Genome-wide identification of neuronal activity-regulated genes in Drosophila

Activity-regulated genes (ARGs) are important for neuronal functions like long-term memory and are well-characterized in mammals but poorly studied in other model organisms like Drosophila. Here we stimulated fly neurons with different paradigms and identified ARGs using high-throughput sequencing from brains as well as from sorted neurons: they included a narrow set of circadian neurons as well as dopaminergic neurons. Surprisingly, many ARGs are specific to the stimulation paradigm and very specific to neuron type. In addition and unlike mammalian immediate early genes (IEGs), fly ARGs do not have short gene lengths and are less enriched for transcription factor function. Chromatin assays using ATAC-sequencing show that the transcription start sites (TSS) of ARGs do not change with neural firing but are already accessible prior to stimulation. Lastly based on binding site enrichment in ARGs, we identified transcription factor mediators of firing and created neuronal activity reporters. DOI: http://dx.doi.org/10.7554/eLife.19942.001

[1]  M. Rosbash,et al.  Circadian Neuron Feedback Controls the Drosophila Sleep-Activity Profile , 2016, Nature.

[2]  T. Holy,et al.  Synchronous Drosophila circadian pacemakers display nonsynchronous Ca2+ rhythms in vivo , 2016, Science.

[3]  Alan R. Mardinly,et al.  Sensory experience regulates cortical inhibition by inducing IGF-1 in VIP neurons , 2016, Nature.

[4]  Rui F. Oliveira,et al.  Brain Transcriptomic Response to Social Eavesdropping in Zebrafish (Danio rerio) , 2015, PloS one.

[5]  Leslie C Griffith,et al.  A single pair of neurons links sleep to memory consolidation in Drosophila melanogaster , 2015, eLife.

[6]  G. Nagel,et al.  Channelrhodopsin-2–XXL, a powerful optogenetic tool for low-light applications , 2014, Proceedings of the National Academy of Sciences.

[7]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[8]  M. Rosbash,et al.  PDF neuron firing phase-shifts key circadian activity neurons in Drosophila , 2014, eLife.

[9]  Alan R. Mardinly,et al.  Npas4 Regulates Excitatory-Inhibitory Balance within Neural Circuits through Cell-Type-Specific Gene Programs , 2014, Cell.

[10]  Stefan R. Pulver,et al.  Independent Optical Excitation of Distinct Neural Populations , 2014, Nature Methods.

[11]  D. Whitmore,et al.  Circadian Rhythmicity and Light Sensitivity of the Zebrafish Brain , 2014, PloS one.

[12]  M. Rosbash,et al.  CLOCK:BMAL1 is a pioneer-like transcription factor , 2014, Genes & development.

[13]  Mark D. Robinson,et al.  Robustly detecting differential expression in RNA sequencing data using observation weights , 2013, Nucleic acids research.

[14]  M. Greenberg,et al.  The activity-dependent transcription factor NPAS4 regulates domain-specific inhibition , 2013, Nature.

[15]  Makoto Sato,et al.  Visualization of Neural Activity in Insect Brains Using a Conserved Immediate Early Gene, Hr38 , 2013, Current Biology.

[16]  M. Rosbash,et al.  Short Neuropeptide F Is a Sleep-Promoting Inhibitory Modulator , 2013, Neuron.

[17]  V. Pieribone,et al.  Genetically Targeted Optical Electrophysiology in Intact Neural Circuits , 2013, Cell.

[18]  G. Robinson,et al.  Activity-dependent gene expression in honey bee mushroom bodies in response to orientation flight , 2013, Journal of Experimental Biology.

[19]  M. Rosbash,et al.  Nascent-Seq analysis of Drosophila cycling gene expression , 2013, Proceedings of the National Academy of Sciences.

[20]  Kenji F. Tanaka,et al.  Identification of Optogenetically Activated Striatal Medium Spiny Neurons by Npas4 Expression , 2012, PloS one.

[21]  Jerry C. P. Yin,et al.  In Vivo Circadian Oscillation of dCREB2 and NF-κB Activity in the Drosophila Nervous System , 2012, PloS one.

[22]  Kei Ito,et al.  Identification of a dopamine pathway that regulates sleep and arousal in Drosophila , 2012, Nature Neuroscience.

[23]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[24]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[25]  Davis J. McCarthy,et al.  Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.

[26]  Ananda L Roy,et al.  Regulation of primary response genes. , 2011, Molecular cell.

[27]  M. Greenberg,et al.  Neuronal activity-regulated gene transcription in synapse development and cognitive function. , 2011, Cold Spring Harbor perspectives in biology.

[28]  Nico Stuurman,et al.  Computer Control of Microscopes Using µManager , 2010, Current protocols in molecular biology.

[29]  Ravi Allada,et al.  Surprising gene expression patterns within and between PDF-containing circadian neurons in Drosophila , 2010, Proceedings of the National Academy of Sciences.

[30]  G. Kreiman,et al.  Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.

