1932

Abstract

My laboratory investigations have been driven by an abiding interest in understanding the consequences of genetic rearrangement in evolution and disease, and in using viruses to elucidate fundamental mechanisms in biology. Starting with bacteriophages and moving to the retroviruses, my use of the tools of genetics, molecular biology, biochemistry, and biophysics has spanned more than half a century—from the time when DNA structure was just discovered to the present day of big data and epigenetics. Both riding and contributing to the successive waves of technology, my laboratory has elucidated fundamental mechanisms in DNA replication, repair, and recombination. We have made substantial contributions in the area of retroviral oncogenesis, delineated mechanisms that control retroviral gene expression, and elucidated critical details of the structure and function of the retroviral enzymes—reverse transcriptase, protease, and integrase—and have had the satisfaction of knowing that the fundamental knowledge gained from these studies contributed important groundwork for the eventual development of antiviral drugs to treat AIDS. While pursuing laboratory research as a principal investigator, I have also been a science administrator—moving from laboratory head to department chair and, finally, to institute director. In addition, I have undertaken a number of community service, science-related “extracurricular” activities during this time. Filling all of these roles, while being a wife and mother, has required family love and support, creative management, and, above all, personal flexibility—with not too much long-term planning. I hope that this description of my journey, with various roles, obstacles, and successes, will be both interesting and informative, especially to young female scientists.

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2017-09-29
2024-04-18
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Literature Cited

  1. Brattstrom BH, Sturn A. 1.  1959. A new species of fossil turtle from the Pliocene of Oregon, with notes on other fossil Clemmys from Western North America. Bull. S. Calif. Acad. Sci. 58:65–71 [Google Scholar]
  2. Sturn A, Brattstrom BH. 2.  1958. A serial abnormality in the painted turtle. Herpetologica 13:277–78 [Google Scholar]
  3. Hurwitz J. 3.  2005. The discovery of RNA polymerase. J. Biol. Chem. 280:42477–85 [Google Scholar]
  4. Hurwitz J, Bresler AE, Diringer R. 4.  1960. The enzymatic incorporation of ribonucleotides into polyribonucleotides and the effect of DNA. Biochem. Biophys. Res. Commun. 3:15–19 [Google Scholar]
  5. Stevens A. 5.  1960. Incorporation of the adenine ribonucleotide into RNA by cell fractions from E.coli B. Biochem. Biophys. Res. Commun. 3:92–96 [Google Scholar]
  6. Hurwitz J, Evans A, Baninet C, Skalka AM. 6.  1963. On the copying of DNA in the RNA polymerase reaction. Cold Spring Harb. Symp. Quant. Biol. 28:59–65 [Google Scholar]
  7. Skalka AM, Fowler AV, Hurwitz J. 7.  1966. The effect of histones on the enzymatic synthesis of RNA. J. Biol. Chem. 241:558 [Google Scholar]
  8. Cairns J. 8.  1963. The bacterial chromosome and its manner of replication as seen by autoradiography. J. Mol. Biol. 6:208–13 [Google Scholar]
  9. Hershey AD, Burgi E, Davern CI. 9.  1965. Preparative density-gradient centrifugation of the molecular halves of lamda DNA. Biochem. Biophys. Res. Commun. 18:675–78 [Google Scholar]
