified two novel isoforms of SSHs, termed SSH-2L and SSH-3L and characterized them in comparison with SSH-1L that was previously reported. SSH-1L and SSH-2L, but not SSH-3L, tightly bound to and co-localized with actin filaments. When expressed in cultured cells, SSH-1L, SSH-2L and SSH-3L decreased the level of Ser-3-phosphorylated cofilin (P-cofilin) in cells and suppressed LIM-kinase-induced actin reorganization, although SSH-3L was less effective than SSH-1L and SSH-2L. In cell-free assays, SSH-1L and SSH-2L efficiently dephosphorylated P-cofilin, whereas SSH-3L did do so only weakly. Using deleted mutants of SSH-1L and SSH-2L, we found that the N-terminal and C-terminal extracatalytic regions are critical for cofilin-phosphatase and F-actin-binding activities, respectively. In situ hybridization analyses revealed characteristic patterns of expression of each of the mouse Ssh genes in both neuronal and non-neuronal tissues; in particular, expression of Ssh-3 in epithelial tissues is evident. Conclusion: SSH-1L, SSH-2L and SSH-3L have the potential to dephosphorylate P-cofilin, but subcellular distribution, F-actin-binding activity, specific phosphatase activity and expression patterns significantly differ, which suggests that they have related but distinct functions in various cellular and developmental events.

Drosophila Flamingo (Fmi) is an evolutionally conserved seven-pass transmembrane receptor of the cadherin superfamily. Fmi plays multiple roles in patterning neuronal processes and epithelial planar cell polarity. To explore the in vivo roles of Fmi homologs in mammals, we previously cloned one of the mouse homologs, mouse flamingo1/Celsr2. Here, we report the results of our study of its embryonic and postnatal expression patterns together with those of two other paralogs, Celsr1 and Celsr3. Celsr1-3 expression was initiated broadly in the nervous system at early developmental stages, and each paralog showed characteristic expression patterns in the developing CNS. These genes were also expressed in several other organs, including the cochlea, where hair cells develop planar polarity, the kidney, and the whisker. The Celsr2 protein was distributed at intercellular boundaries in the whisker and on processes of neuronal cells such as hippocampal pyramidal cells, Purkinje cells, and olfactory neurons. Celsr2 is mapped to a distal region of the mouse chromosome 3. We discussed possible functions of seven-pass transmembrane cadherins in mouse development.

Cerebellar granule cells constitute the majority of neurons in the brain and are the primary conveyors of sensory and motor-related mossy fiber information to Purkinje cells. The functional capability of the cerebellum hinges on whether individual granule cells receive mossy fiber inputs from multiple precerebellar nuclei or are instead unimodal; this distinction is unresolved. Using cell-type-specific projection mapping with synaptic resolution, we observed the convergence of separate sensory (upper body proprioceptive) and basilar pontine pathways onto individual granule cells and mapped this convergence across cerebellar cortex. These findings inform the long-standing debate about the multimodality of mammalian granule cells and substantiate their associative capacity predicted in the Marr-Albus theory of cerebellar function. We also provide evidence that the convergent basilar pontine pathways carry corollary discharges from upper body motor cortical areas. Such merging of related corollary and sensory streams is a critical component of circuit models of predictive motor control. DOI: http://dx.doi.org/10.7554/eLife.00400.001, eLife digest Learning a new motor skill, from riding a bicycle to eating with chopsticks, involves the cerebellum—a structure located at the base of the brain underneath the cerebral hemispheres. Although its name translates as ‘little brain' in Latin, the cerebellum contains more neurons than all other regions of the mammalian brain combined. Most cerebellar neurons are granule cells which, although numerous, are simple neurons with an average of only four excitatory inputs, from axons called mossy fibers. These inputs are diverse in nature, originating from virtually every sensory system and from command centers at multiple levels of the motor hierarchy. However, it is unclear whether individual granule cells receive inputs from only a single sensory source or can instead mix modalities. This distinction has important implications for the functional capabilities of the cerebellum. Now, Huang et al. have addressed this question by mapping, at extremely high resolution, the projections of two pathways onto individual granule cells—one carrying sensory feedback from the upper body (the proprioceptive stream), and another carrying motor-related information (the pontine stream). Using a combination of genetic and viral techniques to label the pathways, Huang and co-workers identified regions where the two types of fiber terminated in close proximity. They then showed that around 40% of proprioceptive granule cells formed junctions, or synapses, with two (or more) fibers carrying different types of input. These cells were not uniformly distributed throughout the cerebellum but tended to occur in ‘hotspots’. Lastly, Huang et al. examined the type of information conveyed by the sensory and motor-related input streams whenever they contacted a single granule cell. They confirmed that when the sensory input consisted of feedback from the upper body, the motor input consisted of copies of motor commands related to the same body region. Because it is thought that the cerebellum converts sensory information into representations of the body's movements, directing motor commands to these same circuits may allow the cerebellum to predict the consequences of a planned movement prior to, or without, the actual movement occurring. The work of Huang et al. provides evidence to support the previously controversial idea that granule cells in the mammalian cerebellum receive both sensory and motor-related inputs. The labeling technique that they used could also be deployed to study the inputs to the cerebellum in greater detail, which should yield new insights into the functioning of this part of the brain. DOI: http://dx.doi.org/10.7554/eLife.00400.002

