@article {5423, title = {A GAL4-driver line resource for Drosophila neurobiology.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {991-1001}, abstract = {

We established a collection of 7,000 transgenic lines of Drosophila melanogaster. Expression of GAL4 in each line is controlled by a different, defined fragment of genomic DNA that serves as a transcriptional enhancer. We used confocal microscopy of dissected nervous systems to determine the expression patterns driven by each fragment in the adult brain and ventral nerve cord. We present image data on 6,650 lines. Using both manual and machine-assisted annotation, we describe the expression patterns in the most useful lines. We illustrate the utility of these data for identifying novel neuronal cell types, revealing brain asymmetry, and describing the nature and extent of neuronal shape stereotypy. The GAL4 lines allow expression of exogenous genes in distinct, small subsets of the adult nervous system. The set of DNA fragments, each driving a documented expression pattern, will facilitate the generation of additional constructs for manipulating neuronal function. synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For the overall strategy and methods used to produce the GAL4 lines:
Pfeiffer, B.D., Jenett, A., Hammonds, A.S., Ngo, T.T., Misra, S., Murphy, C., Scully, A., Carlson, J.W., Wan, K.H., Laverty, T.R., Mungall, C., Svirskas, R., Kadonaga, J.T., Doe, C.Q., Eisen, M.B., Celniker, S.E., Rubin, G.M. (2008). Tools for neuroanatomy and neurogenetics in Drosophila. Proc. Natl. Acad. Sci. USA 105, 9715-9720. http://www.pnas.org/content/105/28/9715.full.pdf+html synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in the embryo:
Manning, L., Purice, M.D., Roberts, J., Pollard, J.L., Bennett, A.L., Kroll, J.R., Dyukareva, A.V., Doan, P.N., Lupton, J.R., Strader, M.E., Tanner, S., Bauer, D., Wilbur, A., Tran, K.D., Laverty, T.R., Pearson, J.C., Crews, S.T., Rubin, G.M., and Doe, C.Q. (2012) Annotated embryonic CNS expression patterns of 5000 GMR GAL4 lines: a resource for manipulating gene expression and analyzing cis-regulatory motifs. Cell Reports (2012) Doi: 10.1016/j.celrep.2012.09.009 http://www.cell.com/cell-reports/fulltext/S2211-1247(12)00290-2 synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in imaginal discs:
Jory, A., Estella, C., Giorgianni, M.W., Slattery, M., Laverty, T.R., Rubin, G.M., and Mann, R.S. (2012) A survey of 6300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Reports (2012) Doi: 10.1016/j.celrep.2012.09.010 http://www.cell.com/cell-reports/fulltext/S2211-1247(12)00291-4 synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in the larval nervous system:
Li, H.-H., Kroll, J.R., Lennox, S., Ogundeyi, O., Jeter, J., Depasquale, G., and Truman, J.W. (2013) A GAL4 driver resource for developmental and behavioral studies on the larval CNS of Drosophila. Cell Reports (submitted).

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.011}, author = {Jenett, Arnim and Rubin, Gerald M and Ngo, Teri-T B and Shepherd, David and Murphy, Christine and Dionne, Heather and Pfeiffer, Barret D and Cavallaro, Amanda and Hall, Donald and Jeter, Jennifer and Iyer, Nirmala and Fetter, Dona and Hausenfluck, Joanna H and Peng, Hanchuan and Trautman, Eric T and Svirskas, Robert R and Myers, Eugene W and Iwinski, Zbigniew R and Aso, Yoshinori and Depasquale, Gina M and Enos, Adrianne and Hulamm, Phuson and Lam, Shing Chun Benny and Li, Hsing-Hsi and Laverty, Todd R and Long, Fuhui and Qu, Lei and Murphy, Sean D and Rokicki, Konrad and Safford, Todd and Shaw, Kshiti and Simpson, Julie H and Sowell, Allison and Tae, Susana and Yu, Yang and Zugates, Christopher T} } @article {6515, title = {A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {1002-13}, abstract = {

Here, we describe the embryonic central nervous system expression of 5,000 GAL4 lines made using molecularly defined cis-regulatory DNA inserted into a single attP genomic location. We document and annotate the patterns in early embryos when neurogenesis is at its peak, and in older embryos where there is maximal neuronal diversity and the first neural circuits are established. We note expression in other tissues, such as the lateral body wall (muscle, sensory neurons, and trachea) and viscera. Companion papers report on the adult brain and larval imaginal discs, and the integrated data sets\ are available online (http://www.janelia.org/gal4-gen1). This collection of embryonically expressed GAL4 lines will be valuable for determining neuronal morphology and function. The 1,862 lines expressed in small subsets of neurons (\<20/segment) will be especially valuable for characterizing\ interneuronal diversity and function, because although interneurons comprise the majority of all central nervous system neurons, their gene expression profile and function remain virtually unexplored.