  10. Skalka A. 10.  1966. Regional and temporal control of genetic transcription in phage lambda. PNAS 55:1190–95 [Google Scholar]
  11. Skalka A. 11.  1966. Multiple units of transcription in phage lambda. Cold Spring Harb. Symp. Quant. Biol. 31:377–79 [Google Scholar]
  12. Skalka A, Burgi E, Hershey AD. 12.  1968. Segmental distribution of nucleotides in the DNA of bacteriophage lambda. J. Mol. Biol. 34:1–16 [Google Scholar]
  13. Skalka AM, Butler B, Echols H. 13.  1967. Genetic control of transcription during development of phage λ. PNAS 58:576–83 [Google Scholar]
  14. Bear PD, Skalka A. 14.  1969. The molecular origin of lambda prophage mRNA. PNAS 62:385–88 [Google Scholar]
  15. Smith MG, Skalka AM. 15.  1966. Some properties of DNA from phage-infected bacteria. J. Gen. Physiol. 49:127–42 [Google Scholar]
  16. Skalka AM. 16.  1971. Origin of DNA concatemers during growth. The Bacteriophage Lambda AD Hershey, pp. 535–47 Cold Spring Harbor, NY: Cold Spring Harbor Lab. [Google Scholar]
  17. Gilbert W, Dressler D. 17.  1968. DNA replication: the rolling circle model. Cold Spring Harb. Symp. Quant. Biol. 33:473–84 [Google Scholar]
  18. Udenfriend SA. 18.  1995. Camelot in Nutley, NJ: Roche Institute of Molecular Biology remembered. The Scientist Oct. 30. http://www.the-scientist.com/?articles.view/articleNo/17625/title/Camelot-In-Nutley–N-J—Roche-Institute-Of-Molecular-Biology-Remembered/
  19. Weissbach H. 19.  1987. The Roche Institute of Molecular Biology. BioEssays 7:243–45 [Google Scholar]
  20. Enquist LW, Skalka AM. 20.  1973. Replication of bacteriophage λ DNA dependent on the function of host and viral genes: I. Interaction of red, gam and rec. J. Mol. Biol. 75:185–212 [Google Scholar]
  21. Skalka AM, Enquist LW. 21.  1974. Overlapping pathways for replication, recombination and repair in bacteriophage lambda. Mechanism and Regulation of DNA Replication AR Kolber, M Kohiyama 181–200 New York: Plenum [Google Scholar]
  22. Skalka AM. 22.  1974. A replicator's view of recombination and repair. Mechanisms in Recombination RF Grell 421–32 New York: Plenum [Google Scholar]
  23. Skalka AM, Poonian M, Bartl P. 23.  1972. Concatemers in DNA replication: electron microscopic studies of partially denatured intracellular lambda DNA. J. Mol. Biol. 64:541–50 [Google Scholar]
  24. Sogo JM, Greenstein M, Skalka AM. 24.  1976. The circle mode of replication of bacteriophage lambda: the role of covalently closed templates and the formation of mixed catenated dimers. J. Mol. Biol. 103:537–62 [Google Scholar]
  25. Gianni AM, Smotkin D, Weinberg RA. 25.  1975. Murine leukemia virus: detection of unintegrated double-stranded DNA forms of the provirus. PNAS 72:447–51 [Google Scholar]
  26. Skalka AM. 26.  1978. A current status of coliphage EK2 vectors. Gene 3:29–38 [Google Scholar]
  27. Leder P, Tiemeier D, Enquist L. 27.  1977. EK2 derivatives of bacteriophage lambda useful in the cloning of DNA from higher organisms: the lambdagtWES system. Science 196:175–77 [Google Scholar]
  28. McClements W, Skalka AM. 28.  1977. Analysis of chicken ribosomal RNA genes and construction of lambda hybrids containing gene fragments. Science 196:195–97 [Google Scholar]
  29. McClements W, Tilghman S, Crouch R, Skalka AM. 29.  1978. Cloning and analysis of rRNA from higher eukaryotes. Proceedings of the International Symposium on Genetic Engineering HW Boyer, S Nicosia 117–26 Amsterdam: Elsevier [Google Scholar]
