Localized inhibition of protein phosphatase 1 by NUAK1 promotes spliceosome activity and reveals a MYC-sensitive feedback control of transcription

[1]  Michael A. Cortazar,et al.  Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a "Sitting Duck Torpedo" Mechanism. , 2019, Molecular cell.

[2]  J. Workman,et al.  Identification of a nuclear localization signal and importin beta members mediating NUAK1 nuclear import inhibited by oxidative stress. , 2019, Journal of cellular biochemistry.

[3]  P. Cramer,et al.  MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation , 2019, Molecular cell.

[4]  S. Carr,et al.  TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach* , 2019, Molecular & Cellular Proteomics.

[5]  R. Versteeg,et al.  Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA polymerase , 2019, Nature.

[6]  T. Laajala,et al.  Pharmacological reactivation of MYC-dependent apoptosis induces susceptibility to anti-PD-1 immunotherapy , 2019, Nature Communications.

[7]  G. Capranico,et al.  DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells , 2018, Proceedings of the National Academy of Sciences.

[8]  P. Boutros,et al.  MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis. , 2018, Molecular cell.

[9]  The Gene Ontology Consortium,et al.  The Gene Ontology Resource: 20 years and still GOing strong , 2018, Nucleic Acids Res..

[10]  M. Carmo-Fonseca,et al.  RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing , 2018, Molecular cell.

[11]  S. Mohammed,et al.  Elongation/Termination Factor Exchange Mediated by PP1 Phosphatase Orchestrates Transcription Termination , 2018, Cell reports.

[12]  Kathleen E. Houlahan,et al.  MYC dephosphorylation by the PP1/PNUTS phosphatase complex regulates chromatin binding and protein stability , 2018, Nature Communications.

[13]  M. Walter,et al.  Spliceosome Mutations Induce R Loop-Associated Sensitivity to ATR Inhibition in Myelodysplastic Syndromes. , 2018, Cancer research.

[14]  Xingyue He,et al.  Anti‐tumor efficacy of a novel CLK inhibitor via targeting RNA splicing and MYC‐dependent vulnerability , 2018, EMBO molecular medicine.

[15]  Gregory T. Booth,et al.  A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II , 2018, Nature.

[16]  M. Drysdale,et al.  Colorectal Tumors Require NUAK1 for Protection from Oxidative Stress. , 2018, Cancer discovery.

[17]  A. Trumpp,et al.  AMPK promotes survival of c‐Myc‐positive melanoma cells by suppressing oxidative stress , 2018, The EMBO journal.

[18]  Nan Li,et al.  Capturing the interactome of newly transcribed RNA , 2018, Nature Methods.

[19]  C. Shao,et al.  The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations. , 2018, Molecular cell.

[20]  Andrea J. Kriz,et al.  Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP. , 2018, Molecular cell.

[21]  D. Rickman,et al.  Association with Aurora-A Controls N-MYC-Dependent Promoter Escape and Pause Release of RNA Polymerase II during the Cell Cycle , 2017, Cell reports.

[22]  R. Young,et al.  Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation. , 2017, Nature chemical biology.

[23]  O. Sansom,et al.  Calcium signalling links MYC to NUAK1 , 2017, Oncogene.

[24]  M. Pelizzola,et al.  Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation , 2017, Genome research.

[25]  P. Jennings,et al.  Redirecting SR Protein Nuclear Trafficking through an Allosteric Platform. , 2017, Journal of molecular biology.

[26]  M. Eilers,et al.  The MYC mRNA 3′‐UTR couples RNA polymerase II function to glutamine and ribonucleotide levels , 2017, The EMBO journal.

[27]  M. Bollen,et al.  Biogenesis and activity regulation of protein phosphatase 1. , 2017, Biochemical Society transactions.

[28]  K. Cimprich,et al.  Conflict Resolution in the Genome: How Transcription and Replication Make It Work , 2016, Cell.

[29]  Jüergen Cox,et al.  The MaxQuant computational platform for mass spectrometry-based shotgun proteomics , 2016, Nature Protocols.

