DOCSLIB.ORG

Figure S1 a 24Hpi 48Hpi 72Hpi 96Hpi B 2.0

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Figure S1 a 24Hpi 48Hpi 72Hpi 96Hpi B 2.0 B A SRA_A427 SRA_Caco2 SRA_Calu3 SRA_Detroit562 SRA_H1299 SRA_H522 SRA_H596 SRA_HCC827 SRA_KYSE30 ACE2 SRA_OE21 SRA_PC9 SRA_SCC25 SRA_Vero E6 UNC_H522 UNC_A427 SRA_H522 UNC_Detroit562 UNC_A427 UNC_H1299 UNC_H522 SRA_A427 UNC_H596 UNC_H1299 UNC_HCC827 UNC_KYSE30 SRA_H1299 UNC_OE21 WashU_Vero E6 UNC_PC9 SRA_Vero E6 UNC_SCC25 WashU_Vero E6 UNC_KYSE30 SRA_KYSE30 SRA_PC9 UNC_PC9 UNC_HCC827 SRA_A427 SRA_Caco2 SRA_HCC827 SRA_Calu3 SRA_Caco2 SRA_Detroit562 SRA_H1299 SRA_Calu3 SRA_H522 UNC_H596 SRA_H596 SRA_H596 SRA_HCC827 GAPDH ACTB SRA_KYSE30 SRA_Detroit562 SRA_OE21 UNC_Detroit562 SRA_PC9 SRA_SCC25 UNC_OE21 SRA_Vero E6 SRA_OE21 UNC_A427 UNC_Detroit562 UNC_SCC25 UNC_H1299 SRA_SCC25 UNC_H522 UNC_H596 UNC_HCC827 UNC_KYSE30 UNC_OE21 UNC_PC9 UNC_SCC25 WashU_Vero E6 SRA_A427 SRA_Caco2 SRA_Calu3 SRA_Detroit562 SRA_H1299 SRA_H522 SRA_H596 SRA_HCC827 SRA_KYSE30 SRA_OE21 SRA_PC9 SRA_SCC25 SRA_Vero E6 UNC_A427 Figure S1 Figure UNC_Detroit562 UNC_H1299 UNC_H522 UNC_H596 UNC_HCC827 UNC_KYSE30 UNC_OE21 UNC_PC9 UNC_SCC25 WashU_Vero E6 A 24hpi 48hpi 72hpi 96hpi B 2.0 1.5 MOI=0.015 1.0 vRNA punctae/cell vRNA 0.5 0.0 0.015 0.06 0.25 1 MOI=0.06 MOI MOI=0.25 MOI=1 100M Figure S2 A ACE2 CRISPR KO Polyclonal Populations H522 H522 H522 Calu-3 ACE2 ACE2 ACE2 ACE2 WT-1 WT-2 KO KO -+-+ -+-+Detection Enzyme 500 bp - Parental band 300 bp - 200 bp - Cleaved bands 44% 51% Cleavage Efficiency B ACE2 CRISPR KO Monoclonal Populations cut site ACE2 sgRNA Ref: 5’-AACTTTTCCAGTACTGTAGATGGTGCTCATTGT ACE2+/+ MC: 5’-AACTTTTCCAGTACTGTAGATGGTGCTCATTGT ACE2-/- MC-1: 5’-AACTTTTCC-----TGTAGATGGTGCTCATTGT ACE2-/- MC-2: 5’-AACTTTTCCAGTA-----GATGGTGCTCATTGT ACE2+/- MC: 5’-AACTTTTCCAGTACTGTAGATGGTGCTCATTGT Figure S3 Bafilomycin A SGC-AAK1-1 E64D Apilimod Camostat mesylate 10uM 5uM 5uM 0.1uM 50uM *** 150 150 150 150 300 250 100 100 100 100 200 * 150 50 50 ** 50 50 100 ** * ** 50 0 0 0 0 0 RNA copies relative to DMSO (%) H522 H522 H522 H522 H522 ACE2 ACE2 ero E6 ACE2 ero E6 ACE2 ACE2 Vero E6 − Vero E6 − V − V − Vero E6 − H522 H522 H522 H522 H522 Figure S4 ECT2-KIF23-RACGAP1 complex p27-cyclinE-CDK2 complex CDC2-CCNA2-CDK2 complex RasGAP-AURKA-survivin complex actomyosin contractile ring assembly G1/S transition of mitotic cell cycle cell cycle mitotic cell cycle spindle midzone G-protein coupled