  30. McClements W, Hanafusa H, Tilghman S, Skalka AM. 30.  1979. Structural studies on oncornavirus-related sequences in chicken genomic DNA: two-step analyses of EcoRI and Bgl I restriction digests and tentative mapping of a ubiquitous endogenous provirus. PNAS 76:2165–69 [Google Scholar]
  31. Boone LR, Skalka A. 31.  1980. Two species of full-length cDNA are synthesized in high yield by melittin-treated avian retrovirus particles. PNAS 77:847–51 [Google Scholar]
  32. Boone LR, Skalka AM. 32.  1981. Viral DNA synthesized in vitro by avian retrovirus particles permeabilized with melittin. I. Kinetics of synthesis and size of minus- and plus-strand transcripts. J. Virol. 37:109–16 [Google Scholar]
  33. Boone LR, Skalka AM. 33.  1981. Viral DNA synthesized in vitro by avian retrovirus particles permeabilized with melittin. II. Evidence for a strand displacement mechanism in plus-strand synthesis. J. Virol. 37:117–26 [Google Scholar]
  34. Ju G, Boone L, Skalka AM. 34.  1980. Isolation and characterization of recombinant DNA clones of avian retroviruses: size heterogeneity and instability of the direct repeat. J. Virol. 33:1026–33 [Google Scholar]
  35. Ju G, Skalka AM. 35.  1980. Nucleotide sequence analysis of the long terminal repeat (LTR) of avian retroviruses: structural similarities with transposable elements. Cell 22:379–86 [Google Scholar]
  36. Hishinuma F, DeBona PJ, Astrin S, Skalka AM. 36.  1981. Nucleotide sequence of acceptor site and termini of integrated avian endogenous provirus ev1: integration creates a 6 bp repeat of host DNA. Cell 23:155–64 [Google Scholar]
  37. Ju G, Hishinuma F, Skalka AM. 37.  1982. Nucleotide sequence analysis of avian retroviruses: structural similarities with transposable elements. Fed. Proc 412659–61 [Google Scholar]
  38. Skalka AM, Ju G, Hishinuma F, DeBona PJ, Astrin S. 38.  1981. Structural analogies among avian retroviral DNAs and transposable elements. Cold Spring Harb. Symp. Quant. Biol. 45:Pt. 2739–46 [Google Scholar]
  39. Skalka AM. 39.  1979. Second report of the COGENE working group on risk assessment. Recombinant DNA and Genetic Experimentation J Morgan, WJ Whelan Oxford, UK: Pergamon [Google Scholar]
  40. Junghans RP, Boone LR, Skalka AM. 40.  1982. Products of reverse transcription in avian retrovirus analyzed by electron microscopy. J. Virol. 43:544–54 [Google Scholar]
  41. Junghans RP, Boone LR, Skalka AM. 41.  1982. Retroviral DNA H structures: displacement-assimilation model of recombination. Cell 30:53–62 [Google Scholar]
  42. Duyk G, Leis J, Longiaru M, Skalka AM. 42.  1983. Selective cleavage in the avian retroviral long terminal repeat sequence by the endonuclease associated with the αβ form of avian reverse transcriptase. PNAS 80:6745–49 [Google Scholar]
  43. Duyk G, Longiaru M, Cobrinik D, Kowal R, deHaseth P. 43.  et al. 1985. Circles with two tandem long terminal repeats are specifically cleaved by pol gene-associated endonuclease from avian sarcoma and leukosis viruses: nucleotide sequences required for site-specific cleavage. J. Virol. 56:589–99 [Google Scholar]
  44. Skalka AM, Duyk G, Longiaru M, DeHaseth P, Terry R, Leis J. 44.  1984. Integrative recombination—a role for the retroviral reverse transcriptase. Cold Spring Harb. Symp. Quant. Biol. 49:651–59 [Google Scholar]
  45. Brown PO, Bowerman B, Varmus HE, Bishop JM. 45.  1987. Correct integration of retroviral DNA in vitro. Cell 49:347–56 [Google Scholar]