[31]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[32]  M. Ardehali,et al.  Tracking rates of transcription and splicing in vivo , 2009, Nature Structural &Molecular Biology.

[33]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[34]  Israel Steinfeld,et al.  BMC Bioinformatics BioMed Central , 2008 .

[35]  M. Greenberg,et al.  A Biological Function for the Neuronal Activity-Dependent Component of Bdnf Transcription in the Development of Cortical Inhibition , 2008, Neuron.

[36]  Athar N. Malik,et al.  Activity-dependent regulation of inhibitory synapse development by Npas4 , 2008, Nature.

[37]  J. Lis,et al.  Rapid, Transcription-Independent Loss of Nucleosomes over a Large Chromatin Domain at Hsp70 Loci , 2008, Cell.

[38]  Mark D. Robinson,et al.  Moderated statistical tests for assessing differences in tag abundance , 2007, Bioinform..

[39]  S. Kasif,et al.  Immediate-Early and Delayed Primary Response Genes Are Distinct in Function and Genomic Architecture* , 2007, Journal of Biological Chemistry.

[40]  M. Robinson,et al.  Small-sample estimation of negative binomial dispersion, with applications to SAGE data. , 2007, Biostatistics.

[41]  T. Kubo,et al.  Increased Neural Activity of a Mushroom Body Neuron Subtype in the Brains of Forager Honeybees , 2007, PloS one.

[42]  Zohar Yakhini,et al.  Discovering Motifs in Ranked Lists of DNA Sequences , 2007, PLoS Comput. Biol..

[43]  J. Littleton,et al.  Genome-Wide Transcriptional Changes Associated with Enhanced Activity in the Drosophila Nervous System , 2005, Neuron.

[44]  J. Keifer,et al.  Expression of the immediate-early gene-encoded protein Egr-1 (zif268) during in vitro classical conditioning. , 2005, Learning & memory.

[45]  R. Fernald,et al.  Evolutionary conservation of the egr‐1 immediate‐early gene response in a teleost , 2005, The Journal of comparative neurology.

[46]  José Agosto,et al.  Coupled oscillators control morning and evening locomotor behaviour of Drosophila , 2004, Nature.

[47]  E. Kandel The Molecular Biology of Memory Storage: A Dialog Between Genes and Synapses , 2004, Bioscience reports.

[48]  Sara Salinas,et al.  Immediate-early gene induction by the stresses anisomycin and arsenite in human osteosarcoma cells involves MAPK cascade signaling to Elk-1, CREB and SRF , 2003, Oncogene.

[49]  A. Wong,et al.  Two-Photon Calcium Imaging Reveals an Odor-Evoked Map of Activity in the Fly Brain , 2003, Cell.

[50]  E. Kandel The molecular biology of memory storage: a dialog between genes and synapses. , 2001, Bioscience reports.

[51]  Eric J. Nestler,et al.  Molecular basis of long-term plasticity underlying addiction , 2001, Nature Reviews Neuroscience.

[52]  C. Shatz,et al.  Functional requirement for class I MHC in CNS development and plasticity. , 2000, Science.

[53]  N. Spitzer,et al.  Coding of neuronal differentiation by calcium transients , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[54]  Carl Wu Chromatin Remodeling and the Control of Gene Expression* , 1997, The Journal of Biological Chemistry.

[55]  R. Douglas Fields,et al.  Action Potential-Dependent Regulation of Gene Expression: Temporal Specificity in Ca2+, cAMP-Responsive Element Binding Proteins, and Mitogen-Activated Protein Kinase Signaling , 1997, The Journal of Neuroscience.

[56]  C. Helfrich-Förster,et al.  Development of pigment‐dispersing hormone‐immunoreactive neurons in the nervous system of Drosophila melanogaster , 1997, The Journal of comparative neurology.

[57]  Jeffrey C. Hall,et al.  Novel Features of Drosophila period Transcription Revealed by Real-Time Luciferase Reporting , 1996, Neuron.

[58]  V. Budnik,et al.  Genetic dissection of dopamine and serotonin synthesis in the nervous system of Drosophila melanogaster. , 1987, Journal of neurogenetics.

[59]  M. Greenberg,et al.  Stimulation of neuronal acetylcholine receptors induces rapid gene transcription. , 1986, Science.

[60]  Abigail Zadina,et al.  RNA-seq profiling of small numbers of Drosophila neurons. , 2015, Methods in enzymology.

[61]  S. Nelson,et al.  Dissecting differential gene expression within the circadian neuronal circuit of Drosophila , 2010, Nature Neuroscience.

[62]  E. Nestler,et al.  Molecular basis of long-term plasticity underlying addiction , 2001, Nature Reviews Neuroscience.

[63]  H. Herschman Primary response genes induced by growth factors and tumor promoters. , 1991, Annual review of biochemistry.

[64]  B. Rollins,et al.  Platelet-derived growth factor generates at least two distinct intracellular signals that modulate gene expression. , 1988, Cold Spring Harbor symposia on quantitative biology.