A network of heterochronic genes including Imp1 regulates temporal changes in stem cell properties

Stem cell properties change over time to match the changing growth and regeneration demands of tissues. We showed previously that adult forebrain stem cell function declines during aging because of increased expression of let-7 microRNAs, evolutionarily conserved heterochronic genes that reduce HMGA2 expression. Here we asked whether let-7 targets also regulate changes between fetal and adult stem cells. We found a second let-7 target, the RNA binding protein IMP1, that is expressed by fetal, but not adult, neural stem cells. IMP1 expression was promoted by Wnt signaling and Lin28a expression and opposed by let-7 microRNAs. Imp1-deficient neural stem cells were prematurely depleted in the dorsal telencephalon due to accelerated differentiation, impairing pallial expansion. IMP1 post-transcriptionally inhibited the expression of differentiation-associated genes while promoting the expression of self-renewal genes, including Hmga2. A network of heterochronic gene products including Lin28a, let-7, IMP1, and HMGA2 thus regulates temporal changes in stem cell properties. DOI: http://dx.doi.org/10.7554/eLife.00924.001

[1]  A. Chenn,et al.  Cell-Autonomous β-Catenin Signaling Regulates Cortical Precursor Proliferation , 2006, The Journal of Neuroscience.

[2]  Andrew P McMahon,et al.  A mitogen gradient of dorsal midline Wnts organizes growth in the CNS. , 2002, Development.

[3]  Ayellet V. Segrè,et al.  The Lin28/let-7 Axis Regulates Glucose Metabolism , 2011, Cell.

[4]  R. Krumlauf,et al.  Evidence for a mitogenic effect of Wnt-1 in the developing mammalian central nervous system. , 1994, Development.

[5]  A. McMahon,et al.  Inactivation of the beta-catenin gene by Wnt1-Cre-mediated deletion results in dramatic brain malformation and failure of craniofacial development. , 2001, Development.

[6]  F. Nielsen,et al.  A Family of Insulin-Like Growth Factor II mRNA-Binding Proteins Represses Translation in Late Development , 1999, Molecular and Cellular Biology.

[7]  Sruthi K. Swaminathan,et al.  Persistent expression of stabilized beta-catenin delays maturation of radial glial cells into intermediate progenitors. , 2007, Developmental biology.

[8]  S. Fuchs,et al.  CRD-BP mediates stabilization of betaTrCP1 and c-myc mRNA in response to beta-catenin signalling. , 2006, Nature.

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

[10]  S. Anderson,et al.  β-catenin–mediated Wnt signaling regulates neurogenesis in the ventral telencephalon , 2008, Nature Neuroscience.

[11]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[12]  G. Daley,et al.  Lin28: A MicroRNA Regulator with a Macro Role , 2010, Cell.

[13]  G. Daley,et al.  A role for Lin28 in primordial germ cell development and germ cell malignancy , 2009, Nature.

[14]  Fatima Al-Shahrour,et al.  Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia , 2010, Nature Medicine.

[15]  L. Smirnova,et al.  A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment , 2008, Nature Cell Biology.

[16]  Carmen Birchmeier,et al.  beta-Catenin signals regulate cell growth and the balance between progenitor cell expansion and differentiation in the nervous system. , 2003, Developmental biology.

[17]  A. Antebi,et al.  A Steroid Receptor–MicroRNA Switch Regulates Life Span in Response to Signals from the Gonad , 2012, Science.

[18]  G. Fishell,et al.  Division-coupled astrocytic differentiation and age-related depletion of neural stem cells in the adult hippocampus. , 2011, Cell stem cell.

[19]  C. Niehrs,et al.  Loss of Dickkopf-1 restores neurogenesis in old age and counteracts cognitive decline. , 2013, Cell stem cell.

[20]  Andrew P. McMahon,et al.  The Wnt-1 (int-1) proto-oncogene is required for development of a large region of the mouse brain , 1990, Cell.

[21]  B. Reinhart,et al.  Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA , 2000, Nature.

[22]  Christopher Gregg,et al.  Aging Results in Reduced Epidermal Growth Factor Receptor Signaling, Diminished Olfactory Neurogenesis, and Deficits in Fine Olfactory Discrimination , 2004, The Journal of Neuroscience.

[23]  J. Rinn,et al.  Lin28a transgenic mice manifest size and puberty phenotypes identified in human genetic association studies , 2010, Nature Genetics.

[24]  Choun-Ki Joo,et al.  Wnt/β-Catenin/Tcf Signaling Induces the Transcription of Axin2, a Negative Regulator of the Signaling Pathway , 2002, Molecular and Cellular Biology.

[25]  K. Ikeda,et al.  3'UTR-truncated Hmga2 cDNA causes MPN-like hematopoiesis by conferring a clonal growth advantage at the level of HSC in mice. , 2011, Blood.

