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Up-regulated accession # Development M93275 ADFP, adipose differentiation related protein D43694 MATH-1, homolog of atonal 1 M64068 Bmi-1, zinc finger protein AW124785 Midnolin, midbrain nucleolar protein AI843178 Cla3, Cerebellar ataxia 3 D10712 Nedd1, Neural precursor cell expressed, developmentally down-regulated gene 1 AB011678 Doublecortin, for neurogenesis M57683 mPDGF-alpha-R, PDGF alpha receptor U41626 DSS1, deleted in split hand/split foot 1 homolog (Dss1), for limb development AB010833 PTCH2, patched 2, Mouse homolog of yeast CDC46 NP_034226 Ebf3, early B-cell factor 3 AI846695 Qk, Quaking U63386 Edr1 Early development regulator 1 (homolog of polyhomeotic 1), Mph1 AI043016 Rnf2, Ring finger protein 2 X69942 Enhancer-trap-locus 1, for transcription regulation AF100694 Ruvbl1, Ruv-B like protein 1, DNA helicase AW123618 Fzd2, Frizzled homolog 2 U88566 Sfrp1, secreted frizzled related protein 1 AA681520 Geminin-pending, for embryogenesis and morphogenesis U88567 Sfrp2, secreted frizzled related protein 2 AB025922 Gli1, GLI-Kruppel family member 1 AF089721 Smo, Smoothened X99104 Gli2, GLI-Kruppel family member 2 AF009414 SOX11, SRY-box containing gene 11 U61362 Grg1, groucho-related gene 1, Tle1, transducin-like enhancer of split 1 U85614 SRG3, Smarcc1, SWI/SNF related, matrix associated, action dependent regulator of chromatin, subfamily, member 1 M97506 Hen1, helix-loop-helix protein AI837838 Tmeff1, Transmembrane protein with EGF-like and two follistatin-like domains 1 U79748 Madh4, MAD homolog 4, for transcription regulation AV109962 Traf4, TNF receptor associated factor 4 NM_007896 Mapre1, Microtubule-associated protein, RP/EB family, member 1 Y10026 Transcription factor TEF-1, Tead2, TEA domain family member 2 M60474 MARCKS, myristoylated alanine-rich C-kinase substrate, for brain development accession # Cell cycle/maintenance AV309347 Ki67, Antigen identified by monoclonal antibody Ki 67 D63784 MIDA1, mouse Id associate 1, Zrf2 Zuotin related factor 2 NM_008506 L-myc U83902 Mad2, Mitotic checkpoint component Mad2 L32751 (clone M1) GTPase (Ran) M12848 Myb, myeloblastosis oncogene, proto-oncogene mRNA encoding 71 kd myb protein AI842771 Anp32b, Acidic nuclear phosphoprotein 32 family, member B M12731 N-myc U80932 Ayk1, serine/threonine kinase Ayk1, Stk6, serine/threonine kinase 6 AI843682 Nras, neuroblastoma ras oncogene U32446 Brca1 M38724 p34 Cdc2, Cdc2a, AF002823 Bud1, mitotic checkpoint protein kinase AA764261 Pim1, Proviral integration site 1, protein kinase L16926 Cdc25c, cell division cycle 25 homolog c U01063 pLK, serine/threonine kinase, Polo-like kinase homolog, protein serine/threonine kinase AW061324 Cdc20, cell division cycle 20 AF069051 Pttg1, Pituitary tumor-transforming 1 AJ223087 Cdc6, Cell division cycle 6 homolog CAC14659 Retinoblastoma-associated protein homolog p107 L01640 Cdk4, Cyclin-dependent kinase 4, D-type G1 cyclin catalytic subunit (PSK-J3/CDK4) M34094 MK, retinoic acid-responsive protein AF011644 Cdkap1, CDK2 (cyclin-dependent kinase 2)-asscoaited protein 1 AW048730 Sgpl1, Sphingosine phosphate lyase 1, sphinganine-1-phosphate aldolase AF016583 Chk1, checkpoint kinase chk1 AF062378 SHA1, Calmbp1, calmodulin-binding protein 1 AF086905 Chk2, Rad53, protein serine/threonine kinase AB025409 sid1334p, Cks1, CDC28 protein kinase 1 L00039 c-Myc AF038848 Sin3B, tnrascriptional repressor Sin3B, X75483 Cyclin A2 AF008914 sst2A, somatostatin receptor type 2 X64713 Cyclin B1 L29480 Stk18, Serine/threonine kinase 18 X66032 Cyclin B2 AW209238 Tacc3, Transforming, acidic coiled-coil containing protein 3 AI849928 Cyclin D1, cyclin-like protein, induced by colony-stimulating factor 1 AJ249987 TAFII30, Taf10 TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30 kDa M83749 Cyclin D2 X02891 Growth hormone NM_007900 