DOCSLIB.ORG

Supplemental Material.Pdf

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplemental Material.Pdf Inventory of Supplemental information Supplementary table I related to figure 4. Supplementary figure 1 related to figure 1. Supplementary figure 2 related to figure 2. Supplementary figure 3 related to figure 3. Supplementary figure 4 related to figure 4. Supplementary figure 5 related to figure 4. Supplementary figure 6 related to figure 4. Supplementary figure 7 related to figure 5. Supplementary figure 8 related to figure 6. Supplementary figure 9 related to figure 7. Supplementary figure 10 related to figure 8. Supplementary figure 11 related to discussion. Supplementary experimental procedures. Supplementary table I. Senescence associated phosphoprotein degradation (SAPD) Peptide/ Protein Fold Functions (Phospho SitePlus) AF4 SSSPGKPQAVSSLNSSHSR 3.03 RNA pol II transcription (P(PMIDMID 21574958). Calcium and PKC signaling (PMID: 19497879) TVIRLPSGSGAASPTGSAVDIR (S210-p) 14 Actin cytoskeleton dynamics and pseudopodia AHNAK LKSEDGVEGDLGETQSR (S135-p) formation (PMID: 20388789). AKT1S1 SSDEENGPPSSPDLDR (S212-p) 2.36 AKT/Tor signaling, (PMID: 18372248) IYLEENPEKSETIQDTDTQSLVGSPSTR (S341-p) 1.4 Cell motility and invasion, (PMID: 17575049) ARHGEF12 HLSTPSSVSPEPQDSAK (S637) ARHGAP1 SSSPELVTHLK (S51-p) 1.8 Cdc42 and Rho signaling, (PMID: 16157885) ARHGAP17 SPSPPTQHTGQPPGQPSAPSQLSAPR (S676) 2.3 Rho signaling and cell polarity, (PMID: 16678097) VPPAPVPCPPPSPGPSAVPSSPKSVATEER (S377-p, S386-p) Chaperone in complex with Hsp70, (PMID: BAG3 SSTPLHSPSPIR (T285-p, S291) 9.2 12750378), mediates ERK inactivation by DUSP6, AASPFR (S264) (PMID: 22310281) Bind acetylated histones and stimulate transcription KADTTTPTPTAILAPGSPASPPGSLEPK (S298-p) * BRD2 (PMID: 18406326) CALD1 RGSIGENQGEEK (S202-p) 1.9 Cell migration and lamellipodia (PMID:16800003) Genomic stability, (PMID: 22363533). ERK target at ILQEKLDQPVSAPPSPR (S240-p, S244-p) 2.9 CCDC6 S244) (PMID: 14712216) ALVEFESNPEETREPGSPPSVQR (S47-p) RLGGLRPESPESLTSVSR (S18-p) 6.2 Nucleolar protein with coiled coil domain, (PMID: CCDC86 AGLGSPERPPK (S58-p) 17300783) LVINSGNGAVEDR (S686-p) LVINSGNGAVEDRKPSGLNGEASK (S697-p) Cell migration and lamellipodia component PMID: CD44 LVINSGNGAVEDRKPSGLNGEASK (S704-p) 9 12145196 KPSGLNGEASKSQEMVHLVNK (S706-p) KPSGLNGEASKSQEMVHLVNK (S697-p, S706-p) Cytoskeletal protein, cell motility, (PMID: Cortactin TQTPPVSPAPQPTEERLPSSPVYEDAASFK (T401-p, S405-p) 4.4 18406052), ERK1/2 target (S405), lamellipodia and N-WASP regulator, (PMID: 21079800) CYBRD1 NLALDEAGQRSTM (T285-p) 3.0 Iron metabolism (PMID: 18194661). LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK (S171-p) 12.3 Nucleolar RNA helicase, pre-rRNA processing, DDX21 VTKNEEPSEEEIDAPKPK (S121-p) (PMID: 19106111) SPGKAEAESDALPDDTVIESEALPSDIAAEAR (S287-p) 13.0 RNA helicase DDX24 AQAVSEEEEEEEGK (S82-p) DDX42 YMAENPTAGVVQEEEEDNLEYDSDGNPIAPTKK (S185-p) 1.7 RNA helicase Nucleolar