[26]  Sean J Morrison,et al.  Mechanisms of stem cell self-renewal. , 2009, Annual review of cell and developmental biology.

[27]  T. Hansen,et al.  Expression of IGF-II mRNA-binding proteins (IMPs) in gonads and testicular cancer. , 2005, Reproduction.

[28]  N. Copeland,et al.  A highly efficient recombineering-based method for generating conditional knockout mutations. , 2003, Genome research.

[29]  C. Joo,et al.  Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. , 2008, Molecular cell.

[30]  S. Fuchs,et al.  CRD-BP mediates stabilization of βTrCP1 and c-myc mRNA in response to β-catenin signalling , 2006, Nature.

[31]  Cole Trapnell,et al.  Improving RNA-Seq expression estimates by correcting for fragment bias , 2011, Genome Biology.

[32]  R. Darnell,et al.  Two ZBP1 KH domains facilitate β-actin mRNA localization, granule formation, and cytoskeletal attachment , 2003, The Journal of cell biology.

[33]  Charles R. Tessier,et al.  Mammary Tumor Induction in Transgenic Mice Expressing an RNA-Binding Protein , 2004, Cancer Research.

[34]  S. Krauss,et al.  A dynamic gradient of Wnt signaling controls initiation of neurogenesis in the mammalian cortex and cellular specification in the hippocampus. , 2007, Developmental biology.

[35]  Scott B. Dewell,et al.  Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP , 2010, Cell.

[36]  G. Nasioulas,et al.  Expression of the RNA-binding protein CRD-BP in brain and non-small cell lung tumors. , 2004, Cancer letters.

[37]  Amber L. Wells,et al.  Feedback Regulation between Zipcode Binding Protein 1 and β-Catenin mRNAs in Breast Cancer Cells , 2008, Molecular and Cellular Biology.

[38]  W. Huttner,et al.  Cdk4/cyclinD1 overexpression in neural stem cells shortens G1, delays neurogenesis, and promotes the generation and expansion of basal progenitors. , 2009, Cell stem cell.

[39]  T. Noda,et al.  Rapid colorectal adenoma formation initiated by conditional targeting of the Apc gene. , 1997, Science.

[40]  A. Álvarez-Buylla,et al.  For the Long Run Maintaining Germinal Niches in the Adult Brain , 2004, Neuron.

[41]  J. Rubenstein,et al.  Neuronal production and precursor proliferation defects in the neocortex of mice with loss of function in the canonical Wnt signaling pathway , 2006, Neuroscience.

[42]  Gene W. Yeo,et al.  LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. , 2012, Molecular cell.

[43]  Anjen Chenn,et al.  Regulation of Cerebral Cortical Size by Control of Cell Cycle Exit in Neural Precursors , 2002, Science.

[44]  F. Gage,et al.  Mechanisms and Functional Implications of Adult Neurogenesis , 2008, Cell.

[45]  Jérôme Larghero,et al.  Transfusion independence and HMGA2 activation after gene therapy of human β-thalassaemia , 2010, Nature.

[46]  Xianjin Zhou,et al.  Mutation responsible for the mouse pygmy phenotype in the developmentally regulated factor HMGI-C , 1995, Nature.

[47]  G. Daley,et al.  Selective Blockade of MicroRNA Processing by Lin28 , 2008, Science.

[48]  Nancy A. Jenkins,et al.  Recombineering: a powerful new tool for mouse functional genomics , 2001, Nature Reviews Genetics.

[49]  Gene W. Yeo,et al.  Wnt-mediated activation of NeuroD1 and retro-elements during adult neurogenesis , 2009, Nature Neuroscience.

[50]  T. Palmer,et al.  Neurogenesis in the dentate gyrus of the adult rat: age-related decrease of neuronal progenitor proliferation , 1996, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[51]  S. Krauss,et al.  Role of β-catenin in the developing cortical and hippocampal neuroepithelium , 2003, Neuroscience.

[52]  A. Chenn,et al.  Beta-Catenin Signaling Negatively Regulates Intermediate Progenitor Population Numbers in the Developing Cortex , 2010, PloS one.

[53]  O. Kretz,et al.  Disruption of the glucocorticoid receptor gene in the nervous system results in reduced anxiety , 1999, Nature Genetics.

[54]  K. Ligon,et al.  p16INK4a induces an age-dependent decline in islet regenerative potential , 2006, Nature.

[55]  H. Okano,et al.  Function of RNA-binding protein Musashi-1 in stem cells. , 2005, Experimental cell research.

[56]  Robert L. Judson,et al.  Opposing microRNA families regulate self-renewal in mouse embryonic stem cells , 2010, Nature.

[57]  E. Elliott,et al.  The insulin‐like growth factor mRNA binding‐protein IMP‐1 and the Ras‐regulatory protein G3BP associate with tau mRNA and HuD protein in differentiated P19 neuronal cells , 2004, Journal of neurochemistry.