Ect2, oncogene Ect2 AK002576 Int6, mammary tumor integration site 6 M21828 Gas2, Growth arrest specific 2 accession # Checkpoint/repair 1 NM_009687 APEX nuclease, Apurinic/apyrimidinic endonuclease U93583 RAD51-binding protein U89652 Brca2 D13803 RecA-like protein MmRad51 X66323 p80 Ku autoantigen AF069519 T:G mismatch-specific thymine-DNA glycosylase TDGb isoform accession # Apoptosis U54803 Caspase 3 AB013819 TIAP, Birc5, Baculoviral IAP repeat-containing 5 AF027707 Mtd, Bok, Bcl-2 related ovarian killer protein X06407 Tpt1 Tumor protein, translationally-controlled 1 AF033115 Siva accession # Signal transduction L32752 (clone M2) GTPase (Ran), Rasl2-9 RAS-like, family 2, locus 9 X69722 Insulin receptor substrate 1 AB020202 Ak2, adenylate kinase isozyme 2 AI317205 MAP3K1, mitogen activated protein kinase kinase kinase 1 M86377 Esk kinase, Ttk protein kinase U88984 MAP4K4, Mitogen-activated protein kinase kinase kinase kinase 4 AW123850 F2r, Coagulation factor II (thrombin) receptor L21707 MRK, receptor tyrosine kinase mrk, Ryk Receptor-like tyrosine kinase X61399 F52 for a novel protein, Mlp, MARCKS-like protein AW047978 Prss25, Protease, serine, 25, serine-type endopeptidase D29802 Gnb2-rs1, Guanine nucleotide binding protein, beta 2, related sequence 1 AW122347 Racgap1, Rac GTPase-activating protein 1 AI957190 Gnai3, guanine nucleotide binding protein, alpha inhibiting 3 XP_122425 Smoc1, secreted modular calcium binding protein 1 AI843396 Gng10, Guanine nucleotide binding protein (G protein), gamma 10 AI840130 Srcasm, Src activating and signaling molecule AW123750 Gng2, Guanine nucleotide binding protein (G protein), gamma 2 subunit L09562 PTPRG, protein tyrosine phosphatase, receptor type, G AI841654 Gpr56, G protein-coupled receptor 56 AB006141 IGFBP-like protein, insulin-like growth factor binding protein like protein accession # DNA/RNA processing D00812 Rpa2, 30-kDa subunit of replication protein A AF022465 HMG-4, Hmgb3, high mobility group box 3 L32836 Ahcy, S-adenosylhomocysteine hydrolase AF031568 hnRNPG, heterogeneous nuclear ribonucleoprotein G AF041476 Baf53a-pending, BRG1/brm-associated factor 53A AAM14132 Hnrpd, Heterogeneous nuclear ribonucleoprotein D AB025349 Bcrp1-pending, Breakpoint cluster region protein 1, BAF M33934 IMP dehydrogenase (EC 1.2.1.14 Z35401 C3H gene for histone H2A.X, H2afx H2A histone family, member X AA823653 Incenp, inner centromere protein AF012710 Cenp-a, centromere protein A , histone H3 variant AA929330 Mcmd, Mini chromosome maintenance deficient, P1 protein X77731 Deoxycytidine kinase D26089 Mcmd4, Mini chromosome maintenance deficient 4 homolog AB013912 Ruvbl2, RuvB-like protein 2, DNA helicase D26090 Mcmd5, mini chromosome maintenance deficient 5, CDC46 D13546 Pola2, Polymerase (DNA directed), alpha 2 D26091 Mcmd7, Mini chromosome maintenance deficient 7 D13543 Pola1, Polymerase (DNA directed), alpha 1 D86725 mMCM2, Mini chromosome maintenance deficient 2 AF036008 DNMT1, DNA (cytosine-5)-methyltransferase (Dnmt1) AW107230 Nap1l1, Nucleosome assembly protein 1-like 1 AI845934 Ebp2, EBNA1 binding protein 2 AF034610 NASP, nuclear autoantigenic sperm protein (histone binding) AB025015 Elongin A, Tceb3 Transcription elongation factor B (SIII), polypeptide 3 (110kD) AI836205 Nme4, expressed in non-metastatic cells 4 NM_007971 Ezh2, ehnancer of zeste homolog 2, transcriptional regulator AI846392 Nsap1-pending, NS1-associated protein 1 Z22593 Fibrillarin X68193 Nme2, Expressed in non-metastatic cells 2, protein (NM23B) (nucleoside diphosphate kinase) AF073993 hnRNP A2/B1, Heterogenous nuclear ribonucleoprotein A2/B1 D14336 Paf53, RNA polymerase I associated factor (PAF53) AW120557 Lsm4-pending, U6 snRNA-associated SM-like protein 4 X57800 PCNA, proliferating cell nuclear antigen AI837853 Snrpd2, Small nuclear ribonucleoprotein D2 AF024570 