  46. Stehelin D, Varmus HE, Bishop JM, Vogt PK. 46.  1976. DNA related to the transforming gene(s) of avian sarcoma viruses is present in normal avian DNA. Nature 260:170–73 [Google Scholar]
  47. Takeya T, Hanafusa H, Junghans RP, Ju G, Skalka AM. 47.  1981. Comparison between the viral transforming gene (src) of recovered avian sarcoma virus and its cellular homolog. Mol. Cell. Biol. 1:1024–37 [Google Scholar]
  48. Bizub D, Wood AW, Skalka AM. 48.  1986. Mutagenesis of the Ha-ras oncogene in mouse skin tumors induced by polycyclic aromatic hydrocarbons. PNAS 83:6048–52 [Google Scholar]
  49. Bizub D, Blair D, Alvord G, Skalka AM. 49.  1988. Correlation between H-ras p21TLeu61 protein content and tumorigenicity of NIH3T3 cells. Oncogene 3:443–48 [Google Scholar]
  50. Bizub D, Fischberg-Bender E, Heimer EP, Felix A, Skalka AM. 50.  1989. Detection of transforming ras proteins containing leucine at position 61 by a new mouse monoclonal antibody. ras53–69 Leu61 Cancer Res 49:6425–31 [Google Scholar]
  51. Reddy EP, Skalka AM, Curran T. 51.  1988. The Oncogene Handbook New York: Elsevier
  52. Neel BG, Gasic GP, Rogler CE, Skalka AM, Ju G. 52.  et al. 1982. Molecular analysis of the c-myc locus in normal tissue and in avian leukosis virus-induced lymphomas. J. Virol. 44:158–66 [Google Scholar]
  53. Tsichlis PN, Donehower L, Hager G, Zeller N, Malavarca R. 53.  et al. 1982. Sequence comparison in the crossover region of an oncogenic avian retrovirus recombinant and its nononcogenic parent: genetic regions that control growth rate and oncogenic potential. Mol. Cell. Biol. 2:1331–38 [Google Scholar]
  54. Cullen BR, Skalka AM, Ju G. 54.  1983. Endogenous avian retroviruses contain deficient promoter and leader sequences. PNAS 80:2946–50 [Google Scholar]
  55. Smith EJ, Bizub D, Scholl DR, Skalka AM. 55.  1984. Characterization of a solitary long terminal repeat of avian endogenous virus origin. Virology 134:493–96 [Google Scholar]
  56. Bizub D, Katz RA, Skalka AM. 56.  1984. Nucleotide sequence of noncoding regions in Rous-associated virus-2: Comparisons delineate conserved regions important in replication and oncogenesis. J. Virol. 49:557–65 [Google Scholar]
  57. Kramer RA, Schaber MD, Skalka AM, Ganguly K, Wong-Staal F, Reddy EP. 57.  1986. HTLV-III gag protein is processed in yeast cells by the virus pol-protease. Science 231:1580–84 [Google Scholar]
  58. Kotler M, Katz RA, Danho W, Leis J, Skalka AM. 58.  1988. Synthetic peptides as substrates and inhibitors of a retroviral protease. PNAS 85:4185–89 [Google Scholar]
  59. Shoeman RL, Young D, Pottathil R, Victor J, Conroy RR. 59.  et al. 1987. Comparison of recombinant human immunodeficiency virus gag precursor and gagenv fusion proteins and a synthetic env peptide as diagnostic reagents. Anal. Biochem. 161:370–79 [Google Scholar]
  60. Kotler M, Katz RA, Skalka AM. 60.  1988. Activity of avian retroviral protease expressed in Escherichia coli. J. Virol. 62:2696–700 [Google Scholar]
  61. Kotler M, Danho W, Katz RA, Leis J, Skalka AM. 61.  1989. Avian retroviral protease and cellular aspartic proteases are distinguished by activities on peptide substrates. J. Biol. Chem. 264:3428–35 [Google Scholar]
  62. Weber IT, Miller M, Jaskolski M, Leis J, Skalka AM, Wlodawer A. 62.  1989. Molecular modeling of the HIV-1 protease and its substrate binding site. Science 243:928–31 [Google Scholar]
