STAU2 protein level is controlled by caspases and the CHK1 pathway and regulates cell cycle progression in the non-transformed hTERT-RPE1 cells

Background Staufen2 (STAU2) is an RNA binding protein involved in the posttranscriptional regulation of gene expression. In neurons, STAU2 is required to maintain the balance between differentiation and proliferation of neural stem cells through asymmetric cell division. However, the importance of controlling STAU2 expression for cell cycle progression is not clear in non-neuronal dividing cells. We recently showed that STAU2 transcription is inhibited in response to DNA-damage due to E2F1 displacement from the STAU2 gene promoter. We now study the regulation of STAU2 steady-state levels in unstressed cells and its consequence for cell proliferation. Results CRISPR/Cas9-mediated and RNAi-dependent STAU2 depletion in the non-transformed hTERT-RPE1 cells both facilitate cell proliferation suggesting that STAU2 expression influences pathway(s) linked to cell cycle controls. Such effects are not observed in the CRISPR STAU2-KO cancer HCT116 cells nor in the STAU2-RNAi-depleted HeLa cells. Interestingly, a physiological decrease in the steady-state level of STAU2 is controlled by caspases. This effect of peptidases is counterbalanced by the activity of the CHK1 pathway suggesting that STAU2 partial degradation/stabilization fines tune cell cycle progression in unstressed cells. A large-scale proteomic analysis using STAU2/biotinylase fusion protein identifies known STAU2 interactors involved in RNA translation, localization, splicing, or decay confirming the role of STAU2 in the posttranscriptional regulation of gene expression. In addition, several proteins found in the nucleolus, including proteins of the ribosome biogenesis pathway and of the DNA damage response, are found in close proximity to STAU2. Strikingly, many of these proteins are linked to the kinase CHK1 pathway, reinforcing the link between STAU2 functions and the CHK1 pathway. Indeed, inhibition of the CHK1 pathway for 4 h dissociates STAU2 from proteins involved in translation and RNA metabolism. Conclusions These results indicate that STAU2 is involved in pathway(s) that control(s) cell proliferation, likely via mechanisms of posttranscriptional regulation, ribonucleoprotein complex assembly, genome integrity and/or checkpoint controls. The mechanism by which STAU2 regulates cell growth likely involves caspases and the kinase CHK1 pathway.

[1]  N. Perrimon,et al.  Efficient proximity labeling in living cells and organisms with TurboID , 2018, Nature Biotechnology.

[2]  M. Oeffinger,et al.  Senescence-associated ribosome biogenesis defects contributes to cell cycle arrest through the Rb pathway , 2018, Nature Cell Biology.

[3]  B. Kile,et al.  Apoptotic Caspases: Multiple or Mistaken Identities? , 2018, Trends in cell biology.

[4]  Min Su,et al.  LncRNAs in DNA damage response and repair in cancer cells , 2018, Acta biochimica et biophysica Sinica.

[5]  Liying Meng,et al.  Transcriptome-wide discovery of coding and noncoding RNA-binding proteins , 2018, Proceedings of the National Academy of Sciences.

[6]  G. Kusek,et al.  Staufen2 deficiency leads to impaired response to novelty in mice , 2018, Neurobiology of Learning and Memory.

[7]  J. Bartek,et al.  Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis , 2018, Oncogene.

[8]  Alfredo Castello,et al.  Expanding horizons: new roles for non-canonical RNA-binding proteins in cancer , 2018, Current opinion in genetics & development.

[9]  D. C. Xu,et al.  Non-apoptotic Caspase regulation of stem cell properties , 2017, Seminars in cell & developmental biology.

[10]  Suntaek Hong RNA Binding Protein as an Emerging Therapeutic Target for Cancer Prevention and Treatment , 2017, Journal of cancer prevention.

[11]  J. Delgado-García,et al.  Forebrain-specific, conditional silencing of Staufen2 alters synaptic plasticity, learning, and memory in rats , 2017, Genome Biology.

[12]  O. Schwartz,et al.  HEXIM1 and NEAT1 Long Non-coding RNA Form a Multi-subunit Complex that Regulates DNA-Mediated Innate Immune Response. , 2017, Molecular cell.

[13]  L. DesGroseillers,et al.  The M-phase specific hyperphosphorylation of Staufen2 involved the cyclin-dependent kinase CDK1 , 2017, BMC Cell Biology.

[14]  Raquel Almeida,et al.  RNA-Binding Proteins in Cancer: Old Players and New Actors. , 2017, Trends in cancer.

[15]  S. Ghafouri-Fard,et al.  The Role of Long Non Coding RNAs in the Repair of DNA Double Strand Breaks , 2017, International journal of molecular and cellular medicine.

[16]  Mark R Cookson,et al.  RNA‐binding proteins implicated in neurodegenerative diseases , 2017, Wiley interdisciplinary reviews. RNA.

