Vesicle localization

Abstract: Genome-wide experiments routinely generate large amounts of data that can be hard to interpret biologically. A common approach to interpreting these results is to employ enrichment analyses of controlled languages, known as ontologies, that describe various biological parameters such as gene molecular or biological function. In C. elegans, three distinct ontologies, the Gene Ontology (GO), Anatomy Ontology (AO), and the Worm Phenotype Ontology (WPO) are used to annotate gene function, expression and phenotype, respectively (Ashburner et al. 2000; Lee and Sternberg, 2003; Schindelman et al. 2011). Previously, we developed software to test datasets for enrichment of anatomical terms, called the Tissue Enrichment Analysis (TEA) tool (Angeles-Albores and Sternberg, 2016). Using the same hypergeometric statistical method, we extend enrichment testing to include WPO and GO, offering a unified approach to enrichment testing in C. elegans. The WormBase Enrichment Suite can be accessed via a user-friendly interface at http://www.wormbase.org/tools/enrichment/tea/tea.cgi. To validate the tools, we analyzed a previously published extracellular vesicle (EV)-releasing neuron (EVN) signature gene set derived from dissociated ciliated EV neurons (Wang et al. 2015) using WormBase Enrichment Suite based on the WS262 WormBase release. TEA correctly identified the CEM, hook sensillum and IL2 neuron as enriched tissues. The top phenotype associated with the EVN signature was chemosensory behavior. Gene Ontology enrichment analysis showed that cell projection and cell body were the most enriched cellular components in this gene set, followed by the biological processes neuropeptide signaling pathway and vesicle localization further down. The tutorial script used to generate the figure above can be viewed at: https://github.com/dangeles/TissueEnrichmentAnalysis/blob/master/tutorial/Tutorial.ipynb The addition of Gene Enrichment Analysis (GEA) and Phenotype Enrichment Analysis (PEA) to WormBase marks an important step towards a unified set of analyses that can help researchers to understand genomic datasets. These enrichment analyses will allow the community to fully benefit from the data curation ongoing at WormBase.

Abstract: Presynaptic compartments are formed through the recruitment of preassembled clusters of proteins to points of cell—cell contact, however, the molecular mechanism(s) underlying this process remains unclear. We demonstrate that clusters of polymerized actin can recruit and maintain synaptic vesicles to discrete sites along the axon, and that cadherin/β-catenin/scribble/β-pix complexes play an important role in this event. Previous work has demonstrated that β-catenin and scribble are important for the clustering of vesicles at synapses. We demonstrate that β-pix, a Rac/Cdc42 guanine nucleotide exchange factor (GEF), forms a complex with cadherin, β-catenin, and scribble at synapses and enhances localized actin polymerization in rat hippocampal neurons. In cells expressing β-pix siRNA or dominant-negative β-pix that lacks its GEF activity, actin polymerization at synapses is dramatically reduced, and synaptic vesicle localization is disrupted. This β-pix phenotype can be rescued by cortactin overexpression, suggesting that β-pix-mediated actin polymerization at synapses regulates vesicle localization.