  63. Bizub D, Weber IT, Cameron CE, Leis JP, Skalka AM. 63.  1991. A range of catalytic efficiencies with avian retroviral protease subunits genetically linked to form single polypeptide chains. J. Biol. Chem. 266:4951–58 [Google Scholar]
  64. Burstein H, Bizub D, Kotler M, Schatz G, Vogt VM, Skalka AM. 64.  1992. Processing of avian retroviral gag polyprotein precursors is blocked by a mutation at the NC-PR cleavage site. J. Virol. 66:1781–85 [Google Scholar]
  65. Burstein H, Bizub D, Skalka AM. 65.  1991. Assembly and processing of avian retroviral gag polyproteins containing linked protease dimers. J. Virol. 65:6165–72 [Google Scholar]
  66. Grinde B, Cameron CE, Leis J, Weber IT, Wlodawer A. 66.  et al. 1992. Mutations that alter the activity of the Rous sarcoma virus protease. J. Biol. Chem. 267:9481–90 [Google Scholar]
  67. Grinde B, Cameron CE, Leis J, Weber IT, Wlodawer A. 67.  et al. 1992. Analysis of substrate interactions of the Rous sarcoma virus wild type and mutant proteases and human immunodeficiency virus-1 protease using a set of systematically altered peptide substrates. J. Biol. Chem. 267:9491–98 [Google Scholar]
  68. Cameron CE, Ridky TW, Shulenin S, Leis J, Weber IT. 68.  et al. 1994. Mutational analysis of the substrate binding pockets of the Rous sarcoma virus and human immunodeficiency virus-1 proteases. J. Biol. Chem. 269:11170–77 [Google Scholar]
  69. Katzman M, Katz RA, Skalka AM, Leis J. 69.  1989. The avian retroviral integration protein cleaves the terminal sequences of linear viral DNA at the in vivo sites of integration. J. Virol. 63:5319–27 [Google Scholar]
  70. Katz RA, Merkel G, Kulkosky J, Leis J, Skalka AM. 70.  1990. The avian retroviral IN protein is both necessary and sufficient for integrative recombination in vitro. Cell 63:87–95 [Google Scholar]
  71. Craigie R, Fujiwara T, Bushman F. 71.  1990. The IN protein of Moloney murine leukemia virus processes the viral DNA ends and accomplishes their integration in vitro. Cell 62:829–37 [Google Scholar]
  72. Khan E, Mack JP, Katz RA, Kulkosky J, Skalka AM. 72.  1991. Retroviral integrase domains: DNA binding and the recognition of LTR sequences. Nucleic Acids Res 19:851–60 [Google Scholar]
  73. Kulkosky J, Jones KS, Katz RA, Mack JP, Skalka AM. 73.  1992. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol. Cell. Biol. 12:2331–38 [Google Scholar]
  74. Kulkosky J, Katz RA, Merkel G, Skalka AM. 74.  1995. Activities and substrate specificity of the evolutionarily conserved central domain of retroviral integrase. Virology 206:448–56 [Google Scholar]
  75. Asante-Appiah E, Seeholzer SH, Skalka AM. 75.  1998. Structural determinants of metal-induced conformational changes in HIV-1 integrase. J. Biol. Chem. 273:35078–87 [Google Scholar]
  76. Asante-Appiah E, Skalka AM. 76.  1997. A metal-induced conformational change and activation of HIV-1 integrase. J. Biol. Chem. 272:16196–205 [Google Scholar]
  77. Yi J, Asante-Appiah E, Skalka AM. 77.  1999. Divalent cations stimulate preferential recognition of a viral DNA end by HIV-1 integrase. Biochemistry 38:8458–68 [Google Scholar]
  78. Yi J, Cheng H, Andrake MD, Dunbrack RL Jr., Roder H, Skalka AM. 78.  2002. Mapping the epitope of an inhibitory monoclonal antibody to the C-terminal DNA-binding domain of HIV-1 integrase. J. Biol. Chem. 277:12164–74 [Google Scholar]
  79. Yi J, Skalka AM. 79.  2000. Mapping epitopes of monoclonal antibodies against HIV-1 integrase with limited proteolysis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Biopolymers 55:308–18 [Google Scholar]
