title: A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy Studies.
abstract: Transgenic methods enable the selective manipulation of neurons for functional mapping of neuronal circuits. Using confocal microscopy, we have imaged the cellular-level expression of 109 transgenic lines in live 6 day post fertilization larvae, including 80 Gal4 enhancer trap lines, 9 Cre enhancer trap lines and 20 transgenic lines that express fluorescent proteins in defined gene-specific patterns. Image stacks were acquired at single micron resolution, together with a broadly expressed neural marker, which we used to align enhancer trap reporter patterns into a common 3-dimensional reference space. To facilitate use of this resource, we have written software that enables searching for transgenic lines that label cells within a selectable 3-dimensional region of interest (ROI) or neuroanatomical area. This software also enables the intersectional expression of transgenes to be predicted, a feature which we validated by detecting cells with co-expression of Cre and Gal4. Many of the imaged enhancer trap lines show intrinsic brain-specific expression. However, to increase the utility of lines that also drive expression in non-neuronal tissue we have designed a novel UAS reporter, that suppresses expression in heart, muscle, and skin through the incorporation of microRNA binding sites in a synthetic 3' untranslated region. Finally, we mapped the site of transgene integration, thus providing molecular identification of the expression pattern for most lines. Cumulatively, this library of enhancer trap lines provides genetic access to 70% of the larval brain and is therefore a powerful and broadly accessible tool for the dissection of neural circuits in larval zebrafish.
authors.affiliation: Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health Bethesda, MD, USA ; Neuroscience and Cognitive Science Program, University of Maryland College Park, MD, USA.
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Marquart
authors.affiliation: Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health Bethesda, MD, USA.
authors.forename: Kathryn M
authors.initials: KM
authors.lastname: Tabor
authors.affiliation: Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health Bethesda, MD, USA.
authors.forename: Mary
authors.initials: M
authors.lastname: Brown
authors.affiliation: Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health Bethesda, MD, USA.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Strykowski
authors.affiliation: Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health Bethesda, MD, USA.
authors.forename: Gaurav K
authors.initials: GK
authors.lastname: Varshney
authors.affiliation: Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health Bethesda, MD, USA.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: LaFave
authors.affiliation: Division of Biology, Kansas State University Manhattan, KS, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Mueller
authors.affiliation: Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health Bethesda, MD, USA.
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Burgess
authors.affiliation: National Institutes of Natural Sciences, Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences Aichi, Japan.
authors.forename: Shin-Ichi
authors.initials: S
authors.lastname: Higashijima
authors.affiliation: Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health Bethesda, MD, USA ; Neuroscience and Cognitive Science Program, University of Maryland College Park, MD, USA.
authors.forename: Harold A
authors.initials: HA
authors.lastname: Burgess
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified / Q000033:anatomy & histology / Q000254:growth & development / Q000378:metabolism; D001921:Brain / Q000166:cytology / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D016208:Databases, Factual; D015870:Gene Expression; D021621:Imaging, Three-Dimensional / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D018613:Microscopy, Confocal / Q000379:methods; D009132:Muscles / Q000166:cytology / Q000378:metabolism; D009206:Myocardium / Q000166:cytology / Q000378:metabolism; D012867:Skin / Q000166:cytology / Q000378:metabolism; D012984:Software; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D015027:Zebrafish / Q000033:anatomy & histology* / Q000254:growth & development / Q000378:metabolism*; D029961:Zebrafish Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; C542436:Gal4 protein, zebrafish; D035683:MicroRNAs; D014157:Transcription Factors; D029961:Zebrafish Proteins
keywords: 3D registration; Cre; Gal4; microRNA; transgenic; zebrafish