}, keywords = {Animals, Central Nervous System, Databases, Drosophila, Drosophila Proteins, Embryo, Factual, Female, Gene Expression, Genes, Genetically Modified, Internet, Male, Nonmammalian, Regulatory Elements, Reporter, Transcription Factors, Transcriptional}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.009}, author = {Manning, Laurina and Heckscher, Ellie S and Purice, Maria D and Roberts, Jourdain and Bennett, Alysha L and Kroll, Jason R and Pollard, Jill L and Strader, Marie E and Lupton, Josh R and Dyukareva, Anna V and Doan, Phuong Nam and Bauer, David M and Wilbur, Allison N and Tanner, Stephanie and Kelly, Jimmy J and Lai, Sen-Lin and Tran, Khoa D and Kohwi, Minoree and Laverty, Todd R and Pearson, Joseph C and Crews, Stephen T and Rubin, Gerald M and Doe, Chris Q} } @article {6506, title = {A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {1014-24}, abstract = {

Over 6,000 fragments from the genome of Drosophila melanogaster were analyzed for their ability to drive expression of GAL4 reporter genes in the third-instar larval imaginal discs. About 1,200 reporter genes drove expression in the eye, antenna, leg, wing, haltere, or genital imaginal discs. The patterns ranged from large regions to individual cells. About 75\% of the active fragments drove expression in multiple discs; 20\% were expressed in ventral, but not dorsal, discs (legs, genital, and antenna), whereas \~{}23\% were expressed in dorsal but not ventral discs (wing, haltere, and eye). Several patterns, for example, within the leg chordotonal organ, appeared a surprisingly large\ number of times. Unbiased searches for DNA sequence motifs suggest candidate transcription factors that may regulate enhancers with shared activities. Together, these expression patterns provide a valuable resource to the community and offer a broad overview of how transcriptional regulatory information is distributed in the Drosophila genome.

}, keywords = {Animals, Arthropod Antennae, Blastodisc, Databases, Drosophila melanogaster, Drosophila Proteins, Eye, Factual, Genes, Genetically Modified, Genome, Imaginal Discs, Regulatory Elements, Reporter, Transcription Factors, Transcriptional, Wing}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.010}, author = {Jory, Aur{\'e}lie and Estella, Carlos and Giorgianni, Matt W and Slattery, Matthew and Laverty, Todd R and Rubin, Gerald M and Mann, Richard S} } @article {4278, title = {A Drosophila resource of transgenic RNAi lines for neurogenetics.}, journal = {Genetics}, volume = {182}, year = {2009}, month = {2009 Aug}, pages = {1089-100}, abstract = {

Conditional expression of hairpin constructs in Drosophila is a powerful method to disrupt the activity of single genes with a spatial and temporal resolution that is impossible, or exceedingly difficult, using classical genetic methods. We previously described a method (Ni et al. 2008) whereby RNAi constructs are targeted into the genome by the phiC31-mediated integration approach using Vermilion-AttB-Loxp-Intron-UAS-MCS (VALIUM), a vector that contains vermilion as a selectable marker, an attB sequence to allow for phiC31-targeted integration at genomic attP landing sites, two pentamers of UAS, the hsp70 core promoter, a multiple cloning site, and two introns. As the level of gene activity knockdown associated with transgenic RNAi depends on the level of expression of the hairpin constructs, we generated a number of derivatives of our initial vector, called the "VALIUM" series, to improve the efficiency of the method. Here, we report the results from the systematic analysis of these derivatives and characterize VALIUM10 as the most optimal vector of this series. A critical feature of VALIUM10 is the presence of gypsy insulator sequences that boost dramatically the level of knockdown. We document the efficacy of VALIUM as a vector to analyze the phenotype of genes expressed in the nervous system and have generated a library of 2282 constructs targeting 2043 genes that will be particularly useful for studies of the nervous system as they target, in particular, transcription factors, ion channels, and transporters.