  80. Levy-Mintz P, Duan L, Zhang H, Hu B, Dornadula G. 80.  et al. 1996. Intracellular expression of single-chain variable fragments to inhibit early stages of the viral life cycle by targeting human immunodeficiency virus type 1 integrase. J. Virol. 70:8821–32 [Google Scholar]
  81. Neamati N, Lin Z, Karki RG, Orr A, Cowansage K. 81.  et al. 2002. Metal-dependent inhibition of HIV-1 integrase. J. Med. Chem 455661–70 [Google Scholar]
  82. Bujacz G, Jaskolski M, Alexandratos J, Wlodawer A, Merkel G. 82.  et al. 1995. High-resolution structure of the catalytic domain of avian sarcoma virus integrase. J. Mol. Biol. 253:333–46 [Google Scholar]
  83. Dyda F, Hickman AB, Jenkins TM, Engelman A, Craigie R, Davies DR. 83.  1994. Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 266:1981–86 [Google Scholar]
  84. Bujacz G, Alexandratos J, Wlodawer A, Merkel G, Andrake M. 84.  et al. 1997. Binding of different divalent cations to the active site of avian sarcoma virus integrase and their effects on enzymatic activity. J. Biol. Chem. 272:18161–68 [Google Scholar]
  85. Lubkowski J, Yang F, Alexandratos J, Wlodawer A, Zhao H. 85.  et al. 1998. Structure of the catalytic domain of avian sarcoma virus integrase with a bound HIV-1 integrase-targeted inhibitor. PNAS 95:4831–36 [Google Scholar]
  86. Lubkowski J, Yang F, Alexandratos J, Merkel G, Katz RA. 86.  et al. 1998. Structural basis for inactivating mutations and pH-dependent activity of avian sarcoma virus integrase. J. Biol. Chem. 273:32685–89 [Google Scholar]
  87. Lubkowski J, Dauter Z, Yang F, Alexandratos J, Merkel G. 87.  et al. 1999. Atomic resolution structures of the core domain of avian sarcoma virus integrase and its D64N mutant. Biochemistry 38:13512–22 [Google Scholar]
  88. Beese LS, Steitz TA. 88.  1991. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J 10:25–33 [Google Scholar]
  89. Jones KS, Coleman J, Merkel GW, Laue TM, Skalka AM. 89.  1992. Retroviral integrase functions as a multimer and can turn over catalytically. J. Biol. Chem. 267:16037–40 [Google Scholar]
  90. Andrake MD, Skalka AM. 90.  1995. Multimerization determinants reside in both the catalytic core and C terminus of avian sarcoma virus integrase. J. Biol. Chem. 270:29299–306 [Google Scholar]
  91. Bao KK, Skalka AM, Wong I. 91.  2002. Presteady-state analysis of avian sarcoma virus integrase. I. A splicing activity and structure-function implications for cognate site recognition. J. Biol. Chem. 277:12089–98 [Google Scholar]
  92. Bao KK, Skalka AM, Wong I. 92.  2002. Presteady-state analysis of avian sarcoma virus integrase. II. Reverse-polarity substrates identify preferential processing of the U3-U5 pair. J. Biol. Chem. 277:12099–108 [Google Scholar]
  93. Bao KK, Wang H, Miller JK, Erie DA, Skalka AM, Wong I. 93.  2003. Functional oligomeric state of avian sarcoma virus integrase. J. Biol. Chem. 278:1323–27 [Google Scholar]
  94. Li M, Mizuuchi M, Burke TR Jr., Craigie R. 94.  2006. Retroviral DNA integration: reaction pathway and critical intermediates. EMBO J 25:1295–304 [Google Scholar]
  95. Bojja RS, Andrake MD, Weigand S, Merkel G, Yarychkivska O. 95.  et al. 2011. Architecture of a full-length retroviral integrase monomer and dimer, revealed by small angle X-ray scattering and chemical cross-linking. J. Biol. Chem. 286:17047–59 [Google Scholar]