[30]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[31]  Jesse J. Lipp,et al.  P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates , 2016, Genes & development.

[32]  Britta A. M. Bouwman,et al.  Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination. , 2015, Molecular cell.

[33]  A. Sabò,et al.  MYC: connecting selective transcriptional control to global RNA production , 2015, Nature Reviews Cancer.

[34]  David C. Norris,et al.  Integrated genome browser: visual analytics platform for genomics , 2015, bioRxiv.

[35]  Sarah J. Kurley,et al.  The spliceosome is a therapeutic vulnerability in MYC-driven cancer , 2015, Nature.

[36]  Sean J Humphrey,et al.  High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics , 2015, Nature Biotechnology.

[37]  A. McCallion,et al.  Targeted inhibition of tumor-specific glutaminase diminishes cell-autonomous tumorigenesis. , 2015, The Journal of clinical investigation.

[38]  M. Bollen,et al.  Genome-wide promoter binding profiling of protein phosphatase-1 and its major nuclear targeting subunits , 2015, Nucleic acids research.

[39]  C. Koh,et al.  MYC regulates the core pre-mRNA splicing machinery as an essential step in lymphomagenesis , 2015, Nature.

[40]  H. Kimura,et al.  Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing , 2015, Cell.

[41]  Yan Liu,et al.  Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor. , 2014, Cancer cell.

[42]  Liuqing Yang,et al.  lncRNA Directs Cooperative Epigenetic Regulation Downstream of Chemokine Signals , 2014, Cell.

[43]  Heiner Koch,et al.  Comprehensive and Reproducible Phosphopeptide Enrichment Using Iron Immobilized Metal Ion Affinity Chromatography (Fe-IMAC) Columns , 2014, Molecular & Cellular Proteomics.

[44]  Bandana Sharma,et al.  CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer , 2014, Cell.

[45]  G. Evan,et al.  BIM is the primary mediator of MYC-induced apoptosis in multiple solid tissues. , 2014, Cell reports.

[46]  A. Quinlan.  BEDTools: The Swiss‐Army Tool for Genome Feature Analysis , 2014, Current protocols in bioinformatics.

[47]  Darjus F. Tschaharganeh,et al.  CDK9-mediated transcription elongation is required for MYC addiction in hepatocellular carcinoma , 2014, Genes & development.

[48]  L. Zender,et al.  Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles , 2014, Nature.

[49]  Marco Y. Hein,et al.  Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ * , 2014, Molecular & Cellular Proteomics.

[50]  A. Prescott,et al.  Interplay between Polo kinase, LKB1-activated NUAK1 kinase, PP1βMYPT1 phosphatase complex and the SCFβTrCP E3 ubiquitin ligase , 2014, The Biochemical journal.

[51]  Eric Nestler,et al.  ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases , 2014, BMC Genomics.

[52]  Jiyong Liang,et al.  Liver kinase B1 regulates the centrosome via PLK1 , 2014, Cell Death and Disease.

[53]  J. Beggs,et al.  A Splicing-Dependent Transcriptional Checkpoint Associated with Prespliceosome Formation , 2014, Molecular cell.

[54]  Rafael C. Jimenez,et al.  The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases , 2013, Nucleic Acids Res..

[55]  N. Gray,et al.  Characterization of WZ4003 and HTH-01-015 as selective inhibitors of the LKB1-tumour-suppressor-activated NUAK kinases , 2013, The Biochemical journal.

[56]  L. Alphey,et al.  PNUTS/PP1 Regulates RNAPII-Mediated Gene Expression and Is Necessary for Developmental Growth , 2013, PLoS genetics.

[57]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[58]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[59]  D. Bentley,et al.  mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. , 2012, Molecular cell.

[60]  I. Korf,et al.  R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. , 2012, Molecular cell.

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

[62]  L. Zender,et al.  Deregulated MYC expression induces dependence upon AMPK-related kinase 5 , 2012, Nature.

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

[64]  H. Urlaub,et al.  Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion , 2012, Nature Communications.

[65]  X. Hou,et al.  A new role of NUAK1: directly phosphorylating p53 and regulating cell proliferation , 2011, Oncogene.