Pold1, DNA polymerase delta catalytic X67668 High mobility group 2 protein NM_008774 poly(A) binding protein, cytoplasmic 1 M29260 histone 1-0 J04620 Prim1, DNA primase, p49 subunit M33988 Histone H2A.1 D13545 Prim2, DNA primase, p58 subunit U62674 Histone H2a.2-615 (H2a-615), and histone H3.2-615 (H3-615 AA690061 Rbm8, RNA binding motif protein U70494 Histone H2A.Z, H2afz H2A histone family, member Z NM_009103 Rrm1, Ribonucleotide reductase subunit M1 2 X53476 HMG-14, Hmgn1, high mobility group nucleosomal binding domain 1 L32836 S-adenosyl homocysteine hydrolase (ahcy), copper binding protein X12944 HMG-17, Hmgn2, high mobility group nucleosomal binding domain 2 AI838274 Slc29a1, solute carrier family 29 (nucleoside transporters), member 1 U01915 Topo-2a, DNA topoisomerase II alpha X65704 Small nuclear ribonucleoprotein E AU044050 Tyms, Thymidylate synthase X60980 TK1, thymidine kinase 1 X96767 Snrp1c, U1 small nuclear ribonucleoprotein 1C U1 snRNP-specific protein C AA624336 Tmk, Thymidylate kinase X63020 Snrpb2 U2 small nuclear ribonucleoprotein B accession # Gene expression AAD28370 ATFx , Activating transcription factor 5 U31758 Hdac2, Histone deacetylase 2 AI844392 2e2, General transcription factor IIE, polypeptide 2 (beta subunit, 34kD BAA92776 Mlt1, IA-1, insulinoma-associated protein 1 U89876 Aly, transcriptional coactivator ALY X89749 mTGIF, TG interacting factor M88301 brain-4 class III POU-domain Y07686 NfiB3-protein, nuclear factor I/B, splice variant, splice variant, missing exons 9,10 & 11, 12 is in different ORF AAM20126 Cebpa-rs1, CCAAT/enhancer binding protein alpha (C/EBP), related sequence 1 U28656 PHAS-1, Eif4ebp1, eukaryotic translation initiation factor 4E (eIF-4E) binding protein1 L03279 Core-binding factor beta AB001927 G3bp-pending, ras-GTPase-activating protein SH3-domain binding protein X72310 DRTF-polypeptide-1 (DP-1), Tfdp1 Transcription factor Dp 1 L35032 SOX18,
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  • The Nucleolus – a Gateway to Viral Infection? Brief Review

    The Nucleolus – a Gateway to Viral Infection? Brief Review

    Arch Virol (2002) 147: 1077–1089 DOI 10.1007/s00705-001-0792-0 The nucleolus – a gateway to viral infection? Brief Review J. A. Hiscox School of Animal and Microbial Sciences, University of Reading, U.K. Received August 24, 2001; accepted December 26, 2001 Published online March 18, 2002, © Springer-Verlag 2002 Summary. A number of viruses and viral proteins interact with a dynamic sub- nuclear structure called the nucleolus. The nucleolus is present during interphase in mammalian cells and is the site of ribosome biogenesis, and has been implicated in controlling regulatory processes such as the cell cycle. Viruses interact with the nucleolus and its antigens; viral proteins co-localise with factors such as nucleolin, B23 and fibrillarin, and can cause their redistribution during infection. Viruses can use these components as part of their replication process, and also use the nucleolus as a site of replication itself. Many of these properties are not restricted to any particular type of virus or replication mechanism, and examples of these processes can be found in DNA, RNA and retroviruses. Evidence suggests that viruses may target the nucleolus and its components to favour viral transcription, translation and perhaps alter the cell cycle in order to promote virus replication. Autoimmunity to nucleolin and fibrillarin have been associated with a number of diseases, and by targeting the nucleolus and displacing nucleolar antigens, virus infection might play a role in the initiation of these conditions. Introduction The eukaryotic nucleus contains a number of domains or subcompartments, which include nucleoli, nuclear Cajal bodies, nuclear speckles, transcription and replica- tion foci, and chromosome territories [34].