  96. Bojja RS, Andrake MD, Merkel G, Weigand S, Dunbrack RL Jr., Skalka AM. 96.  2013. Architecture and assembly of HIV integrase multimers in the absence of DNA substrates. J. Biol. Chem. 288:7373–86 [Google Scholar]
  97. Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P. 97.  2010. Retroviral intasome assembly and inhibition of DNA strand transfer. Nature 464:232–36 [Google Scholar]
  98. Yin Z, Shi K, Banerjee S, Pandey KK, Bera S. 98.  et al. 2016. Crystal structure of the Rous sarcoma virus intasome. Nature 530:362–66 [Google Scholar]
  99. Katz RA, Kotler M, Skalka AM. 99.  1988. cis-acting intron mutations that affect the efficiency of avian retroviral RNA splicing: implication for mechanisms of control. J. Virol. 62:2686–95 [Google Scholar]
  100. Bouck J, Fu XD, Skalka AM, Katz RA. 100.  1995. Genetic selection for balanced retroviral splicing: Novel regulation involving the second step can be mediated by transitions in the polypyrimidine tract. Mol. Cell. Biol. 15:2663–71 [Google Scholar]
  101. Bouck J, Fu XD, Skalka AM, Katz RA. 101.  1998. Role of the constitutive splicing factors U2AF65 and SAP49 in suboptimal RNA splicing of novel retroviral mutants. J. Biol. Chem. 273:15169–76 [Google Scholar]
  102. Fu XD, Katz RA, Skalka AM, Maniatis T. 102.  1991. The role of branchpoint and 3′-exon sequences in the control of balanced splicing of avian retrovirus RNA. Genes Dev 5:211–20 [Google Scholar]
  103. Katz RA, Skalka AM. 103.  1990. Control of retroviral RNA splicing through maintenance of suboptimal processing signals. Mol. Cell. Biol. 10:696–704 [Google Scholar]
  104. Kukolj G, Katz RA, Skalka AM. 104.  1998. Characterization of the nuclear localization signal in the avian sarcoma virus integrase. Gene 223:157–63 [Google Scholar]
  105. Greger JG, Katz RA, Taganov K, Rall GF, Skalka AM. 105.  2004. Transduction of terminally differentiated neurons by avian sarcoma virus. J. Virol. 78:4902–6 [Google Scholar]
  106. Katz RA, Greger JG, Darby K, Boimel P, Rall GF, Skalka AM. 106.  2002. Transduction of interphase cells by avian sarcoma virus. J. Virol. 76:5422–34 [Google Scholar]
  107. Katz RA, Greger JG, Boimel P, Skalka AM. 107.  2003. Human immunodeficiency virus type 1 DNA nuclear import and integration are mitosis independent in cycling cells. J. Virol. 77:13412–17 [Google Scholar]
  108. Daniel R, Katz RA, Skalka AM. 108.  1999. A role for DNA-PK in retroviral DNA integration. Science 284:644–47 [Google Scholar]
  109. Daniel R, Kao G, Taganov K, Greger JG, Favorova O. 109.  et al. 2003. Evidence that the retroviral DNA integration process triggers an ATR-dependent DNA damage response. PNAS 100:4778–83 [Google Scholar]
  110. Daniel R, Katz RA, Merkel G, Hittle JC, Yen TJ, Skalka AM. 110.  2001. Wortmannin potentiates integrase-mediated killing of lymphocytes and reduces the efficiency of stable transduction by retroviruses. Mol. Cell. Biol. 21:1164–72 [Google Scholar]
  111. Daniel R, Litwin S, Katz RA, Skalka AM. 111.  2001. Computational analysis of retrovirus-induced scid cell death. J. Virol. 75:3121–28 [Google Scholar]
  112. Taganov K, Daniel R, Katz RA, Favorova O, Skalka AM. 112.  2001. Characterization of retrovirus-host DNA junctions in cells deficient in nonhomologous-end joining. J. Virol. 75:9549–52 [Google Scholar]
  113. Daniel R, Myers CB, Kulkosky J, Taganov K, Greger JG. 113.  et al. 2004. Characterization of a naphthalene derivative inhibitor of retroviral integrases. AIDS Res. Hum. Retrovir. 20:135–44 [Google Scholar]