receptor signaling pathway KIF23 CCNE1 CDK1 RASA1 RACGAP1 CDKN1B CDK2 BIRC5 CCNA2 AURKA ECT2 CDK2 AuroraB-AuroraC-INCENP complex RasGAP-AURKB-survivin complex BRIC5-AURKB-INCEN-EVI5 complex CRM1-Survivin-AuroraB mitotic complex protein folding and stabilization mitotic cell cycle cytokinesis mitotic cell cycle G-protein coupled receptor signaling pathway barrier septum assembly nuclear transport AURKB RASA1 INCENP AURKB INCENP AURKB BIRC5 AURKB BIRC5 AURKA BIRC5 EVI5 XPO1 Chromosomal passenger complex BRCA1-IRIS-pre-replication complex MIS18 complex GINS complex mitotic cell cycle DNA replication centromere complex assembly Pre-replicative complex assembly spindle assembly regulation of CENP-A containing nucleosome assembly GINS2 AURKB GMNN MIS18BP1 OIP5 GINS4 CDCA8 BRCA1 INCENP ORC1 GINS3 BIRC5 CDC6 MIS18A GINS1 Chromatin assembly complex (CAF-1) BRD7-EZH2-SUZ12 complex BRCC complex KNL1-MIS12-NDC80-SPC24-ZWINT complex DNA replication DNA repair mitotic cell cycle checkpoint mitotic S phase BRD7 cell cycle checkpoint chromosome organization EZH2 protein ubiquitination SPC24 NDC80 CHAF1A BRCA2 CHAF1B BRCA1 KNL1 SUZ12 BRCC3 ZWINT RAD51 MIS12 RBBP4 BABAM2 BARD1-BRCA1-CSTF64 complex NDC80 kinetochore complex E3 ubiquitin ligase - UbcH5c complex BRCA1 B complex RNA 3'-end processing mitotic cell cycle protein ubiquitination DNA recombination chromosome segregation DNA damage response CSTF2 BARD1 NDC80 UBE2D3 BACH1 BARD1 BARD1 NUF2 SPC24 BRCA1 SPC25 BRCA1 BRCA1 BRCA1-BARD1-POLR2A complex BRAC1-BARD1-UbcH7c complex APP-APBB1-LRP1 complex Interferon-stimulated gene factor regulation of RNA biosynthetic process DNA damage response protein processing (proteolytic) transcription complex 3 regulation of transcription UBE2L3 APBB1 STAT2 POLR2A BARD1 BARD1 LRP1 IRF9 ORF7b BRCA1 STAT1 BRCA1 APP DTX3L-PARP9-STAT1 complex Defense response to viruses SARS-CoV-2 protein Protein ubiquitination Non-differentially expressed PARP9 DTX3L Undetected Figure S5 STAT1 siRNA knockdown efficiency RIG−I MDA5 LGP−2 MAVS 1.0 1.0 1.0 1.0 0.8 0.8 0.8 0.8 0.6 0.6 0.6 0.6 0.4 0.4 0.4 0.4 0.2 0.2 0.2 0.2 0 0 0 0 24 96 120 24 96 120 24 96 120 24 96 120 TLR3 TLR7 TLR9 TRIF MyD88 1.0 1.0 1.0 1.0 1.0 0.8 0.8 0.8 0.8 0.8 Relative copies (siRNA / siNT) * * * 0.6 ND x2 ND x2 0.6 ND x1 0.6 0.6 0.6 0.4 0.4 0.4 0.4 0.4 0.2 0.2 0.2 0.2 0.2 0 0 0 0 0 24 96 120 24 96 120 24 96 120 24 96 120 24 96 120 Hours post−infection Figure S6.