[58]  R. DePinho,et al.  Stem-cell ageing modified by the cyclin-dependent kinase inhibitor p16INK4a , 2006, Nature.

[59]  S. Morrison,et al.  Increasing p16INK4a expression decreases forebrain progenitors and neurogenesis during ageing , 2006, Nature.

[60]  A. Maslov,et al.  Neural Stem Cell Detection, Characterization, and Age- Related Changes in the Subventricular Zone of Mice , 2022 .

[61]  Federico Calegari,et al.  Cell cycle control of mammalian neural stem cells: putting a speed limit on G1. , 2010, Trends in cell biology.

[62]  S. Morrison,et al.  Bmi-1 promotes neural stem cell self-renewal and neural development but not mouse growth and survival by repressing the p16Ink4a and p19Arf senescence pathways. , 2005, Genes & development.

[63]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[64]  T. Hansen,et al.  Dwarfism and Impaired Gut Development in Insulin-Like Growth Factor II mRNA-Binding Protein 1-Deficient Mice , 2004, Molecular and Cellular Biology.

[65]  F. Slack,et al.  The let-7 family of microRNAs. , 2008, Trends in cell biology.

[66]  Yoosik Kim,et al.  LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells , 2012, Cell.

[67]  Yunyu Zhang,et al.  An HMGA2-IGF2BP2 axis regulates myoblast proliferation and myogenesis. , 2012, Developmental cell.

[68]  David J. Anderson,et al.  Isolation of a stem cell for neurons and glia from the mammalian neural crest , 1992, Cell.

[69]  M. Götz,et al.  Neuronal or Glial Progeny Regional Differences in Radial Glia Fate , 2003, Neuron.

[70]  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.

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

[72]  S. Mcconnell,et al.  BMP ligands act redundantly to pattern the dorsal telencephalic midline , 2003, Genesis.

[73]  Sean J. Morrison,et al.  Hmga2 Promotes Neural Stem Cell Self-Renewal in Young but Not Old Mice by Reducing p16Ink4a and p19Arf Expression , 2008, Cell.

[74]  Gerald J. Sun,et al.  In Vivo Clonal Analysis Reveals Self-Renewing and Multipotent Adult Neural Stem Cell Characteristics , 2011, Cell.

[75]  J. Kimble,et al.  Controls of germline stem cells, entry into meiosis, and the sperm/oocyte decision in Caenorhabditis elegans. , 2007, Annual review of cell and developmental biology.

[76]  Henry Kennedy,et al.  Cell-cycle control and cortical development , 2007, Nature Reviews Neuroscience.

[77]  A. Krogh,et al.  Molecular Composition of IMP1 Ribonucleoprotein Granules*S , 2007, Molecular & Cellular Proteomics.

[78]  Guoqiang Sun,et al.  MicroRNA let-7b regulates neural stem cell proliferation and differentiation by targeting nuclear receptor TLX signaling , 2010, Proceedings of the National Academy of Sciences.

[79]  A. McMahon,et al.  Wnt signalling required for expansion of neural crest and CNS progenitors , 1997, Nature.

[80]  H. Okano,et al.  RNA-binding protein Musashi family: Roles for CNS stem cells and a subpopulation of ependymal cells revealed by targeted disruption and antisense ablation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[81]  A. Joyner,et al.  The midbrain-hindbrain phenotype of Wnt-1− Wnt-1− mice results from stepwise deletion of engrailed-expressing cells by 9.5 days postcoitum , 1992, Cell.

[82]  C. Burge,et al.  Identification of let-7-regulated oncofetal genes. , 2008, Cancer research.

[83]  J. Yisraeli VICKZ proteins: a multi‐talented family of regulatory RNA‐binding proteins , 2005, Biology of the cell.

[84]  L. Behar,et al.  Dynamic association with polysomes during P19 neuronal differentiation and an untranslated‐region‐dependent translation regulation of the tau mRNA by the tau mRNA‐associated proteins IMP1, HuD, and G3BP1 , 2007, Journal of neuroscience research.

[85]  J. M. Thomson,et al.  Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing. , 2008, RNA.

[86]  F. Nielsen,et al.  Cytoplasmic trafficking of IGF-II mRNA-binding protein by conserved KH domains. , 2002, Journal of cell science.

[87]  Reynaldo Sequerra,et al.  High-efficiency deleter mice show that FLPe is an alternative to Cre-loxP , 2000, Nature Genetics.

[88]  J. Giovannoni,et al.  Uniting Germline and Stem Cells : The Function of Piwi Proteins and the piRNA Pathway in Diverse Organisms , 2015 .

[89]  S. Krauss,et al.  Role of beta-catenin in the developing cortical and hippocampal neuroepithelium. , 2003, Neuroscience.