component. Ribosomal RNA maturation, RVNDAEPGSPEAPQGK (S83-p) 2.6 DDX51 (PMID: 20404093) MHLPSPTDSNFYR (S991-p), EGFR GSHQISLDNPDYQQDFFPK (S1166-p) 10 Growth factor signaling GSHQISLDNPDYQQDFFPK (S1162-p) EIF3G GIPLATGDTSPEPELLPGAPLPPPKEVINGNIK (S42-p) 3.9 Translation initiation, (PMID: 17094969) TEPAAEAEAASGPSESPSPPAAEELPGSHAEPPVPAQGEAPGE QARDER (S85-p) 10 Translation initiation EIF3B TEPAAEAEAASGPSESPSPPAAEELPGSHAEPPVPAQGEAPGE QARDER (S81-p) SFSKEVEER (S1185-p), SFSKEVEER (S1187-p) EAALPPVSPLK 2.4 Protein synthesis (PMID: 9418880). EIF4G1 (S1231-p) EIF4G2 TQTPPLGQTPQLGLK (T506-p) 1.3 Protein synthesis Signaling and cell motility, S910 is phosphorylated FAK/PTK2 LQPQEISPPPTANLDR (S910-p) 2.3 by ERK, (PMID: 12692126), pseudopodia protein (PMID: 15985431) KMEESDEEAVQAK (S692-p) 9.5 Histone demethylase of K36H3, knockdown induces FBXL11 SCDEPLTPPPHSPTSMLQLIHDPVSPR (T713-p, S718-p) senescence (PMID: 18836456) Actin binding protein, RalA effector to induce LVSPGSANETSSILVESVTR (S-2478-p) 12 FLNB filopodia, (PMID: 10051605) hnRNA-binding protein, Ras and NF-kB signaling NLEELEEKSTTPPPAEPVSLPQEPPKPR (T227-p) 12 G3BP2 (PMID: 10969074) Nuclear protein, Methyl lysine histone binding ARGDSEALDEES (S664-p) 1.7 HDGF2 (PMID: 19162039) Stabilizes proteins against aggregation during cellular stress and mediate the folding of newly GGSGSGPTIEEVD (S631-p) 14.8 HSPA1A translated polypeptides (PMID: 21874533). Controls OIS (PMID: 19001088). Involved in stress resistance, actin organization AQLGGPEAAKSDETAAK (S199-p) (PMID: 19593530) and mitochondrial quality control QLSSGVSEIR (S82-p) 48.2 HSPB1 (PMID: 21641551). Phosphorylated by MAPKAP GPSWDPFRDWYPHSR (S15-p) kinase 2 at S15 and S82, (PMID: 1332886) Involved in translational control, mRNA localization QGSPVAAGAPAK (S181-p) 1.5 IGF2BP1 and cell migration (PMID: 22279049 RNA binding protein, nucleolar protein, CDK2 target DSSKGEDSAEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAE at S382) (PMID: 18847512), regulates DNA damage QGPILTK (S482-p) 2.3 ILF3/NF90 repair and non-homologous end joining, (PMID: RPMEEDGEEKSPSK (S382-p) 21969602) Involved in the transport of phosphorylated LVSFHDDSDEDLLHI (S2484-p) lysosomal enzymes from the Golgi and the cell IGF2R/M6PR 2.6 TVSSTKLVSFHDDSDEDLLHI (S2484-p) surface to lysosomes (PMID: 20615935, 11058096, 2541923). Transcriptional repressor of IRF-2, (PMID: RKPSPEPEGEVGPPK (S360-p) IRF2BP2 12799427) Involved in cell adhesion to collagens, modulation of collagen and collagenase gene expression. It ITGA2 NPDEIDETTELSS (S1180-p) 1.7 regulates generation and organization of newly synthesized extracellular matrix (PMID: 2545729). JUN LASPELER (S73-p) 25 Transcription factor (PMID: 20132737). JunB SRDATPPVSPINMEDQER (T255-p) 1.4 Transcription factor (PMID: 20132737). Heterochromatin and gene repression (PMID: SRSGEGEVSGLMR (S473-p) 7 KAP1 STAPSAAASASASAAASSPAGGGAEALELLEHCGVCR (S50-p) 8769649). ETPHSPGVEDAPIAK (S490-p) Cystoskeletal protein, ERK