Load more

Recommended publications
  • Symplekin and Transforming Acidic Coiled-Coil Containing Protein 3 Support the Cancer Cell Mitotic Spindle
    SYMPLEKIN AND TRANSFORMING ACIDIC COILED-COIL CONTAINING PROTEIN 3 SUPPORT THE CANCER CELL MITOTIC SPINDLE Kathryn M. Cappell A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctorate of Philosophy in the Department of Pharmacology, School of Medicine. Chapel Hill 2011 Approved by: Advisor: Dr. Angelique Whitehurst Reader: Dr. David Siderovski Reader: Dr. Channing Der Reader: Dr. Pilar Blancafort Reader: Dr. Mohanish Deshmukh ABSTRACT KATHRYN CAPPELL: Symplekin and Transforming Acidic Coiled-Coil Containing Protein 3 Support the Cancer Cell Mitotic Spindle (Under the direction of Dr. Angelique Whitehurst) An increased rate of proliferation in cancer cells, combined with abnormalities in spindle architecture, places tumors under increased mitotic stress. Previously, our laboratory performed a genome-wide paclitaxel chemosensitizer screen to identify genes whose depletion sensitizes non- small cell lung cancer (NSCLC) cells to mitotic stress induced by paclitaxel treatment. This screen uncovered a cohort of genes that are required for viability only in the presence of paclitaxel. Two genes uncovered in this screen were the polyadenylation scaffold symplekin and the gametogenic protein transforming acidic coiled-coil containing protein 3 (TACC3). Herein, we examine the impact of polyadenylation and gametogenesis on the tumor cell mitotic spindle. First, we demonstrate that depletion of SYMPK and other polyadenylation components sensitizes many NSCLC cells, but not normal immortalized lines, to paclitaxel by inducing mitotic errors and leading to abnormal mitotic progression. Second, we demonstrate that multiple gametogenic genes are required for normal microtubule dynamics and mitotic spindle formation in the presence of paclitaxel.
    [Show full text]
  • Anti-CSTF2 / Cstf 64 Antibody (ARG58549)
    Product datasheet [email protected] ARG58549 Package: 50 μl anti-CSTF2 / CstF 64 antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes CSTF2 / CstF 64 Tested Reactivity Hu Predict Reactivity Ms, Rat, Cow, Dog, Gpig, Hrs, Rb Tested Application IHC-P, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name CSTF2 / CstF 64 Antigen Species Human Immunogen Synthetic peptide around the N-terminal region of Human CSTF2 / CstF 64. (within the following sequence: VDPEIALKILHRQTNIPTLIAGNPQPVHGAGPGSGSNVSMNQQNPQAPQA) Conjugation Un-conjugated Alternate Names CstF-64; CF-1 64 kDa subunit; Cleavage stimulation factor 64 kDa subunit; CSTF 64 kDa subunit; Cleavage stimulation factor subunit 2 Application Instructions Predict Reactivity Note Predicted homology based on immunogen sequence: Cow: 85%; Dog: 85%; Guinea Pig: 86%; Horse: 86%; Mouse: 86%; Rabbit: 100%; Rat: 93% Application table Application Dilution IHC-P 4 - 8 µg/ml WB 0.2 - 1 µg/ml Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control 293T Calculated Mw 61 kDa Properties Form Liquid Purification Affinity purified. Buffer PBS, 0.09% (w/v) Sodium azide and 2% Sucrose. Preservative 0.09% (w/v) Sodium azide Stabilizer 2% Sucrose www.arigobio.com 1/3 Concentration Batch dependent: 0.5 - 1 mg/ml Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C or below. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening.
    [Show full text]
  • Quantitative SUMO Proteomics Reveals the Modulation of Several
    www.nature.com/scientificreports OPEN Quantitative SUMO proteomics reveals the modulation of several PML nuclear body associated Received: 10 October 2017 Accepted: 28 March 2018 proteins and an anti-senescence Published: xx xx xxxx function of UBC9 Francis P. McManus1, Véronique Bourdeau2, Mariana Acevedo2, Stéphane Lopes-Paciencia2, Lian Mignacca2, Frédéric Lamoliatte1,3, John W. Rojas Pino2, Gerardo Ferbeyre2 & Pierre Thibault1,3 Several regulators of SUMOylation have been previously linked to senescence but most targets of this modifcation in senescent cells remain unidentifed. Using a two-step purifcation of a modifed SUMO3, we profled the SUMO proteome of senescent cells in a site-specifc manner. We identifed 25 SUMO sites on 23 proteins that were signifcantly regulated during senescence. Of note, most of these proteins were PML nuclear body (PML-NB) associated, which correlates with the increased number and size of PML-NBs observed in senescent cells. Interestingly, the sole SUMO E2 enzyme, UBC9, was more SUMOylated during senescence on its Lys-49. Functional studies of a UBC9 mutant at Lys-49 showed a decreased association to PML-NBs and the loss of UBC9’s ability to delay senescence. We thus propose both pro- and anti-senescence functions of protein SUMOylation. Many cellular mechanisms of defense have evolved to reduce the onset of tumors and potential cancer develop- ment. One such mechanism is cellular senescence where cells undergo cell cycle arrest in response to various stressors1,2. Multiple triggers for the onset of senescence have been documented. While replicative senescence is primarily caused in response to telomere shortening3,4, senescence can also be triggered early by a number of exogenous factors including DNA damage, elevated levels of reactive oxygen species (ROS), high cytokine signa- ling, and constitutively-active oncogenes (such as H-RAS-G12V)5,6.
