Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stability

The numerous neurons and glia that form the brain originate from tightly controlled growth and division of neural stem cells, regulated systemically by known extrinsic signals. However, the intrinsic mechanisms that control the characteristic proliferation rates of individual neural stem cells are unknown. Here, we show that the size and division rates of Drosophila neural stem cells (neuroblasts) are controlled by the highly conserved RNA binding protein Imp (IGF2BP), via one of its top binding targets in the brain, myc mRNA. We show that Imp stabilises myc mRNA leading to increased Myc protein levels, larger neuroblasts, and faster division rates. Declining Imp levels throughout development limit myc mRNA stability to restrain neuroblast growth and division, while heterogeneous Imp expression correlates with myc mRNA stability between individual neuroblasts in the brain. We propose that Imp-dependent regulation of myc mRNA stability fine-tunes individual neural stem cell proliferation rates.

[1]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[2]  E. Wahle,et al.  Control of c-myc mRNA stability by IGF2BP1-associated cytoplasmic RNPs. , 2008, RNA.

[3]  D. Prober,et al.  Drosophila myc Regulates Cellular Growth during Development , 1999, Cell.

[4]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[5]  Juergen A. Knoblich,et al.  Long-Term Live Cell Imaging and Automated 4D Analysis of Drosophila Neuroblast Lineages , 2013, PloS one.

[6]  B. Edgar,et al.  The Transcriptional Repressor dMnt Is a Regulator of Growth in Drosophila melanogaster , 2005, Molecular and Cellular Biology.

[7]  P. Gallant.  Myc function in Drosophila. , 2013, Cold Spring Harbor perspectives in medicine.

[8]  C. Desplan,et al.  Temporal patterning of Drosophila medulla neuroblasts controls neural fates , 2013, Nature.

[9]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[10]  C. Doe,et al.  Steroid hormone induction of temporal gene expression in Drosophila brain neuroblasts generates 2 neuronal and glial diversity 3 4 5 6 Summary : Hormone induction of temporal gene expression in neural progenitors 7 8 9 10 11 , 2017 .

[11]  R. Delanoue,et al.  The steroid hormone ecdysone controls systemic growth by repressing dMyc function in Drosophila fat cells. , 2010, Developmental cell.

[12]  B. Edgar,et al.  Myc-dependent regulation of ribosomal RNA synthesis during Drosophila development , 2005, Nature Cell Biology.

[13]  C. Doe,et al.  Steroid hormone induction of temporal gene expression in Drosophila brain neuroblasts generates neuronal and glial diversity , 2017, bioRxiv.

[14]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[15]  D. Levens.  You Don't Muck with MYC. , 2010, Genes & cancer.

[16]  Ilan Davis,et al.  Drosophila Syncrip modulates the expression of mRNAs encoding key synaptic proteins required for morphology at the neuromuscular junction , 2014, RNA.

[17]  S. Bowman,et al.  The tumor suppressors Brat and Numb regulate transit-amplifying neuroblast lineages in Drosophila. , 2008, Developmental cell.

[18]  P. Macdonald,et al.  Imp Associates with Squid and Hrp48 and Contributes to Localized Expression of gurken in the Oocyte , 2006, Molecular and Cellular Biology.

[19]  A. Teleman,et al.  Nutritional control of protein biosynthetic capacity by insulin via Myc in Drosophila. , 2008, Cell metabolism.

[20]  E. Lanet,et al.  Two distinct mechanisms silence chinmo in Drosophila neuroblasts and neuroepithelial cells to limit their self-renewal , 2017, Development.

[21]  Arnold Kriegstein,et al.  The glial nature of embryonic and adult neural stem cells. , 2009, Annual review of neuroscience.

[22]  A C C Gibbs,et al.  Data Analysis , 2009, Encyclopedia of Database Systems.

[23]  R. Sears,et al.  MYC degradation. , 2014, Cold Spring Harbor perspectives in medicine.

[24]  Volker Hartenstein,et al.  Neural Lineages of the Drosophila Brain: A Three-Dimensional Digital Atlas of the Pattern of Lineage Location and Projection at the Late Larval Stage , 2006, The Journal of Neuroscience.

[25]  Andres Ramos,et al.  A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets , 2018, Nature Communications.

[26]  Mirana Ramialison,et al.  Imp Promotes Axonal Remodeling by Regulating profilin mRNA during Brain Development , 2014, Current Biology.

[27]  H. Reichert,et al.  The asymmetrically segregating lncRNA cherub is required for transforming stem cells into malignant cells , 2018, eLife.

[28]  K. Mechtler,et al.  Asymmetric Segregation of the Tumor Suppressor Brat Regulates Self-Renewal in Drosophila Neural Stem Cells , 2006, Cell.

[29]  Philippe Andrey,et al.  MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ , 2016, Bioinform..

[30]  Thomas R. Burkard,et al.  Ecdysone and Mediator Change Energy Metabolism to Terminate Proliferation in Drosophila Neural Stem Cells , 2014, Cell.

[31]  D. St Johnston,et al.  A repeated IMP-binding motif controls oskar mRNA translation and anchoring independently of Drosophila melanogaster IMP , 2006, The Journal of cell biology.

[32]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[33]  A. Brand,et al.  Nutrition-Responsive Glia Control Exit of Neural Stem Cells from Quiescence , 2010, Cell.

[34]  N. Sokol,et al.  Neural stem cell-encoded temporal patterning delineates an early window of malignant susceptibility in Drosophila , 2016, eLife.