target at S360, cell SEVQQPVHPKPLSPDSR (S362-p) 5 LIMA1/EPLIN motility, (PMID: 17875928) ASSLSESSPPK (S374-p) Nucleocytoplasmic shuttling protein (PMID: LMO7 ATLSSTSGLDLMSESGEGEISPQREVSR (S1026-p) 15 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK (T990-p, S991-p) 17067998), cell migration, (PMID: 21670154) EVAATEEDVTRLPSPTSPFSSLSQDQAATSK (S988) SHSPSASQSGSQLR (S1593-p) LRWD1 ANSPEKPPEAGAAHKPR (S212-p) * Origin of replication, (PMID: 20932478) CLSPDDSTVK (S986-p) MASPPPSGPPSATHTPFHQSPVEEKSEPQDFQEADSWGDTK (S1013-p) WPEVSPEDTQSLSLSEESPSKETSLDVSSK (S1203-p) QLSPESLGTLQFGELNLGK (S1218-p) YLPGAITSPDEHILTPDSSFSK (S1311-p) WLAESPVGLPPEEEDKLTR (S1776-p) Structural protein that interacts with MAPK (PMID: 14 MAP1A SPFEIISPPASPPEMVGQR (S1797-p, S1801-p) 20936779). SPFEIISPPASPPEMVGQRVPSAPGQESPIPDPK (S1801-p) VPSAPGQESPIPDPK (S1818) NTSAEKELSSPISPK (S2019-p, S2022-p) GELSPSFLNPPLPPSIDDR (S2449-p) SPTPGKGPADR (S2629-p) DVMSDETNNEETESPSQEFVNITK (S1154-p) SPSLSPSPPSPLEK (S1262-p) SPSLSPSPPSPLEK (S1265-p) VSAEAEVAPVSPEVTQEVVEEHCASPEDK (S1298-p) ASVSPMDEPVPDSESPIEK (S1378-p, S1389-p) GAESPFEEKSGK (S1427) MAP1B QGSPDQVSPVSEMTSTSLYQDKQEGK (S1438-p, S1443-p) 6 Cytoskeleton (PMID: 17292797) KLGDVSPTQIDVSQFGSFK (S1501) VQSLEGEKLSPK (S1779-p) SDISPLTPR (S185) ESSPLYSPTFSDSTSAVKEK (S1793-p) ESSPLYSPTFSDSTSAVKEK (S1797-p) TATCHSSSSPPIDAASAEPYGFR (S1819-p) DMESPTKLDVTLAK (S280-p) DMESPTKLDVTLAK (T282-p) DMSPLSETEMALGKDVTPPPETEVVLIK (S507-p) DMSPLSETEMALGKDVTPPPETEVVLIK (S510-p) 29 Microtubules dynamics, (PMID:15840946) MAP4 DVTPPPETEVVLIK (T521-p) GISEDSHLESLQDVGQSAAPTFMISPETITGTGKK (S624-p) KCSLPAEEDSVLEK (S636-p) RASPSKPASAPASR (S793-p, S797-p) VGSTENIKHQPGGGR (S941-p) AAATPESQEPQAK (T148-p) 15 PKC signaling MARCKSL1 GDVTAEEAAGASPAKANGQENGHVK (S22-p) RVASGPSPGEGISPQSAQAPQAPGDNHVVPVLR (S873-p) MVP RVASGPSPGEGISPQSAQAPQAPGDNHVVPVLR (S867-p, S876- 3 Vault ribonucleoproteins p) TLLEAENSRLQTPGGGSK (T315-p) QEASTGQSPEDHASLAPPLSPDHSSLEAK (S471-p) Nestin 19 Cancer Stem cell marker (PMID: 20429619) TPTLASTPIPPTPQAPSPAVDAEIR (S398-p) ENQEPLRSPEVGDEEALRPLTK (S680-p) WEDTVEKDQELAQESPPGMAGVENEDEAELNLR (S965-p) EAARSPDKPGGSPSASR (S49-p) 10 Nucleolar protein, p53 inhibitor, (PMID: 16322561) NOC2L EAARSPDKPGGSPSASR (S49-p, S56-p) NOLC1 GGSISVQVNSIKFDSE (S698-p) 28 Pol1 coactivator, nucleologenesis (PMID: 7657714) NOL6/NRAP GQSPAGDGSPEPPTPR (S283-p) 7.5 Nucleolar protein (PMID: 11895476) Nucleolar protein, 60S biogenesis, (PMID: HIKEEPLSEEEPCTSTAIASPEK (S502-p) 23 NOP5 11583964) Nucleolar protein, 60S biogenesis, snoRNP FSKEEPVSSGPEEAVGK (S570-p) 21 NOP56 biogenesis, (PMID: 19620283) VVVSPTKK (S67-p) 20 Nucleolar protein and pol I cofactor, (PMID: Nucleolin LELQGPRGSPNAR (S563-p) 17130237), p53 inhibitor, (PMID: 22013067) NUP188 GAPSSPATGVLPSPQGK (S1708-p, S1717-p) 1.5 Nuclear pore, (PMID: 20566687) ODZ2 SLMYWMTVQYDSMGRVIK (S2181) 54 Tenascin family PDLIM4 IHIDPEIQDGSPTTSR (S112-p) 22 Cytoskeletal protein. Competes with other PH domain-containing