    [Show full text]
  • Mechanisms of Mrna Polyadenylation
    Turkish Journal of Biology Turk J Biol (2016) 40: 529-538 http://journals.tubitak.gov.tr/biology/ © TÜBİTAK Review Article doi:10.3906/biy-1505-94 Mechanisms of mRNA polyadenylation Hızlan Hıncal AĞUŞ, Ayşe Elif ERSON BENSAN* Department of Biology, Arts and Sciences, Middle East Technical University, Ankara, Turkey Received: 26.05.2015 Accepted/Published Online: 21.08.2015 Final Version: 18.05.2016 Abstract: mRNA 3’-end processing involves the addition of a poly(A) tail based on the recognition of the poly(A) signal and subsequent cleavage of the mRNA at the poly(A) site. Alternative polyadenylation (APA) is emerging as a novel mechanism of gene expression regulation in normal and in disease states. APA results from the recognition of less canonical proximal or distal poly(A) signals leading to changes in the 3’ untranslated region (UTR) lengths and even in some cases changes in the coding sequence of the distal part of the transcript. Consequently, RNA-binding proteins and/or microRNAs may differentially bind to shorter or longer isoforms. These changes may eventually alter the stability, localization, and/or translational efficiency of the mRNAs. Overall, the 3’ UTRs are gaining more attention as they possess a significant posttranscriptional regulation potential guided by APA, microRNAs, and RNA-binding proteins. Here we provide an overview of the recent developments in the APA field in connection with cancer as a potential oncogene activator and/or tumor suppressor silencing mechanism. A better understanding of the extent and significance of APA deregulation will pave the way to possible new developments to utilize the APA machinery and its downstream effects in cancer cells for diagnostic and therapeutic applications.
    [Show full text]
  • Related Regulators of 3′ UTR Processing with KAPAC Andreas J
    Gruber et al. Genome Biology (2018) 19:44 https://doi.org/10.1186/s13059-018-1415-3 METHOD Open Access Discovery of physiological and cancer- related regulators of 3′ UTR processing with KAPAC Andreas J. Gruber† , Ralf Schmidt†, Souvik Ghosh, Georges Martin, Andreas R. Gruber, Erik van Nimwegen and Mihaela Zavolan* Abstract 3′ Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on poly(A) site choice. Application of PAQR and KAPAC to RNA sequencing data from normal and tumor tissue samples uncovers motifs that can explain changes in cleavage and polyadenylation in specific cancers. In particular, our analysis points to polypyrimidine tract binding protein 1 as a regulator of poly(A) site choice in glioblastoma. Keywords: Cleavage and polyadenylation, APA, CFIm, KAPAC, PAQR, HNRNPC, PTBP1, Prostate adenocarcinoma, Glioblastoma, Colon adenocarcinoma Background signal, consisting of the CPSF1, CPSF4, FIP1L1, and The 3′ ends of most eukaryotic mRNAs are generated WDR33 proteins, has been identified [6, 7]. through endonucleolytic cleavage and polyadenylation Most genes have multiple poly(A) sites (PAS), which (CPA) [1–3]. These steps are carried out in mammalian are differentially processed across cell types [8], likely cells by a 3′ end processing complex composed of the due to cell type-specific interactions with RNA-binding cleavage and polyadenylation specificity factor (which in- proteins (RBPs). The length of 3′ UTRs is most strongly cludes the proteins CPSF1 (also known as CPSF160), dependent on the mammalian cleavage factor I (CFIm), CPSF2 (CPSF100), CPSF3 (CPSF73), CPSF4 (CPSF30), which promotes the use of distal poly(A) sites [5, 9–12].