  • Table S1. List of Oligonucleotide Primers Used

    Table S1. List of Oligonucleotide Primers Used

    Table S1. List of oligonucleotide primers used. Cla4 LF-5' GTAGGATCCGCTCTGTCAAGCCTCCGACC M629Arev CCTCCCTCCATGTACTCcgcGATGACCCAgAGCTCGTTG M629Afwd CAACGAGCTcTGGGTCATCgcgGAGTACATGGAGGGAGG LF-3' GTAGGCCATCTAGGCCGCAATCTCGTCAAGTAAAGTCG RF-5' GTAGGCCTGAGTGGCCCGAGATTGCAACGTGTAACC RF-3' GTAGGATCCCGTACGCTGCGATCGCTTGC Ukc1 LF-5' GCAATATTATGTCTACTTTGAGCG M398Arev CCGCCGGGCAAgAAtTCcgcGAGAAGGTACAGATACGc M398Afwd gCGTATCTGTACCTTCTCgcgGAaTTcTTGCCCGGCGG LF-3' GAGGCCATCTAGGCCATTTACGATGGCAGACAAAGG RF-5' GTGGCCTGAGTGGCCATTGGTTTGGGCGAATGGC RF-3' GCAATATTCGTACGTCAACAGCGCG Nrc2 LF-5' GCAATATTTCGAAAAGGGTCGTTCC M454Grev GCCACCCATGCAGTAcTCgccGCAGAGGTAGAGGTAATC M454Gfwd GATTACCTCTACCTCTGCggcGAgTACTGCATGGGTGGC LF-3' GAGGCCATCTAGGCCGACGAGTGAAGCTTTCGAGCG RF-5' GAGGCCTGAGTGGCCTAAGCATCTTGGCTTCTGC RF-3' GCAATATTCGGTCAACGCTTTTCAGATACC Ipl1 LF-5' GTCAATATTCTACTTTGTGAAGACGCTGC M629Arev GCTCCCCACGACCAGCgAATTCGATagcGAGGAAGACTCGGCCCTCATC M629Afwd GATGAGGGCCGAGTCTTCCTCgctATCGAATTcGCTGGTCGTGGGGAGC LF-3' TGAGGCCATCTAGGCCGGTGCCTTAGATTCCGTATAGC RF-5' CATGGCCTGAGTGGCCGATTCTTCTTCTGTCATCGAC RF-3' GACAATATTGCTGACCTTGTCTACTTGG Ire1 LF-5' GCAATATTAAAGCACAACTCAACGC D1014Arev CCGTAGCCAAGCACCTCGgCCGAtATcGTGAGCGAAG D1014Afwd CTTCGCTCACgATaTCGGcCGAGGTGCTTGGCTACGG LF-3' GAGGCCATCTAGGCCAACTGGGCAAAGGAGATGGA RF-5' GAGGCCTGAGTGGCCGTGCGCCTGTGTATCTCTTTG RF-3' GCAATATTGGCCATCTGAGGGCTGAC Kin28 LF-5' GACAATATTCATCTTTCACCCTTCCAAAG L94Arev TGATGAGTGCTTCTAGATTGGTGTCggcGAAcTCgAGCACCAGGTTG L94Afwd CAACCTGGTGCTcGAgTTCgccGACACCAATCTAGAAGCACTCATCA LF-3' TGAGGCCATCTAGGCCCACAGAGATCCGCTTTAATGC RF-5' CATGGCCTGAGTGGCCAGGGCTAGTACGACCTCG