proteins TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPRTP (S144-p) 9.6 to prevent their binding to membrane lipids (PMID: PHLDA2 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPRTP (T160-p) 9403053). VADAKGDSESEEDEDLEVPVPSR (S78-p, S80-p) 11 Regulatory subunit of cAMP-regulated kinase PRKAR2A RVSVCAETYNPDEEEEDTDPR (S99-p) KEESEESDDDMGFGLFD (S104-p) 3.4 Structural component of ribosome (PMID: RPLP1 KEESEESDDDMGFGLFD (S101-p) 54.7 16572171), bypass senescence (PMID: 19233166). Ribosomal protein RPL23 IRTSPTFR (S43-p) 35 Actin cytoskeleton dynamics and pseudopodia formation (PMID: 20388789). RRBP1 SHVEDGDIAGAPASSPEAPPAEQDPVQLK (S1277-p) 6 Binding of ribosomes to the ER, (PMID: 22156060) Nucleolar protein. Inhibits PTEN and p27 and is RSL1D1 (CSIG) downregulated in replicative senescence (PMID: ATNESEDEIPQLVPIGK (S361-p) 2.4 IPI00642046 18678645). Regulates nucleostemin localization (PMID: 17158916). SCAMP2
Load more

Recommended publications
  • The N-Cadherin Interactome in Primary Cardiomyocytes As Defined Using Quantitative Proximity Proteomics Yang Li1,*, Chelsea D
    © 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs221606. doi:10.1242/jcs.221606 TOOLS AND RESOURCES The N-cadherin interactome in primary cardiomyocytes as defined using quantitative proximity proteomics Yang Li1,*, Chelsea D. Merkel1,*, Xuemei Zeng2, Jonathon A. Heier1, Pamela S. Cantrell2, Mai Sun2, Donna B. Stolz1, Simon C. Watkins1, Nathan A. Yates1,2,3 and Adam V. Kwiatkowski1,‡ ABSTRACT requires multiple adhesion, cytoskeletal and signaling proteins, The junctional complexes that couple cardiomyocytes must transmit and mutations in these proteins can cause cardiomyopathies (Ehler, the mechanical forces of contraction while maintaining adhesive 2018). However, the molecular composition of ICD junctional homeostasis. The adherens junction (AJ) connects the actomyosin complexes remains poorly defined. – networks of neighboring cardiomyocytes and is required for proper The core of the AJ is the cadherin catenin complex (Halbleib and heart function. Yet little is known about the molecular composition of the Nelson, 2006; Ratheesh and Yap, 2012). Classical cadherins are cardiomyocyte AJ or how it is organized to function under mechanical single-pass transmembrane proteins with an extracellular domain that load. Here, we define the architecture, dynamics and proteome of mediates calcium-dependent homotypic interactions. The adhesive the cardiomyocyte AJ. Mouse neonatal cardiomyocytes assemble properties of classical cadherins are driven by the recruitment of stable AJs along intercellular contacts with organizational and cytosolic catenin proteins to the cadherin tail, with p120-catenin β structural hallmarks similar to mature contacts. We combine (CTNND1) binding to the juxta-membrane domain and -catenin β quantitative mass spectrometry with proximity labeling to identify the (CTNNB1) binding to the distal part of the tail.