    [Show full text]
  • Development and Validation of an RNA Binding Protein- Associated Prognostic Model for Hepatocellular Carcinoma
    Journal of Clinical and Translational Hepatology 2021 DOI: 10.14218/JCTH.2020.00103 Original Article Development and Validation of an RNA Binding Protein- associated Prognostic Model for Hepatocellular Carcinoma Hao Zhang , Peng Xia, Weijie Ma and Yufeng Yuan* Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China Received: 7 November 2020 | Revised: 24 February 2021 | Accepted: 26 March 2021 | Published: 13 April 2021 Abstract ated prognostic model for hepatocellular carcinoma. J Clin Transl Hepatol 2021. doi: 10.14218/JCTH.2020.00103. Background and Aims: The survival rate of patients with hepatocellular carcinoma is variable. The abnormal expres- sion of RNA-binding proteins (RBPs) is closely related to the occurrence and development of malignant tumors. The pri- Introduction mary aim of this study was to identify RBPs related to the prognosis of liver cancer and to construct a prognostic model Worldwide, liver cancer is the fourth leading cause of can- of liver cancer. Methods: We downloaded the hepatocellular cer-related deaths and has the sixth highest incidence.1 carcinoma gene sequencing data from The Cancer Genome It is estimated that 840,000 new cases of liver cancer are Atlas (cancergenome.nih.gov/) database, constructed a diagnosed and at least 780,000 people die of liver cancer protein-protein interaction network, and used Cytoscape to every year, with China accounting for 47% of the total num- realize the visualization. From among 325 abnormally ex- ber of liver cancer cases as well as the related mortality.2,3 pressed genes for RBPs, 9 (XPO5, enhancer of zeste 2 poly- Hepatocellular carcinoma (HCC) is the predominant type of comb repressive complex 2 subunit [EZH2], CSTF2, BRCA1, primary liver cancer, accounting for approximately 90% of RRP12, MRPL54, EIF2AK4, PPARGC1A, and SEPSECS) were all liver cancer cases.4 Although great progress has been selected for construction of the prognostic model.
    [Show full text]
  • Antisense Oligonucleotide-Based Therapeutic Against Menin for Triple-Negative Breast Cancer Treatment
    biomedicines Article Antisense Oligonucleotide-Based Therapeutic against Menin for Triple-Negative Breast Cancer Treatment Dang Tan Nguyen 1,†, Thi Khanh Le 1,2,† , Clément Paris 1,†, Chaïma Cherif 1 , Stéphane Audebert 3 , Sandra Oluchi Udu-Ituma 1,Sébastien Benizri 4 , Philippe Barthélémy 4 , François Bertucci 1, David Taïeb 1,5 and Palma Rocchi 1,* 1 Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, 13273 Marseille, France; [email protected] (D.T.N.); [email protected] (T.K.L.); [email protected] (C.P.); [email protected] (C.C.); [email protected] (S.O.U.-I.); [email protected] (F.B.); [email protected] (D.T.) 2 Department of Life Science, University of Science and Technology of Hanoi (USTH), Hanoi 000084, Vietnam 3 Marseille Protéomique, Centre de Recherche en Cancérologie de Marseille, INSERM, CNRS, Institut Paoli-Calmettes, Aix-Marseille University, 13009 Marseille, France; [email protected] 4 ARNA Laboratory, INSERM U1212, CNRS UMR 5320, University of Bordeaux, 33076 Bordeaux, France; [email protected] (S.B.); [email protected] (P.B.) 5 Biophysics and Nuclear Medicine Department, La Timone University Hospital, European Center for Research in Medical Imaging, Aix-Marseille University, 13005 Marseille, France * Correspondence: [email protected]; Tel.: +33-626-941-287 † These authors contributed equally. Citation: Nguyen, D.T.; Le, T.K.; Paris, C.; Cherif, C.; Audebert, S.; Abstract: The tumor suppressor menin has dual functions, acting either as a tumor suppressor or Oluchi Udu-Ituma, S.; Benizri, S.; as an oncogene/oncoprotein, depending on the oncological context.