[17]  Victor L. Willson,et al.  One-Sample T-Test , 2017 .

[18]  A. Aguilera,et al.  Transcription–replication conflicts: how they occur and how they are resolved , 2016, Nature Reviews Molecular Cell Biology.

[19]  N. Zhang,et al.  RNA- binding protein Stau2 is important for spindle integrity and meiosis progression in mouse oocytes , 2016, Cell cycle.

[20]  J. Tainer,et al.  Noncoding RNA joins Ku and DNA-PKcs for DNA-break resistance in breast cancer , 2016, Nature Structural &Molecular Biology.

[21]  Kenneth H. Roux,et al.  An improved smaller biotin ligase for BioID proximity labeling , 2016, Molecular biology of the cell.

[22]  E. Drobetsky,et al.  The downregulation of the RNA-binding protein Staufen2 in response to DNA damage promotes apoptosis , 2016, Nucleic acids research.

[23]  Gwendolyn M. Jang,et al.  Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding. , 2015, Cell host & microbe.

[24]  Edward L. Huttlin,et al.  The BioPlex Network: A Systematic Exploration of the Human Interactome , 2015, Cell.

[25]  K. Cimprich,et al.  The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability. , 2014, DNA repair.

[26]  J. Diffley,et al.  DNA Replication and Oncogene-Induced Replicative Stress , 2014, Current Biology.

[27]  Youwei Zhang,et al.  Roles of Chk1 in cell biology and cancer therapy , 2014, International journal of cancer.

[28]  R. Lothe,et al.  Epigenetic and genetic features of 24 colon cancer cell lines , 2013, Oncogenesis.

[29]  Amber L. Couzens,et al.  The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data , 2013, Nature Methods.

[30]  Bin Tian,et al.  STAU1 binding 3' UTR IRAlus complements nuclear retention to protect cells from PKR-mediated translational shutdown. , 2013, Genes & development.

[31]  Bernd Fischer,et al.  RNA-binding proteins in Mendelian disease. , 2013, Trends in genetics : TIG.

[32]  D. Mittelman,et al.  The fractured genome of HeLa cells , 2013, Genome Biology.

[33]  David R McIlwain,et al.  Caspase functions in cell death and disease. , 2013, Cold Spring Harbor perspectives in biology.

[34]  Mallikarjun Patil,et al.  Checkpoint kinase 1 in DNA damage response and cell cycle regulation , 2013, Cellular and Molecular Life Sciences.

[35]  L. Maquat,et al.  Staufen2 functions in Staufen1-mediated mRNA decay by binding to itself and its paralog and promoting UPF1 helicase but not ATPase activity , 2012, Proceedings of the National Academy of Sciences.

[36]  R. Johnstone,et al.  Oncogenes in cell survival and cell death. , 2012, Cold Spring Harbor perspectives in biology.

[37]  P. Macchi,et al.  The double-stranded RNA-binding protein Staufen 2 regulates eye size , 2012, Molecular and Cellular Neuroscience.

[38]  G. Kusek,et al.  Asymmetric segregation of the double-stranded RNA binding protein Staufen2 during mammalian neural stem cell divisions promotes lineage progression. , 2012, Cell stem cell.

[39]  M. Kiebler,et al.  An asymmetrically localized Staufen2-dependent RNA complex regulates maintenance of mammalian neural stem cells. , 2012, Cell stem cell.

[40]  M. Horb,et al.  Xenopus staufen2 is required for anterior endodermal organ formation , 2012, Genesis.

[41]  E. Kuranaga Beyond apoptosis: caspase regulatory mechanisms and functions in vivo , 2012, Genes to cells : devoted to molecular & cellular mechanisms.

[42]  Sebastian A. Wagner,et al.  A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1 , 2011, Genome Biology.

[43]  J. Lacaille,et al.  Staufen 2 regulates mGluR long-term depression and Map1b mRNA distribution in hippocampal neurons. , 2011, Learning & memory.

[44]  H. Will,et al.  The RNA-binding protein La contributes to cell proliferation and CCND1 expression , 2011, Oncogene.

[45]  Hyungwon Choi,et al.  SAINT: Probabilistic Scoring of Affinity Purification - Mass Spectrometry Data , 2010, Nature Methods.

[46]  M. Meuth,et al.  Chk1 suppressed cell death , 2010, Cell Division.

[47]  T. Helleday,et al.  Chk1 promotes replication fork progression by controlling replication initiation , 2010, Proceedings of the National Academy of Sciences.

[48]  Kotb Abdelmohsen,et al.  Regulation of HuR by DNA Damage Response Kinases , 2010, Journal of nucleic acids.

[49]  L. DesGroseillers,et al.  Molecular Composition of Staufen2-Containing Ribonucleoproteins in Embryonic Rat Brain , 2010, PloS one.