    [Show full text]
  • Ahnaks Are a Class of Giant Propeller-Like Proteins That Associate with Calcium Channel Proteins of Cardiomyocytes and Other Cells
    The AHNAKs are a class of giant propeller-like proteins that associate with calcium channel proteins of cardiomyocytes and other cells Akihiko Komuro*, Yutaka Masuda*, Koichi Kobayashi, Roger Babbitt, Murat Gunel, Richard A. Flavell, and Vincent T. Marchesi† Departments of Pathology and Immunobiology, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, CT 06510 Contributed by Vincent T. Marchesi, December 31, 2003 To explore the function of the giant AHNAK molecule, first de- mechanisms, one operating at the cell surface in collaboration with scribed in 1992 [Shtivelman, E., Cohen, F. E. & Bishop, J. M. (1992) calcium channels, and the second, PLC activation, which is a process Proc. Natl. Acad. Sci. USA 89, 5472–5476], we created AHNAK null that could potentially take place at multiple points throughout the mice by homologous recombination. Homozygous knockouts cell. showed no obvious phenotype, but revealed instead a second The arrangement of channel proteins at the cell surface is AHNAK-like molecule, provisionally designated AHNAK2. Like the believed to be controlled by multidomain polypeptides known as original AHNAK, AHNAK2 is a 600-kDa protein composed of a large scaffolding proteins that link together activated channels at specific number of highly conserved repeat segments. Structural predic- points on the membrane surface. Scaffolding proteins also coordi- tions suggest that the repeat segments of both AHNAKs may have nate the activities of multienzyme complexes by physically linking as their basic framework a series of linked, antiparallel ␤-strands them together, and as in the case with AHNAK, they are often similar to those found in ␤-propeller proteins.
    [Show full text]
  • Overexpression of RNF38 Facilitates TGF-Β Signaling by Ubiquitinating
    Peng et al. Journal of Experimental & Clinical Cancer Research (2019) 38:113 https://doi.org/10.1186/s13046-019-1113-3 RESEARCH Open Access Overexpression of RNF38 facilitates TGF-β signaling by Ubiquitinating and degrading AHNAK in hepatocellular carcinoma Rui Peng1,2†, Peng-Fei Zhang1,3†, Xuan Yang1†, Chuan-Yuan Wei1†, Xiao-Yong Huang1, Jia-Bin Cai1, Jia-Cheng Lu1, Chao Gao1, Hai-Xiang Sun1, Qiang Gao1, Dou-Sheng Bai2, Guo-Ming Shi1*, Ai-Wu Ke1* and Jia Fan1,4* Abstract Background: RING finger protein 38 (RNF38), a member of the RNF protein family, has just emerged as a vital driver of cancer progression. However, the oncogenic mechanisms of RNF38 remain unexplored. Methods: Using frozen tumor tissue and tissue microarray from hepatocellular carcinoma (HCC) patients, we tried to probe the expression of RNF38 in HCC and its clinical value. Then the biological functions of RNF38 were analyzed in vivo and vitro. Stable isotope labeling with amino acids (SILAC) in cell culture and co-immunoprecipitation proteomic analyses were combined to reveal the potential mechanism of RNF38 in HCC progression. Results: We report that RNF38 expression was markedly higher in HCC tissues than in peritumor tissues. Correspondingly, RNF38 overexpression promoted the HCC cell migration and invasion and inhibited apoptosis both in vitro and in vivo. And elevated RNF38 expression induced HCC cell epithelial-mesenchymal transition by facilitating transforming growth factor-β (TGF-β) signaling via ubiquitinating and degrading neuroblast differentiation-associated protein (AHNAK), a well-established inhibitor of TGF-β signaling. Furthermore, AHNAK interference restored the HCC cell invasion and metastasis deprived by RNF38 downregulation.