    [Show full text]
  • Global Analysis of Chromosome X Gene Expression in Primary Cultures of Normal Ovarian Surface Epithelial Cells and Epithelial Ovarian Cancer Cell Lines
    5-17 6/12/06 18:21 Page 5 INTERNATIONAL JOURNAL OF ONCOLOGY 30: 5-17, 2007 5 Global analysis of chromosome X gene expression in primary cultures of normal ovarian surface epithelial cells and epithelial ovarian cancer cell lines MARIE-HÉLÈNE BENOÎT1, THOMAS J. HUDSON1,2,3, GEORGES MAIRE4, JEREMY A. SQUIRE4,5, SUZANNA L. ARCAND6, DIANE PROVENCHER7,8, ANNE-MARIE-MES-MASSON7,9 and PATRICIA N. TONIN1,3,6 1Department of Human Genetics, McGill University, Montreal, Quebec H3A 1A1; 2McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A 1A4; 3Department of Medicine, McGill University, Montreal, Quebec H3G 1A4; 4Applied Molecular Oncology, The Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Ontario M5G 2M9; 5Departments of Medical Biophysics and Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L5; 6The Research Institute of McGill University Health Center, Montreal, Quebec H3G 1A4; 7Centre de Recherche du Centre Hospitalier de l'Université de Montreal (CR-CHUM)/Institut du cancer de Montréal, Montreal, Quebec H2L 4M1; 8Division de gynécologie et obstétrique, and 9Départément de médicine, Université de Montréal, Montreal, Quebec H3C 3J7, Canada Received June 2, 2006; Accepted August 3, 2006 Abstract. The interpretation of loss of heterozygosity (LOH) and TOV21G. The combined evidence is consistent with two in cancers is complicated as genes that map to LOH regions proposed mechanisms to account for absence of Xi in female may be transcriptionally active (Xa) or inactive (Xi) due to X cancers: Xi loss followed by Xa duplication (exemplified by chromosome inactivation (XCI). We have analyzed the TOV112D) and transcriptional reactivation of Xi (exemplified chromosome X transcriptome in four epithelial ovarian by TOV21G).
    [Show full text]
  • Mechanisms of Deadenylation Regulation Under Different Cellular Conditions
    City University of New York (CUNY) CUNY Academic Works All Dissertations, Theses, and Capstone Projects Dissertations, Theses, and Capstone Projects 2-2014 Mechanisms Of Deadenylation Regulation Under Different Cellular Conditions Xiaokan Zhang Graduate Center, City University of New York How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/gc_etds/135 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] MECHANISMS OF DEADENYLATION REGULATION UNDER DIFFERENT CELLULAR CONDITIONS by XIAOKAN ZHANG A dissertation submitted to the Graduate Faculty in Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy, The City University of New York 2014 ii 2014 XIAOKAN ZHANG All Rights Reserved iii This manuscript has been read and accepted for the Graduate Faculty in Biochemistry in satisfaction of the dissertation requirement for the degree of Doctor of Philosophy. Dr. Frida Kleiman, Hunter College of CUNY ____________ __________________________________________________ Date Chair of Examining Committee Dr. Edward Kennelly, The Graduate Center of CUNY ____________ __________________________________________________ Date Executive Officer Dr. Diego Loayza, Hunter College of CUNY Dr. Kevin Ryan, City College of CUNY Dr. Serafin Piñol-Roma, City College of CUNY Dr Hualin Zhong, Hunter College of CUNY Supervisory Committee THE CITY UNIVERSITY OF NEW YORK iv ABSTRACT Mechanisms of Deadenylation Regulation Under Different Cellular Conditions By Xiaokan Zhang Adviser: Professor Frida Esther Kleiman Control of gene expression by regulating mRNA stability after DNA damage has the potential to contribute to the cells rapid response to stress.
