Browsing by Author "Barish, Scott"
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Item Open Access A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity.(PLoS Genet, 2016-01) Li, Qingyun; Barish, Scott; Okuwa, Sumie; Maciejewski, Abigail; Brandt, Alicia T; Reinhold, Dominik; Jones, Corbin D; Volkan, Pelin CayirliogluSensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, the olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1-4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), increases ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2 (Bar), Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitutes a transcription factor (TF) network that patterns the developing olfactory tissue. This network was previously shown to pattern the segmentation of the leg, which suggests that this network is functionally conserved. In antennal imaginal discs, precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines each unique SOP fate. Our results highlight the importance of the early prepatterning gene regulatory network as a modulator of SOP and terminally differentiated ORN diversity. Finally, our model illustrates how conserved developmental strategies are used to generate neuronal diversity.Item Open Access Establishing Neuronal Diversity: Regulation of olfactory receptor neuron specification and axon guidance in Drosophila(2017) Barish, ScottThe human brain contains over 80 billion neurons that make approximately 100 trillion specific connections. Each neuron must acquire a specific identity that includes its, gene expression, morphology, connectivity, and location. The basic logic and mechanisms that are used to coordinate this process on the immense scale of the brain remain largely unknown. We use the Drosophila olfactory system as model to understand nervous system development because of the powerful genetic tools and the workable level of neuronal diversity, which contains 50 classes of olfactory receptor neurons (ORNs). Each class of neurons is defined by the exclusive expression of typically a single olfactory receptor and connect to 50 class-specific glomeruli in the antennal lobe of the brain. Here we demonstrate that a cross regulatory network of transcription factors patterns the antennal disc, which contains ORN precursors and will develop into the antenna. These transcription factors create seven rings that are each labeled by a unique combination of genes, which generate distinct sets of ORN fates. Manipulation of this network changes the ORN fates that are produced in the adult, thereby demonstrating its necessity for generating neuronal diversity. We next show that the DIP/Dpr family of proteins, which are members of the Ig superfamily of genes and heterophilically interact, is required for axon sorting among classes of ORNs to create 50 class specific glomeruli. The members of this family are expressed in a combinatorial code in ORNs at times that correlate to glomerular formation. Computational analysis of DIP/Dpr expression patterns groups ORN classes into clusters that mimics their relative glomerular positioning in the antennal lobe. Class-specific or combinatorial knock down of DIP and dpr genes causes localized axon sorting defects where effected class invade neighboring glomeruli based upon the similarity of the DIP/Dpr expression codes. Our results highlight two functionally conserved strategies for generating and wiring a diverse neural circuit: prepatterning of precursors through combinatorial transcription factor expression, and the generation of differential adhesion force between classes of axons through combinatorial interactions of cell surface molecules. Not only are these strategies conserved in mammals, many of the genes that govern these processes are conserved as well, with genes like Bar, ap, and dac all having mammalian orthologues, and DIPs and Dprs sharing homology with Kirrel proteins. These studies have advanced our knowledge of the underlying logic that governs how a diverse nervous system is generated and coordinately wired.
Item Open Access Examination of Endogenous Rotund Expression and Function in Developing Drosophila Olfactory System Using CRISPR-Cas9-Mediated Protein Tagging.(G3 (Bethesda), 2015-10-23) Li, Qingyun; Barish, Scott; Okuwa, Sumie; Volkan, Pelin CThe zinc-finger protein Rotund (Rn) plays a critical role in controlling the development of the fly olfactory system. However, little is known about its molecular function in vivo. Here, we added protein tags to the rn locus using CRISPR-Cas9 technology in Drosophila to investigate its subcellular localization and the genes that it regulates . We previously used a reporter construct to show that rn is expressed in a subset of olfactory receptor neuron (ORN) precursors and it is required for the diversification of ORN fates. Here, we show that tagged endogenous Rn protein is functional based on the analysis of ORN phenotypes. Using this method, we also mapped the expression pattern of the endogenous isoform-specific tags in vivo with increased precision. Comparison of the Rn expression pattern from this study with previously published results using GAL4 reporters showed that Rn is mainly present in early steps in antennal disc patterning, but not in pupal stages when ORNs are born. Finally, using chromatin immunoprecipitation, we showed a direct binding of Rotund to a previously identified regulatory element upstream of the bric-a-brac gene locus in the developing antennal disc.Item Open Access The microRNA processor DROSHA is a candidate gene for a severe progressive neurological disorder.(Human molecular genetics, 2022-04-11) Barish, Scott; Senturk, Mumine; Schoch, Kelly; Minogue, Amanda L; Lopergolo, Diego; Fallerini, Chiara; Harland, Jake; Seemann, Jacob H; Stong, Nicholas; Kranz, Peter G; Kansagra, Sujay; Mikati, Mohamad A; Jasien, Joan; El-Dairi, Mays; Galluzzi, Paolo; Undiagnosed Diseases Network; Ariani, Francesca; Renieri, Alessandra; Mari, Francesca; Wangler, Michael F; Arur, Swathi; Jiang, Yong-Hui; Yamamoto, Shinya; Shashi, Vandana; Bellen, Hugo JDROSHA encodes a ribonuclease that is a subunit of the Microprocessor complex and is involved in the first step of microRNA (miRNA) biogenesis. To date, DROSHA has not yet been associated with a Mendelian disease. Here we describe two individuals with profound intellectual disability, epilepsy, white matter atrophy, microcephaly, and dysmorphic features, who carry damaging de novo heterozygous variants in DROSHA. DROSHA is constrained for missense variants and moderately intolerant to loss of function (o/e = 0.24). The loss of the fruit fly ortholog drosha causes developmental arrest and death in third instar larvae, a severe reduction in brain size, and loss of imaginal discs in the larva. Loss of drosha in eye clones causes small and rough eyes in adult flies. One of the identified DROSHA variants (p.Asp1219Gly) behaves as a strong loss-of-function allele in flies, while another variant (p.Arg1342Trp) is less damaging in our assays. In worms, a knock-in that mimics the p.Asp1219Gly variant at a worm equivalent residue causes loss of miRNA expression and heterochronicity, a phenotype characteristic of the loss of miRNA. Together, our data show that the DROSHA variants found in the individuals presented here are damaging based on functional studies in model organisms and likely underlie the severe phenotype involving the nervous system.