[66]  M. Seizl,et al.  The Prp19 Complex Is a Novel Transcription Elongation Factor Required for Trex Occupancy at Transcribed Genes Functional Analysis of the Rna Polymerase Ii C-terminal Domain Kinase Ctk1 in the Yeast , 2022 .

[67]  Helga Thorvaldsdóttir,et al.  Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..

[68]  J. Manley,et al.  The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex. , 2011, Genes & development.

[69]  S. Elledge,et al.  Functional identification of optimized RNAi triggers using a massively parallel sensor assay. , 2011, Molecular cell.

[70]  M. Mann,et al.  Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.

[71]  Jason I. Herschkowitz,et al.  The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo , 2011, Proceedings of the National Academy of Sciences.

[72]  W. Tarn,et al.  The Exon Junction Complex Component Y14 Modulates the Activity of the Methylosome in Biogenesis of Spliceosomal Small Nuclear Ribonucleoproteins* , 2011, The Journal of Biological Chemistry.

[73]  D. Skalnik,et al.  Identification and Characterization of a Novel Human PP1 Phosphatase Complex* , 2010, The Journal of Biological Chemistry.

[74]  Christopher B. Burge,et al.  c-Myc Regulates Transcriptional Pause Release , 2010, Cell.

[75]  A. Prescott,et al.  New Roles for the LKB1-NUAK Pathway in Controlling Myosin Phosphatase Complexes and Cell Adhesion , 2010, Science Signaling.

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

[77]  M. Bollen,et al.  Nuclear Inhibitor of Protein Phosphatase-1 (NIPP1) Directs Protein Phosphatase-1 (PP1) to Dephosphorylate the U2 Small Nuclear Ribonucleoprotein Particle (snRNP) Component, Spliceosome-associated Protein 155 (Sap155)* , 2008, Journal of Biological Chemistry.

[78]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[79]  Chris Mungall,et al.  AmiGO: online access to ontology and annotation data , 2008, Bioinform..

[80]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[81]  D. Hartshorne,et al.  Myosin phosphatase target subunit: Many roles in cell function. , 2008, Biochemical and biophysical research communications.

[82]  T. Owa,et al.  Splicing factor SF3b as a target of the antitumor natural product pladienolide , 2007, Nature Chemical Biology.

[83]  M. Hagiwara,et al.  Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA , 2007, Nature Chemical Biology.

[84]  J. Manley,et al.  PP1/PP2A phosphatases are required for the second step of Pre-mRNA splicing and target specific snRNP proteins. , 2006, Molecular cell.

[85]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[86]  Alok J. Saldanha,et al.  Java Treeview - extensible visualization of microarray data , 2004, Bioinform..

[87]  S. Lowe,et al.  Intrinsic tumour suppression , 2004, Nature.

[88]  P. Greengard,et al.  PNUTS, a Protein Phosphatase 1 (PP1) Nuclear Targeting Subunit , 2003, The Journal of Biological Chemistry.

[89]  M. Mann,et al.  Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. , 2003, Analytical chemistry.

[90]  Stella Pelengaris,et al.  c-MYC: more than just a matter of life and death , 2002, Nature Reviews Cancer.

[91]  B. Kuster,et al.  High pH Reversed-Phase Micro-Columns for Simple, Sensitive, and Efficient Fractionation of Proteome and (TMT labeled) Phosphoproteome Digests. , 2017, Methods in molecular biology.

[92]  C. Dang.  A Time for MYC: Metabolism and Therapy. , 2016, Cold Spring Harbor symposia on quantitative biology.

[93]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[94]  C. Dang,et al.  Therapeutic targeting of Myc-reprogrammed cancer cell metabolism. , 2011, Cold Spring Harbor symposia on quantitative biology.

[95]  Cedric E. Ginestet.  ggplot2: Elegant Graphics for Data Analysis , 2011 .

[96]  Tsung-Cheng Chang,et al.  c-Myc suppression of miR-23 enhances mitochondrial glutaminase and glutamine metabolism , 2009, Nature.