Acetoacetyl-CoA thiolase (AT) is an enzyme that catalyses the CoA-dependent thiolytic cleavage of acetoacetyl-CoA to yield 2 molecules of acetyl-CoA, or the reverse condensation reaction. A full-length cDNA clone pBSGT-3, which has homology to known thiolases, was isolated from Dictyostelium cDNA library. Expression of the protein encoded in pBSGT-3 in Escherichia coli, its thiolase enzyme activity, and the amino acid sequence homology search revealed that pBSGT-3 encodes an AT. The recombinant AT (r-thiolase) was expressed in an active form in an E. coli expression system, and purified to homogeneity by selective ammonium sulfate fractionation and two steps of column chromatography. The purified enzyme exhibited a specific activity of 4.70 mU/mg protein. Its N-terminal sequence was (NH2)-Arg-Met-Tyr-Thr-Thr-Ala-Lys-Asn-Leu-Glu-, which corresponds to the sequence from positions 15 to 24 of the amino acid sequence deduced from pBSGT-3 clone. The r-thiolase in the inclusion body expressed highly in E. coli was the precursor form, which is slightly larger than the purified r-thiolase. When incubated with the cell-free extract of Dictyostelium cells, the precursor was converted to the same size to the purified r-thiolase, suggesting that the presequence at the N-terminus is removed by a Dictyostelium processing peptidase.

Actin-depolymerizing factor (ADF) and cofilin constitute a family of key regulators of actin filament dynamics. ADF/cofilin is inactivated by phosphorylation at Ser-3 by LIM-kinases and reactivated by dephosphorylation by Slingshot (SSH) family phosphatases. Defects in LIM kinases or ADF/cofilin have been implicated in morbidity in human or mice; however, the roles of mammalian SSH in vivo have not been addressed. In this study, we examined the endogenous expression of each mouse SSH member in various cell lines and tissues, and showed that SSH-3L protein was strongly expressed in epithelial cells. Our structure-function analysis of SSH-3L suggested the possibility that the C-tail unique to SSH-3L negatively regulates the catalytic activity of this phosphatase. Furthermore we made ssh-3 knockout mice to examine its potential in vivo roles. Unexpectedly, ssh-3 was not essential for viability, fertility, or development of epithelial tissues; and ssh-3 did not genetically modify the corneal disorder of the corn1/ADF/destrin mutant.

The growth of neurites (axon and dendrite) should be appropriately regulated by their interactions in the development of nervous systems where a myriad of neurons and their neurites are tightly packed. We show here that mammalian seven-pass transmembrane cadherins Celsr2 and Celsr3 are activated by their homophilic interactions and regulate neurite growth in an opposing manner. Both gene-silencing and coculture assay with rat neuron cultures showed that Celsr2 enhanced neurite growth, whereas Celsr3 suppressed it, and that their opposite functions were most likely the result of a difference of a single amino acid residue in the transmembrane domain. Together with calcium imaging and pharmacological analyses, our results suggest that Celsr2 and Celsr3 fulfill their functions through second messengers, and that differences in the activities of the homologs results in opposite effects in neurite growth regulation.