    [Show full text]
  • CD29 Identifies IFN-Γ–Producing Human CD8+ T Cells with an Increased Cytotoxic Potential
    + CD29 identifies IFN-γ–producing human CD8 T cells with an increased cytotoxic potential Benoît P. Nicoleta,b, Aurélie Guislaina,b, Floris P. J. van Alphenc, Raquel Gomez-Eerlandd, Ton N. M. Schumacherd, Maartje van den Biggelaarc,e, and Monika C. Wolkersa,b,1 aDepartment of Hematopoiesis, Sanquin Research, 1066 CX Amsterdam, The Netherlands; bLandsteiner Laboratory, Oncode Institute, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; cDepartment of Research Facilities, Sanquin Research, 1066 CX Amsterdam, The Netherlands; dDivision of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; and eDepartment of Molecular and Cellular Haemostasis, Sanquin Research, 1066 CX Amsterdam, The Netherlands Edited by Anjana Rao, La Jolla Institute for Allergy and Immunology, La Jolla, CA, and approved February 12, 2020 (received for review August 12, 2019) Cytotoxic CD8+ T cells can effectively kill target cells by producing therefore developed a protocol that allowed for efficient iso- cytokines, chemokines, and granzymes. Expression of these effector lation of RNA and protein from fluorescence-activated cell molecules is however highly divergent, and tools that identify and sorting (FACS)-sorted fixed T cells after intracellular cytokine + preselect CD8 T cells with a cytotoxic expression profile are lacking. staining. With this top-down approach, we performed an un- + Human CD8 T cells can be divided into IFN-γ– and IL-2–producing biased RNA-sequencing (RNA-seq) and mass spectrometry cells. Unbiased transcriptomics and proteomics analysis on cytokine- γ– – + + (MS) analyses on IFN- and IL-2 producing primary human producing fixed CD8 T cells revealed that IL-2 cells produce helper + + + CD8 Tcells.
    [Show full text]
  • A Genome-Wide Association Study of Idiopathic Dilated Cardiomyopathy in African Americans
    Journal of Personalized Medicine Article A Genome-Wide Association Study of Idiopathic Dilated Cardiomyopathy in African Americans Huichun Xu 1,* ID , Gerald W. Dorn II 2, Amol Shetty 3, Ankita Parihar 1, Tushar Dave 1, Shawn W. Robinson 4, Stephen S. Gottlieb 4 ID , Mark P. Donahue 5, Gordon F. Tomaselli 6, William E. Kraus 5,7 ID , Braxton D. Mitchell 1,8 and Stephen B. Liggett 9,* 1 Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA; [email protected] (A.P.); [email protected] (T.D.); [email protected] (B.D.M.) 2 Center for Pharmacogenomics, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; [email protected] 3 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; [email protected] 4 Division of Cardiovascular Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA; [email protected] (S.W.R.); [email protected] (S.S.G.) 5 Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27708, USA; [email protected] (M.P.D.); [email protected] (W.E.K.) 6 Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD 21218, USA; [email protected] 7 Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA 8 Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration
    [Show full text]
  • Global Analysis of O-Glcnac Glycoproteins in Activated Human T Cells Peder J
    Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells Peder J. Lund, Joshua E. Elias and Mark M. Davis This information is current as J Immunol 2016; 197:3086-3098; Prepublished online 21 of October 2, 2021. September 2016; doi: 10.4049/jimmunol.1502031 http://www.jimmunol.org/content/197/8/3086 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2016/09/20/jimmunol.150203 Material 1.DCSupplemental References This article cites 89 articles, 32 of which you can access for free at: http://www.jimmunol.org/content/197/8/3086.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on October 2, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Author Choice Freely available online through The Journal of Immunology Author Choice option Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells Peder J.
    [Show full text]
  • Building the Vertebrate Codex Using the Gene Breaking Protein Trap Library
    TOOLS AND RESOURCES Building the vertebrate codex using the gene breaking protein trap library Noriko Ichino1, MaKayla R Serres1, Rhianna M Urban1, Mark D Urban1, Anthony J Treichel1, Kyle J Schaefbauer1, Lauren E Greif1, Gaurav K Varshney2,3, Kimberly J Skuster1, Melissa S McNulty1, Camden L Daby1, Ying Wang4, Hsin-kai Liao4, Suzan El-Rass5, Yonghe Ding1,6, Weibin Liu1,6, Jennifer L Anderson7, Mark D Wishman1, Ankit Sabharwal1, Lisa A Schimmenti1,8,9, Sridhar Sivasubbu10, Darius Balciunas11, Matthias Hammerschmidt12, Steven Arthur Farber7, Xiao-Yan Wen5, Xiaolei Xu1,6, Maura McGrail4, Jeffrey J Essner4, Shawn M Burgess2, Karl J Clark1*, Stephen C Ekker1* 1Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States; 2Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States; 3Functional & Chemical Genomics Program, Oklahoma Medical Research Foundation, Oklahoma City, United States; 4Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States; 5Zebrafish Centre for Advanced Drug Discovery & Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto & University of Toronto, Toronto, Canada; 6Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States; 7Department of Embryology, Carnegie Institution for Science, Baltimore, United States; 8Department of Clinical Genomics, Mayo Clinic, Rochester, United States; 9Department of Otorhinolaryngology, Mayo Clinic, Rochester, United States; 10Genomics and Molecular Medicine Unit, CSIR– 11 *For correspondence: Institute of Genomics and Integrative Biology, Delhi, India; Department of [email protected] (KJC); Biology, Temple University, Philadelphia, United States; 12Institute of Zoology, [email protected] (SCE) Developmental Biology Unit, University of Cologne, Cologne, Germany Competing interests: The authors declare that no competing interests exist.