[35]  Stephen Dalton,et al.  The cell cycle and Myc intersect with mechanisms that regulate pluripotency and reprogramming. , 2009, Cell stem cell.

[36]  H. Reichert,et al.  Amplification of neural stem cell proliferation by intermediate progenitor cells in Drosophila brain development , 2008, Neural Development.

[37]  Arturo Alvarez-Buylla,et al.  Mosaic Organization of Neural Stem Cells in the Adult Brain , 2007, Science.

[38]  Hao Zhu,et al.  A network of heterochronic genes including Imp1 regulates temporal changes in stem cell properties , 2013, eLife.

[39]  Ilan Davis,et al.  Single molecule fluorescence in situ hybridisation for quantitating post-transcriptional regulation in Drosophila brains , 2017, bioRxiv.

[40]  Juri Rappsilber,et al.  Drosophila Syncrip binds the gurken mRNA localisation signal and regulates localised transcripts during axis specification , 2012, Biology Open.

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

[42]  N. Betz,et al.  The c-myc coding region determinant-binding protein: a member of a family of KH domain RNA-binding proteins. , 1998, Nucleic acids research.

[43]  V. Caviness,et al.  The cell cycle of the pseudostratified ventricular epithelium of the embryonic murine cerebral wall , 1995, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[44]  Anders Krogh,et al.  Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation , 2015, Genome Biology.

[45]  J. Knoblich,et al.  Drosophila neuroblasts: a model for stem cell biology , 2012, Development.

[46]  A. Gould,et al.  Fat cells reactivate quiescent neuroblasts via TOR and glial Insulin relays in Drosophila , 2011, Nature.

[47]  Hanchuan Peng,et al.  Clonal Development and Organization of the Adult Drosophila Central Brain , 2013, Current Biology.

[48]  E. Levine,et al.  The let-7–Imp axis regulates ageing of the Drosophila testis stem-cell niche , 2012, Nature.

[49]  Robert Gentleman,et al.  rtracklayer: an R package for interfacing with genome browsers , 2009, Bioinform..

[50]  S. Itzkovitz,et al.  Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues. , 2016, Methods.

[51]  Michael P. Snyder,et al.  Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures , 2014, Bioinform..

[52]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

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

[54]  Lu Yang,et al.  CytoCensus: mapping cell identity and division in tissues and organs using machine learning , 2019, bioRxiv.

[55]  Luke P. Lee,et al.  Opposing intrinsic temporal gradients guide neural stem cell production of varied neuronal fates , 2015, Science.

[56]  Ilan Davis,et al.  Imp and Syp RNA-binding proteins govern decommissioning of Drosophila neural stem cells , 2017, Development.

[57]  I. Lemm,et al.  Regulation of c-myc mRNA Decay by Translational Pausing in a Coding Region Instability Determinant , 2002, Molecular and Cellular Biology.

[58]  E. Birney,et al.  Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.

[59]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[60]  Tzumin Lee,et al.  Temporal control of Drosophila central nervous system development , 2019, Current Opinion in Neurobiology.

[61]  P. Driscoll,et al.  Anaplastic Lymphoma Kinase Spares Organ Growth during Nutrient Restriction in Drosophila , 2011, Cell.

[62]  R. Eisenman,et al.  An overview of MYC and its interactome. , 2014, Cold Spring Harbor perspectives in medicine.

[63]  Bruce A. Hay,et al.  Inactivation of Both foxo and reaper Promotes Long-Term Adult Neurogenesis in Drosophila , 2010, Current Biology.

[64]  C. Doe.  Temporal Patterning in the Drosophila CNS. , 2017, Annual review of cell and developmental biology.

[65]  Chris Q Doe,et al.  Identification of Drosophila type II neuroblast lineages containing transit amplifying ganglion mother cells , 2008, Developmental neurobiology.

[66]  Aljoscha Nern,et al.  Stem Cell-Intrinsic, Seven-up-Triggered Temporal Factor Gradients Diversify Intermediate Neural Progenitors , 2017, Current Biology.

[67]  R. Nusse,et al.  Ablation of Insulin-Producing Neurons in Flies: Growth and Diabetic Phenotypes , 2002, Science.

[68]  X. Morin,et al.  Motility Screen Identifies Drosophila IGF-II mRNA-Binding Protein—Zipcode-Binding Protein Acting in Oogenesis and Synaptogenesis , 2008, PLoS genetics.

[69]  Vilaiwan M. Fernandes,et al.  Timing temporal transitions during brain development , 2017, Current Opinion in Neurobiology.

[70]  Chi V Dang,et al.  MYC on the Path to Cancer , 2012, Cell.

[71]  P. Bernstein,et al.  Control of c-myc mRNA half-life in vitro by a protein capable of binding to a coding region stability determinant. , 1992, Genes & Development.

[72]  E. Rulifson,et al.  Remote control of insulin secretion by fat cells in Drosophila. , 2009, Cell metabolism.

[73]  Nicolò Riggi,et al.  IMPs: an RNA-binding protein family that provides a link between stem cell maintenance in normal development and cancer , 2016, Genes & development.

[74]  B. Edgar,et al.  Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. , 2003, Genes & development.

[75]  Giulia Antonazzo,et al.  FlyBase 2.0: the next generation , 2018, Nucleic Acids Res..

[76]  Christophe Zimmer,et al.  FISH-quant: automatic counting of transcripts in 3D FISH images , 2013, Nature Methods.