ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97

[1]  C. Hill,et al.  Active conformation of the p97-p47 unfoldase complex , 2022, Nature Communications.

[2]  S. Carr,et al.  Targeting acute myeloid leukemia dependency on VCP-mediated DNA repair through a selective second-generation small-molecule inhibitor , 2021, Science Translational Medicine.

[3]  Asher Mullard.  Targeted protein degraders crowd into the clinic , 2021, Nature Reviews Drug Discovery.

[4]  E. Oh,et al.  APC/C-dependent control of gene expression and cell identity , 2020, Nature.

[5]  Judith Oehler,et al.  The p97–Ataxin 3 complex regulates homeostasis of the DNA damage response E3 ubiquitin ligase RNF8 , 2019, The EMBO journal.

[6]  J. Bushweller.  Targeting transcription factors in cancer — from undruggable to reality , 2019, Nature Reviews Cancer.

[7]  J. C. Price,et al.  Structure of the Cdc48 segregase in the act of unfolding an authentic substrate , 2019, Science.

[8]  Meng Lei,et al.  Discovery of a new class of valosine containing protein (VCP/P97) inhibitors for the treatment of non-small cell lung cancer. , 2019, Bioorganic & medicinal chemistry.

[9]  R. Maki,et al.  Diagnosis, Prognosis, and Treatment of Alveolar Soft-Part Sarcoma: A Review , 2019, JAMA oncology.

[10]  D. Xia,et al.  Structural Basis of p97 Inhibition by the Site-Selective Anticancer Compound CB-5083 , 2018, Molecular Pharmacology.

[11]  Martin Eisenacher,et al.  The PRIDE database and related tools and resources in 2019: improving support for quantification data , 2018, Nucleic Acids Res..

[12]  M. Ladanyi,et al.  Diagnosis of known sarcoma fusions and novel fusion partners by targeted RNA sequencing with identification of a recurrent ACTB-FOSB fusion in pseudomyogenic hemangioendothelioma , 2018, Modern Pathology.

[13]  X. Teng,et al.  RNA sequencing of Xp11 translocation-associated cancers reveals novel gene fusions and distinctive clinicopathologic correlations , 2018, Modern Pathology.

[14]  Martin J. Aryee,et al.  hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data , 2018, Nature Methods.

[15]  R. Tycko,et al.  Structure of FUS Protein Fibrils and Its Relevance to Self-Assembly and Phase Separation of Low-Complexity Domains , 2017, Cell.

[16]  M. Rivera,et al.  Cancer-Specific Retargeting of BAF Complexes by a Prion-like Domain , 2017, Cell.

[17]  Christopher S. Hughes,et al.  CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion , 2017, Nucleic acids research.

[18]  A. Ballabio,et al.  TFE3 regulates whole‐body energy metabolism in cooperation with TFEB , 2017, EMBO molecular medicine.

[19]  P. Lockhart,et al.  Metalloprotease SPRTN/DVC1 Orchestrates Replication-Coupled DNA-Protein Crosslink Repair , 2016, Molecular cell.

[20]  M. Hirst,et al.  Nucleosome Density ChIP-Seq Identifies Distinct Chromatin Modification Signatures Associated with MNase Accessibility. , 2016, Cell reports.

[21]  M. Selbach,et al.  Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers , 2016, Nature Communications.

[22]  Howard Y. Chang,et al.  HiChIP: efficient and sensitive analysis of protein-directed genome architecture , 2016, Nature Methods.

[23]  Andrew D. Rouillard,et al.  Enrichr: a comprehensive gene set enrichment analysis web server 2016 update , 2016, Nucleic Acids Res..

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

[25]  Daniel J. Anderson,et al.  Discovery of a First-in-Class, Potent, Selective, and Orally Bioavailable Inhibitor of the p97 AAA ATPase (CB-5083). , 2015, Journal of medicinal chemistry.

[26]  Jean-Philippe Vert,et al.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.

[27]  M. Capecchi,et al.  ASPM regulates symmetric stem cell division by tuning Cyclin E ubiquitination , 2015, Nature Communications.

[28]  K. Burke,et al.  Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II. , 2015, Molecular cell.

[29]  Olli S Nevalainen,et al.  Using Peptide-Level Proteomics Data for Detecting Differentially Expressed Proteins. , 2015, Journal of proteome research.

[30]  Krystal M. Straessler,et al.  Modeling alveolar soft part sarcomagenesis in the mouse: a role for lactate in the tumor microenvironment. , 2014, Cancer cell.

[31]  N. Dantuma,et al.  Should I stay or should I go: VCP/p97-mediated chromatin extraction in the DNA damage response. , 2014, Experimental cell research.

[32]  Shawn M. Gillespie,et al.  EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. , 2014, Cancer cell.

[33]  Jeroen Krijgsveld,et al.  Ultrasensitive proteome analysis using paramagnetic bead technology , 2014, Molecular systems biology.

[34]  S. Krause,et al.  The ubiquitin-selective chaperone Cdc48/p97 associates with Ubx3 to modulate monoubiquitylation of histone H2B , 2014, Nucleic acids research.

[35]  D. Corey,et al.  Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading , 2014, Nature Protocols.

[36]  R. Hartmann-Petersen,et al.  Human ASPL/TUG interacts with p97 and complements the proteasome mislocalization of a yeast ubx4 mutant, but not the ER-associated degradation defect , 2014, BMC Cell Biology.