    [Show full text]
  • Requirement for AHNAK1-Mediated Calcium Signaling During T Lymphocyte Cytolysis
    Requirement for AHNAK1-mediated calcium signaling during T lymphocyte cytolysis Didi Matzaa, Abdallah Badoua,1, Mithilesh K. Jhaa, Tim Willingera, Andrey Antova, Shomyseh Sanjabia, Koichi S. Kobayashia,2, Vincent T. Marchesib, and Richard A. Flavella,c,3 aDepartment of Immunobiology, bDepartment of Pathology and Boyer Center for Molecular Medicine, and cThe Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510 Contributed by Richard A. Flavell, April 23, 2009 (sent for review January 20, 2009) ؉ ϩ Cytolytic CD8 T cells (CTLs) kill virally infected cells, tumor cells, or Cav1.1 ␣1 subunits mediated by AHNAK1 in peripheral CD4 other potentially autoreactive T cells in a calcium-dependent man- T cells. AHNAK1 is associated with the regulatory ␤2 subunit of ner. To date, the molecular mechanism that leads to calcium intake Cav1 channels and is required for normal expression of the during CTL differentiation and function has remained unresolved. Cav1.1 ␣1 subunit and intact calcium influx following TCR We demonstrate that desmoyokin (AHNAK1) is expressed in ma- cross-linking (11). Here, we demonstrate that CTLs employ -ture CTLs, but not in naive CD8؉ T cells, and is critical for calcium AHNAK1 to mediate calcium entry required for cytolytic ac entry required for their proper function during immune response. tivity late in primary TCR stimulation through the regulation of We show that mature AHNAK1-deficient CTLs exhibit reduced Cav1.1 channels. Cav1.1 ␣1 subunit expression (also referred to as L-type calcium channels or ␣1S pore-forming subunits), which recently were Results suggested to play a role in calcium entry into CD4؉ T cells.
    [Show full text]
  • A Cluster of Noncoding Rnas Activates the ESR1 Locus During Breast Cancer Adaptation
    ARTICLE Received 7 Jan 2015 | Accepted 20 Mar 2015 | Published 29 Apr 2015 DOI: 10.1038/ncomms7966 OPEN A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation Saori Tomita1,2,*, Mohamed Osama Ali Abdalla1,*, Saori Fujiwara1,2, Haruka Matsumori1, Kazumitsu Maehara3, Yasuyuki Ohkawa3, Hirotaka Iwase2, Noriko Saitoh1 & Mitsuyoshi Nakao1,4,5 Estrogen receptor-a (ER)-positive breast cancer cells undergo hormone-independent proliferation after deprivation of oestrogen, leading to endocrine therapy resistance. Up-regulation of the ER gene (ESR1) is critical for this process, but the underlying mechanisms remain unclear. Here we show that the combination of transcriptome and fluorescence in situ hybridization analyses revealed that oestrogen deprivation induced a cluster of noncoding RNAs that defined a large chromatin domain containing the ESR1 locus. We termed these RNAs as Eleanors (ESR1 locus enhancing and activating noncoding RNAs). Eleanors were present in ER-positive breast cancer tissues and localized at the transcriptionally active ESR1 locus to form RNA foci. Depletion of one Eleanor, upstream (u)-Eleanor, impaired cell growth and transcription of intragenic Eleanors and ESR1 mRNA, indicating that Eleanors cis-activate the ESR1 gene. Eleanor-mediated gene activation represents a new type of locus control mechanism and plays an essential role in the adaptation of breast cancer cells. 1 Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan. 2 Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan. 3 Department of Advanced Initiative Medicine, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.