}, keywords = {Animals, Carrier Proteins, Drosophila, Gene Knockdown Techniques, Ion Channels, Methods, Nervous System, RNA, RNA Interference, Small Interfering, Transcription Factors}, issn = {1943-2631}, doi = {10.1534/genetics.109.103630}, author = {Ni, Jian-Quan and Liu, Lu-Ping and Binari, Richard and Hardy, Robert and Shim, Hye-Seok and Cavallaro, Amanda and Booker, Matthew and Pfeiffer, Barret D and Markstein, Michele and Wang, Hui and Villalta, Christians and Laverty, Todd R and Perkins, Lizabeth A and Perrimon, Norbert} } @article {988, title = {Tools for neuroanatomy and neurogenetics in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Jul 15}, pages = {9715-20}, abstract = {

We demonstrate the feasibility of generating thousands of transgenic Drosophila melanogaster lines in which the expression of an exogenous gene is reproducibly directed to distinct small subsets of cells in the adult brain. We expect the expression patterns produced by the collection of 5,000 lines that we are currently generating to encompass all neurons in the brain in a variety of intersecting patterns. Overlapping 3-kb DNA fragments from the flanking noncoding and intronic regions of genes thought to have patterned expression in the adult brain were inserted into a defined genomic location by site-specific recombination. These fragments were then assayed for their ability to function as transcriptional enhancers in conjunction with a synthetic core promoter designed to work with a wide variety of enhancer types. An analysis of 44 fragments from four genes found that \>80\% drive expression patterns in the brain; the observed patterns were, on average, comprised of \<100 cells. Our results suggest that the D. melanogaster genome contains \>50,000 enhancers and that multiple enhancers drive distinct subsets of expression of a gene in each tissue and developmental stage. We expect that these lines will be valuable tools for neuroanatomy as well as for the elucidation of neuronal circuits and information flow in the fly brain.

}, keywords = {Animals, Biomedical Research, Brain, Developmental, Drosophila melanogaster, Enhancer Elements, Gene Expression Regulation, Genes, Genetic, Genetically Modified, Insect, Neurons, Neurosciences, Recombination}, issn = {1091-6490}, doi = {https://doi.org/10.1073/pnas.0803697105}, author = {Pfeiffer, Barret D and Jenett, Arnim and Hammonds, Ann S and Ngo, Teri-T B and Misra, Sima and Murphy, Christine and Scully, Audra and Carlson, Joseph W and Wan, Kenneth H and Laverty, Todd R and Mungall, Chris and Svirskas, Rob and Kadonaga, James T and Doe, Chris Q and Eisen, Michael B and Celniker, Susan E and Rubin, Gerald M} } @article {46640, title = {Rough eye is a gain-of-function allele of amos that disrupts regulation of the proneural gene atonal during Drosophila retinal differentiation.}, journal = {Genetics}, volume = {160}, year = {2002}, month = {2002 Feb}, pages = {623-35}, abstract = {

The regular organization of the ommatidial lattice in the Drosophila eye originates in the precise regulation of the proneural gene atonal (ato), which is responsible for the specification of the ommatidial founder cells R8. Here we show that Rough eye (Roi), a dominant mutation manifested by severe roughening of the adult eye surface, causes defects in ommatidial assembly and ommatidial spacing. The ommatidial spacing defect can be ascribed to the irregular distribution of R8 cells caused by a disruption of the patterning of ato expression. Disruptions in the recruitment of other photoreceptors and excess Hedgehog production in differentiating cells may further contribute to the defects in ommatidial assembly. Our molecular characterization of the Roi locus demonstrates that it is a gain-of-function mutation of the bHLH gene amos that results from a chromosomal inversion. We show that Roi can rescue the retinal developmental defect of ato1 mutants and speculate that amos substitutes for some of ato{\textquoteright}s function in the eye or activates a residual function of the ato1 allele.

}, keywords = {Alleles, Animals, Basic Helix-Loop-Helix Transcription Factors, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Epistasis, Genetic, Gene Expression Regulation, Developmental, Nerve Growth Factors, Nerve Tissue Proteins, Retina, Signal Transduction, Transgenes}, issn = {0016-6731}, author = {Chanut, Fran{\c c}oise and Woo, Katherine and Pereira, Shalini and Donohoe, Terrence J and Chang, Shang-Yu and Laverty, Todd R and Jarman, Andrew P and Heberlein, Ulrike} }