[37]  Lorne Zinman,et al.  Mutations in the Matrin 3 gene cause familial amyotrophic lateral sclerosis , 2014, Nature Neuroscience.

[38]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[39]  Avi Ma'ayan,et al.  Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool , 2013, BMC Bioinformatics.

[40]  C. Leslie,et al.  Combining integrated genomics and functional genomics to dissect the biology of a cancer‐associated, aberrant transcription factor, the ASPSCR1–TFE3 fusion oncoprotein , 2013, The Journal of pathology.

[41]  David A. Orlando,et al.  Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers , 2013, Cell.

[42]  Michael Benatar,et al.  Prion-like domain mutations in hnRNPs cause multisystem proteinopathy and ALS , 2013, Nature.

[43]  S. Scheres.  RELION: Implementation of a Bayesian approach to cryo-EM structure determination , 2012, Journal of structural biology.

[44]  D. Covell,et al.  Bioinformatic Analysis of Patient-Derived ASPS Gene Expressions and ASPL-TFE3 Fusion Transcript Levels Identify Potential Therapeutic Targets , 2012, PloS one.

[45]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[46]  M. Bug,et al.  Emerging functions of the VCP/p97 AAA-ATPase in the ubiquitin system , 2012, Nature Cell Biology.

[47]  C. Orme,et al.  The Ubiquitin Regulatory X (UBX) Domain-containing Protein TUG Regulates the p97 ATPase and Resides at the Endoplasmic Reticulum-Golgi Intermediate Compartment* , 2011, The Journal of Biological Chemistry.

[48]  Shreya Paliwal,et al.  The ubiquitin-selective segregase VCP/p97 orchestrates the response to DNA double-strand breaks , 2011, Nature Cell Biology.

[49]  E. Halperin,et al.  Matrin 3 Binds and Stabilizes mRNA , 2011, PloS one.

[50]  Sonja W. Scholz,et al.  Exome Sequencing Reveals VCP Mutations as a Cause of Familial ALS , 2010, Neuron.

[51]  Joon-Oh Park,et al.  Expression of MET in alveolar soft part sarcoma , 2010, Medical oncology.

[52]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[53]  D. Piwnica-Worms,et al.  Valosin-containing protein (VCP) is required for autophagy and is disrupted in VCP disease , 2009, The Journal of cell biology.

[54]  C. Peterson,et al.  Dignam and Roeder nuclear extract preparation. , 2009, Cold Spring Harbor protocols.

[55]  J. Laney,et al.  A ubiquitin-selective AAA-ATPase mediates transcriptional switching by remodeling a repressor-promoter DNA complex , 2009, Nature Cell Biology.

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

[57]  M. Pericak-Vance,et al.  Mutations in the FUS/TLS Gene on Chromosome 16 Cause Familial Amyotrophic Lateral Sclerosis , 2009, Science.

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

[59]  A. Nagler,et al.  Myofibroblasts in pulmonary and brain metastases of alveolar soft-part sarcoma: a novel target for treatment? , 2008, Neoplasia.

[60]  A. Lazar,et al.  Angiogenesis-Promoting Gene Patterns in Alveolar Soft Part Sarcoma , 2007, Clinical Cancer Research.

[61]  A. Kudlicki,et al.  Valosin-containing protein (p97) is a regulator of endoplasmic reticulum stress and of the degradation of N-end rule and ubiquitin-fusion degradation pathway substrates in mammalian cells. , 2006, Molecular biology of the cell.

[62]  F. Studier,et al.  Protein production by auto-induction in high density shaking cultures. , 2005, Protein expression and purification.

[63]  Y. Kaneko,et al.  Establishment and characterization of a renal cell carcinoma cell line (FU-UR-1) with the reciprocal ASPL-TFE3 fusion transcript. , 2004, Oncology reports.

[64]  H. Lodish,et al.  Functional cloning of TUG as a regulator of GLUT4 glucose transporter trafficking , 2003, Nature.

[65]  M. Ladanyi,et al.  Aberrant Nuclear Immunoreactivity for TFE3 in Neoplasms With TFE3 Gene Fusions: A Sensitive and Specific Immunohistochemical Assay , 2003, The American journal of surgical pathology.

[66]  M. Ladanyi,et al.  Primary renal neoplasms with the ASPL-TFE3 gene fusion of alveolar soft part sarcoma: a distinctive tumor entity previously included among renal cell carcinomas of children and adolescents. , 2001, The American journal of pathology.

[67]  Alfons Meindl,et al.  The der(17)t(X;17)(p11;q25) of human alveolar soft part sarcoma fuses the TFE3 transcription factor gene to ASPL, a novel gene at 17q25 , 2001, Oncogene.

[68]  D. Botstein,et al.  Yeast cell cycle protein CDC48p shows full-length homology to the mammalian protein VCP and is a member of a protein family involved in secretion, peroxisome formation, and gene expression , 1991, The Journal of cell biology.

[69]  K. Chan,et al.  A direct colorimetric assay for Ca2+ -stimulated ATPase activity. , 1986, Analytical biochemistry.

[70]  R. Roeder,et al.  Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. , 1983, Nucleic acids research.

[71]  B. Delabarre,et al.  Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains , 2003, Nature Structural Biology.

[72]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.

[73]  Heng Li,et al.  BIOINFORMATICS ORIGINAL PAPER , 2022 .