    [Show full text]
  • The Endosome Is a Master Regulator of Plasma Membrane Collagen Fibril Assembly
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.25.436925; this version posted March 25, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The endosome is a master regulator of plasma membrane collagen fibril assembly 1Joan Chang*, 1Adam Pickard, 1Richa Garva, 1Yinhui Lu, 2Donald Gullberg and 1Karl E. Kadler* 1Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medical and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT UK, 2Department of Biomedicine and Center for Cancer Biomarkers, Norwegian Center of Excellence, University of Bergen, Norway. * Co-corresponding authors: JC email: [email protected] (orcid.org/0000-0002-7283- 9759); KEK email: [email protected] (orcid.org/0000-0003-4977-4683) Keywords: collagen-I, endocytosis, extracellular matrix, fibril, fibrillogenesis, integrin-a11, trafficking, VPS33b, [abstract] [149 word max] Collagen fibrils are the principal supporting elements in vertebrate tissues. They account for 25% of total protein mass, exhibit a broad range of size and organisation depending on tissue and stage of development, and can be under circadian clock control. Here we show that the remarkable dynamic pleomorphism of collagen fibrils is underpinned by a mechanism that distinguishes between collagen secretion and initiation of fibril assembly, at the plasma membrane. Collagen fibrillogenesis occurring at the plasma membrane requires vacuolar protein sorting (VPS) 33b (which is under circadian clock control), collagen-binding integrin-a11 subunit, and is reduced when endocytosis is inhibited. Fibroblasts lacking VPS33b secrete soluble collagen without assembling fibrils, whereas constitutive over-expression of VPS33b increases fibril number with loss of fibril rhythmicity.
    [Show full text]
  • Mouse Ahnak Conditional Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Ahnak Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Ahnak conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Ahnak gene (NCBI Reference Sequence: NM_009643 ; Ensembl: ENSMUSG00000069833 ) is located on Mouse chromosome 19. 5 exons are identified, with the ATG start codon in exon 3 and the TAG stop codon in exon 5 (Transcript: ENSMUST00000092956). Exon 4 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Ahnak gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-241A8 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Mice homozygous for one knock-out allele exhibit decreased T cell proliferation and increased susceptibility to parasitic infection. Exon 4 starts from about 0.93% of the coding region. The knockout of Exon 4 will result in frameshift of the gene. The size of intron 3 for 5'-loxP site insertion: 419 bp, and the size of intron 4 for 3'-loxP site insertion: 835 bp. The size of effective cKO region: ~647 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 2 3 4 5 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Ahnak Homology arm cKO region loxP site Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • ANRIL Is Implicated in the Regulation of Nucleus and Potential Transcriptional Target of E2F1
    701-707.qxd 22/7/2010 10:44 Ì ™ÂÏ›‰·701 ONCOLOGY REPORTS 24: 701-707, 2010 701 ANRIL is implicated in the regulation of nucleus and potential transcriptional target of E2F1 KAZUYUKI SATO1, HIROKI NAKAGAWA1, ATSUSHI TAJIMA2, KENICHI YOSHIDA1 and ITURO INOUE2 1Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki; 2Division of Molecular Life Science, School of Medicine, Tokai University, Isehara, Kanagawa, Japan Received April 21, 2010; Accepted June 11, 2010 DOI: 10.3892/or_00000910 Abstract. ANRIL, a large antisense non-coding RNA, is in were shown to act as promoter for ANRIL and p14ARF. the proximity of CDKN2A and overlapped with CDKN2B at Moreover, as well p14ARF, ANRIL promoter was responsive human chromosome 9p21, and has been strongly implicated to transcription factor E2F1 in HeLa and A549 cells. Taken in the association with high risk genetic markers of coronary together, our present results indicate that co-regulation of artery disease (CAD). Mice model harboring large deletion ANRIL and p14ARF could be coupled by their unique of posterior part of ANRIL and CAD high risk genetic markers intergenic region potentially through E2F1. Judged from the resulted in substantial suppression of both CDKN2A and suppressive effect of ANRIL on a subset of mRNAs involved CDKN2B; however, the mechanistic insights of regulation in the nuclear function suggests that ANRIL might have and function of ANRIL have remain elusive. To date multiple silencing effect on a specific gene set that accounts for a splice variants of ANRIL have been reported and expression wide array of gene expression. of specific splice variant of ANRIL has been shown to be tightly associated with 9p21 CAD high risk markers.
    [Show full text]