Drosophila Flamingo is a 7-pass transmembrane cadherin that is necessary for dendritic patterning and axon guidance. How it works at the molecular level and whether homologs of Flamingo play similar roles in mammalian neurons or not have been unanswered questions. Here, we performed loss-of-function analysis using an RNAi system and organotypic brain slice cultures to address the role of a mammalian Flamingo homolog, Celsr2. Knocking down Celsr2 resulted in prominent simplification of dendritic arbors of cortical pyramidal neurons and Purkinje neurons, and this phenotype seemed to be due to branch retraction. Cadherin domain-mediated homophilic interaction appears to be required for the maintenance of dendritic branches. Furthermore, expression of various Celsr2 forms elicited distinct responses that were dependent on an extracellular subregion outside the cadherin domains and on a portion within the carboxyl intracellular tail. Based on these findings, we discuss how Celsr2 may regulate dendritic maintenance and growth.

Cofilin, a key regulator of actin filament dynamics, is inactivated by phosphorylation at Ser-3 by LIM-kinases and is reactivated by dephosphorylation by a family of protein phosphatases, termed Slingshot (SSH).We have identified two novel isoforms of SSHs, termed SSH-2L and SSH-3L and characterized them in comparison with SSH-1L that was previously reported. SSH-1L and SSH-2L, but not SSH-3L, tightly bound to and co-localized with actin filaments. When expressed in cultured cells, SSH-1L, SSH-2L and SSH-3L decreased the level of Ser-3-phosphorylated cofilin (P-cofilin) in cells and suppressed LIM-kinase-induced actin reorganization, although SSH-3L was less effective than SSH-1L and SSH-2L. In cell-free assays, SSH-1L and SSH-2L efficiently dephosphorylated P-cofilin, whereas SSH-3L did do so only weakly. Using deleted mutants of SSH-1L and SSH-2L, we found that the N-terminal and C-terminal extracatalytic regions are critical for cofilin-phosphatase and F-actin-binding activities, respectively. In situ hybridization analyses revealed characteristic patterns of expression of each of the mouse Ssh genes in both neuronal and non-neuronal tissues; in particular, expression of Ssh-3 in epithelial tissues is evident.SSH-1L, SSH-2L and SSH-3L have the potential to dephosphorylate P-cofilin, but subcellular distribution, F-actin-binding activity, specific phosphatase activity and expression patterns significantly differ, which suggests that they have related but distinct functions in various cellular and developmental events.

We identified a seven-pass transmembrane receptor of the cadherin superfamily, designated Flamingo (Fmi), localized at cell–cell boundaries in the Drosophila wing. In the absence of Fmi, planar polarity was distorted. Before morphological polarization of wing cells along the proximal-distal (P-D) axis, Fmi was redistributed predominantly to proximal and distal cell edges. This biased localization of Fmi appears to be driven by an imbalance of the activity of Frizzled (Fz) across the proximal/distal cell boundary. These results, together with phenotypes caused by ectopic expression of fz and fmi, suggest that cells acquire the P-D polarity by way of the Fz-dependent boundary localization of Fmi.

SummaryA key obstacle to understanding neural circuits in the cerebral cortex is that of unraveling the diversity of GABAergic interneurons. This diversity poses general questions for neural circuit analysis: how are these interneuron cell types generated and assembled into stereotyped local circuits and how do they differentially contribute to circuit operations that underlie cortical functions ranging from perception to cognition? Using genetic engineering in mice, we have generated and characterized approximately 20 Cre and inducible CreER knockin driver lines that reliably target major classes and lineages of GABAergic neurons. More select populations are captured by intersection of Cre and Flp drivers. Genetic targeting allows reliable identification, monitoring, and manipulation of cortical GABAergic neurons, thereby enabling a systematic and comprehensive analysis from cell fate specification, migration, and connectivity, to their functions in network dynamics and behavior. As such, this approach will accelerate the study of GABAergic circuits throughout the mammalian brain.