  114. Lau A, Kanaar R, Jackson SP, O'Connor MJ. 114.  2004. Suppression of retroviral infection by the RAD52 DNA repair protein. EMBO J 23:3421–29 [Google Scholar]
  115. Daniel R, Greger JG, Katz RA, Taganov KD, Wu X. 115.  et al. 2004. Evidence that stable retroviral transduction and cell survival following DNA integration depend on components of the nonhomologous end joining repair pathway. J. Virol. 78:8573–81 [Google Scholar]
  116. Skalka AM, Katz RA. 116.  2005. Retroviral DNA integration and the DNA damage response. Cell Death Differ 12:Suppl. 1971–78 [Google Scholar]
  117. Greger JG, Katz RA, Ishov AM, Maul GG, Skalka AM. 117.  2005. The cellular protein Daxx interacts with avian sarcoma virus integrase and viral DNA to repress viral transcription. J. Virol. 79:4610–18 [Google Scholar]
  118. Katz RA, Jack-Scott E, Narezkina A, Palagin I, Boimel P. 118.  et al. 2007. High-frequency epigenetic repression and silencing of retroviruses can be antagonized by histone deacetylase inhibitors and transcriptional activators, but uniform reactivation in cell clones is restricted by additional mechanisms. J. Virol. 81:2592–604 [Google Scholar]
  119. Shalginskikh N, Poleshko A, Skalka AM, Katz RA. 119.  2013. Retroviral DNA methylation and epigenetic repression are mediated by the antiviral host protein Daxx. J. Virol. 87:2137–50 [Google Scholar]
  120. Poleshko A, Einarson MB, Shalginskikh N, Zhang R, Adams PD. 120.  et al. 2010. Identification of a functional network of human epigenetic silencing factors. J. Biol. Chem. 285:422–33 [Google Scholar]
  121. Poleshko A, Palagin I, Zhang R, Boimel P, Castagna C. 121.  et al. 2008. Identification of cellular proteins that maintain retroviral epigenetic silencing: evidence for an antiviral response. J. Virol. 82:2313–23 [Google Scholar]
  122. Poleshko A, Katz RA. 122.  2014. Specifying peripheral heterochromatin during nuclear lamina reassembly. Nucleus 5:32–39 [Google Scholar]
  123. Belyi VA, Levine AJ, Skalka AM. 123.  2010. Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes. PLOS Pathog 6:e1001030 [Google Scholar]
  124. Avril T. 124.  2010. Virus “fossils” offer clues to surviving infection. Philadelphia Inquirer July 30 A3 [Google Scholar]
  125. Palca J. 125.  2010. Vertebrate genomes hide ancient viruses. Science Friday, National Public Radio July 30. http://www.npr.org/templates/story/story.php?storyId=128875905 [Google Scholar]
  126. 126. PLOS. 2010. Unexpected viral ‘fossils’ found in vertebrate genomes. ScienceDaily July 30. https://www.sciencedaily.com/releases/2010/07/100729172330.htm
  127. Keim B. 127.  2010. Genome surprise: Guinea pigs have Ebola!. Wired July 29. http://www.wired.com/2010/07/ebola-in-genomes/ [Google Scholar]
  128. Belyi VA, Levine AJ, Skalka AM. 128.  2010. Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: the Parvoviridae and Circoviridae are more than 40 to 50 million years old. J. Virol. 84:12458–62 [Google Scholar]
  129. 129. ASM. 2010. Upending conventional wisdom, certain virus families are ancient. ScienceDaily Nov. 17. https://www.sciencedaily.com/releases/2010/11/101116162847.htm
  130. Flint SJ, Enquist LW, Krug RM, Racaniello VR, Skalka AM. 130.  2000. Principles of Virology: Molecular Biology, Pathogenesis, and Control Washington, DC: ASM Press, 1st ed..
  131. Flint J, Racaniello VR, Rall GF, Skalka AM. 131.  2015. Principles of Virology Washington, DC: ASM Press, 4th ed..
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