    [Show full text]
  • Alternative Polyadenylation in Triple-Negative Breast Tumors Allows NRAS and C-JUN to Bypass PUMILIO Posttranscriptional Regulation Wayne O
    Published OnlineFirst October 10, 2016; DOI: 10.1158/0008-5472.CAN-16-0844 Cancer Tumor and Stem Cell Biology Research Alternative Polyadenylation in Triple-Negative Breast Tumors Allows NRAS and c-JUN to Bypass PUMILIO Posttranscriptional Regulation Wayne O. Miles1,2, Antonio Lembo3,4, Angela Volorio5, Elena Brachtel5, Bin Tian6, Dennis Sgroi5, Paolo Provero3,4, and Nicholas Dyson1 Abstract Alternative polyadenylation (APA) is a process that changes the targets. mRNA stability and luciferase assays demonstrated APA- posttranscriptional regulation and translation potential of dependent alterations in RNA and protein levels of affected mRNAs via addition or deletion of 30 untranslated region (30 candidate genes. Examination of clinical parameters of these UTR) sequences. To identify posttranscriptional-regulatory events tumors found those with APA of NRAS and c-JUN to be smaller affected by APA in breast tumors, tumor datasets were analyzed and less proliferative, but more invasive than non-APA for recurrent APA events. Motif mapping of the changed 30 UTR tumors. RT-PCR profiling identified elevated levels of poly- regions found that APA-mediated removal of Pumilio regulatory adenylation factor CSTF3 in tumors with APA. Overexpression elements (PRE) was unusually common. Breast tumor subtype– of CSTF3 was common in triple-negative breast cancer cell specific APA profiling identified triple-negative breast tumors as lines, and elevated CSTF3 levels were sufficient to induce APA having the highest levels of APA. To determine the frequency of of NRAS and c-JUN. Our results support the hypothesis that these events, an independent cohort of triple-negative breast PRE-containing mRNAs are disproportionately affected by tumors and normal breast tissue was analyzed for APA.
    [Show full text]
  • A Plant-Like Mechanism Coupling M6a Reading to Polyadenylation
    RESEARCH ARTICLE A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma Dayana C Farhat1, Matthew W Bowler2, Guillaume Communie3, Dominique Pontier4, Lucid Belmudes5, Caroline Mas6, Charlotte Corrao1, Yohann Coute´ 5, Alexandre Bougdour1, Thierry Lagrange4, Mohamed-Ali Hakimi1†*, Christopher Swale1†* 1IAB,Team Host-Pathogen Interactions & Immunity to Infection, INSERMU1209, CNRSUMR5309, Grenoble Alpes University, Grenoble, France; 2European Molecular Biology Laboratory, Grenoble, France; 3Institut Laue-Langevin, Grenoble, France; 4Laboratoire Genome et Developpement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Universitede Perpignan via Domitia (UPVD), Perpignan, France; 5Univ. Grenoble Alpes, INSERM, CEA, UMR BioSante´ U1292, CNRS, CEA, Grenoble, France; 6Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Universite´ Grenoble Alpes, EMBL, Grenoble, France *For correspondence: [email protected] Abstract Correct 3’end processing of mRNAs is one of the regulatory cornerstones of gene (M-AH); expression. In a parasite that must adapt to the regulatory requirements of its multi-host life style, christopher.swale@univ-grenoble- there is a need to adopt additional means to partition the distinct transcriptional signatures of the alpes.fr (CS) closely and tandemly arranged stage-specific genes. In this study, we report our findings in T. †These authors contributed gondii of an m6A-dependent 3’end polyadenylation serving as a transcriptional barrier at these loci. equally to this work We identify the core polyadenylation complex within T. gondii and establish CPSF4 as a reader for Competing interests: The m6A-modified mRNAs, via a YTH domain within its C-terminus, a feature which is shared with authors declare that no plants.
    [Show full text]
  • Autocrine IFN Signaling Inducing Profibrotic Fibroblast Responses By
    Downloaded from http://www.jimmunol.org/ by guest on September 23, 2021 Inducing is online at: average * The Journal of Immunology , 11 of which you can access for free at: 2013; 191:2956-2966; Prepublished online 16 from submission to initial decision 4 weeks from acceptance to publication August 2013; doi: 10.4049/jimmunol.1300376 http://www.jimmunol.org/content/191/6/2956 A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Autocrine IFN Signaling Feng Fang, Kohtaro Ooka, Xiaoyong Sun, Ruchi Shah, Swati Bhattacharyya, Jun Wei and John Varga J Immunol cites 49 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2013/08/20/jimmunol.130037 6.DC1 This article http://www.jimmunol.org/content/191/6/2956.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 23, 2021. The Journal of Immunology A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Inducing Autocrine IFN Signaling Feng Fang,* Kohtaro Ooka,* Xiaoyong Sun,† Ruchi Shah,* Swati Bhattacharyya,* Jun Wei,* and John Varga* Activation of TLR3 by exogenous microbial ligands or endogenous injury-associated ligands leads to production of type I IFN.
    [Show full text]