[50]  Paul W Anderson,et al.  Identification of Small Molecule and Genetic Modulators of AON-Induced Dystrophin Exon Skipping by High-Throughput Screening , 2009, PloS one.

[51]  S. Parapuram,et al.  Differential effects of TGFbeta and vitreous on the transformation of retinal pigment epithelial cells. , 2009, Investigative ophthalmology & visual science.

[52]  J. Bartek,et al.  The DNA-damage response in human biology and disease , 2009, Nature.

[53]  R. Wollman,et al.  A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. , 2009, Molecular cell.

[54]  M. Meuth,et al.  ATR and Chk1 Suppress a Caspase-3–Dependent Apoptotic Response Following DNA Replication Stress , 2009, PLoS genetics.

[55]  T. Helleday,et al.  Essential function of Chk1 can be uncoupled from DNA damage checkpoint and replication control , 2008, Proceedings of the National Academy of Sciences.

[56]  Junying Yuan,et al.  Caspases in apoptosis and beyond , 2008, Oncogene.

[57]  Kai-Wei Chang,et al.  RNA-binding proteins in human genetic disease. , 2008, Trends in genetics : TIG.

[58]  B. Gómez-González,et al.  Genome instability: a mechanistic view of its causes and consequences , 2008, Nature Reviews Genetics.

[59]  L. Furic,et al.  A genome-wide approach identifies distinct but overlapping subsets of cellular mRNAs associated with Staufen1- and Staufen2-containing ribonucleoprotein complexes. , 2007, RNA.

[60]  J. Keene RNA regulons: coordination of post-transcriptional events , 2007, Nature Reviews Genetics.

[61]  J. Malm,et al.  The semenogelins: proteins with functions beyond reproduction? , 2006, Cellular and Molecular Life Sciences CMLS.

[62]  J. Manley,et al.  Cotranscriptional processes and their influence on genome stability. , 2006, Genes & development.

[63]  K. Sampath,et al.  Zebrafish Staufen1 and Staufen2 are required for the survival and migration of primordial germ cells. , 2006, Developmental biology.

[64]  M. Kiebler,et al.  The brain-specific double-stranded RNA-binding protein Staufen2 is required for dendritic spine morphogenesis , 2006, The Journal of cell biology.

[65]  L. DesGroseillers,et al.  The zinc‐finger protein ZFR is critical for Staufen 2 isoform specific nucleocytoplasmic shuttling in neurons , 2006, Journal of neurochemistry.

[66]  M. Meuth,et al.  Chk1 and p21 cooperate to prevent apoptosis during DNA replication fork stress. , 2005, Molecular biology of the cell.

[67]  Jiri Bartek,et al.  ATM- and cell cycle-dependent regulation of ATR in response to DNA double-strand breaks , 2006, Nature Cell Biology.

[68]  M. Kiebler,et al.  A putative nuclear function for mammalian Staufen. , 2005, Trends in biochemical sciences.

[69]  J. Correale,et al.  Staufen recruitment into stress granules does not affect early mRNA transport in oligodendrocytes. , 2004, Molecular biology of the cell.

[70]  Luc DesGroseillers,et al.  The Brain-specific Double-stranded RNA-binding Protein Staufen2 , 2004, Journal of Biological Chemistry.

[71]  J. Gautier,et al.  ATR and ATM regulate the timing of DNA replication origin firing , 2004, Nature Cell Biology.

[72]  F. Vikhanskaya,et al.  Characterization of the 5’flanking Region of the Human chk1 Gene: Identification of E2F1 Functional Sites , 2003, Cell cycle.

[73]  Takashi Horiuchi,et al.  Transcription-dependent recombination and the role of fork collision in yeast rDNA. , 2003, Genes & development.

[74]  Stephen J. Elledge,et al.  Sensing DNA Damage Through ATRIP Recognition of RPA-ssDNA Complexes , 2003, Science.

[75]  M. Kiebler,et al.  Staufen2 isoforms localize to the somatodendritic domain of neurons and interact with different organelles. , 2002, Journal of cell science.

[76]  E. Schuman,et al.  A Role for a Rat Homolog of Staufen in the Transport of RNA to Neuronal Dendrites , 2001, Neuron.

[77]  H. Piwnica-Worms,et al.  ATR-Mediated Checkpoint Pathways Regulate Phosphorylation and Activation of Human Chk1 , 2001, Molecular and Cellular Biology.

[78]  A. Ballabio,et al.  Identification of a novel homolog of the Drosophila staufen protein in the chromosome 8q13-q21.1 region. , 1999, Genomics.

[79]  S. Jackson,et al.  The DNA-dependent protein kinase: Requirement for DNA ends and association with Ku antigen , 1993, Cell.

[80]  J. Henzen Publisher's note , 1979, Brain Research.

[81]  E. Schuman,et al.  Dendrites , 1978, Journal of the Geological Society.