|
1.Hande MP. DNA Repair Factors and Telomere-Chromosome Integrity in Mammalian Cells. Cytogenet Genome Res. 2004;104(1-4):116-22. 2.Tlsty TD, Romanov SR, Kozakiewicz BK, Holst CR, Haupt LM, Crawford YG. Loss of Chromosomal Integrity in Human Mammary Epithelial Cells Subsequent to Escape from Senescence. J Mammary Gland Biol Neoplasia. 2001;6(2):235-43. 3.Goepfert TM, Moreno-Smith M, Edwards DG, Pathak S, Medina D, Brinkley WR. Loss of Chromosomal Integrity Drives Rat Mammary Tumorigenesis. Int J Cancer. 2007;120(5):985-94. 4.Jackson SP, Bartek J. The DNA-Damage Response in Human Biology and Disease. Nature. 2009;461(7267):1071-8. 5.Khanna KK, Jackson SP. DNA Double-Strand Breaks: Signaling, Repair and the Cancer Connection. Nat Genet. 2001;27(3):247-54. 6.Sandell LL, Zakian VA. Loss of a Yeast Telomere: Arrest, Recovery, and Chromosome Loss. Cell. 1993;75(4):729-39. 7.Pimpinelli S, Goday C. Unusual Kinetochores and Chromatin Diminution in Parascaris. Trends Genet. 1989;5(9):310-5. 8.Wang J, Davis RE. Programmed DNA Elimination in Multicellular Organisms. Curr Opin Genet Dev. 2014;27:26-34. 9.Boveri T. Ueber Differenzierung Der Zellkerne Wahrend Der Furchung Des Eies Von Ascaris Megalocephala. Anat Anz. 1887;2:6. 10.Goday C, Pimpinelli S. Chromosome Organization and Heterochromatin Elimination in Parascaris. Science. 1984;224(4647):411-3. 11.Muller F, Tobler H. Chromatin Diminution in the Parasitic Nematodes Ascaris Suum and Parascaris Univalens. Int J Parasitol. 2000;30(4):391-9. 12.Muller F, Bernard V, Tobler H. Chromatin Diminution in Nematodes. Bioessays. 1996;18(2):133-8. 13.Wang J, Mitreva M, Berriman M, Thorne A, Magrini V, Koutsovoulos G, et al. Silencing of Germline-Expressed Genes by DNA Elimination in Somatic Cells. Dev Cell. 2012;23(5):1072-80. 14.Jentsch S, Tobler H, Muller F. New Telomere Formation During the Process of Chromatin Diminution in Ascaris Suum. Int J Dev Biol. 2002;46(1):143-8. 15.Muller F, Wicky C, Spicher A, Tobler H. New Telomere Formation after Developmentally Regulated Chromosomal Breakage During the Process of Chromatin Diminution in Ascaris Lumbricoides. Cell. 1991;67(4):815-22. 16.Goday C, Gonzalez-Garcia JM, Esteban MR, Giovinazzo G, Pimpinelli S. Kinetochores and Chromatin Diminution in Early Embryos of Parascaris Univalens. J Cell Biol. 1992;118(1):23-32. 17.Etter A, Aboutanos M, Tobler H, Muller F. Eliminated Chromatin of Ascaris Contains a Gene That Encodes a Putative Ribosomal Protein. Proc Natl Acad Sci U S A. 1991;88(5):1593-6. 18.Etter A, Bernard V, Kenzelmann M, Tobler H, Muller F. Ribosomal Heterogeneity from Chromatin Diminution in Ascaris Lumbricoides. Science. 1994;265(5174):954-6. 19.Spicher A, Etter A, Bernard V, Tobler H, Muller F. Extremely Stable Transcripts May Compensate for the Elimination of the Gene Fert-1 from All Ascaris Lumbricoides Somatic Cells. Dev Biol. 1994;164(1):72-86. 20.Baroin A, Prat A, Caron F. Telomeric Site Position Heterogeneity in Macronuclear DNA of Paramecium Primaurelia. Nucleic Acids Res. 1987;15(4):1717-28. 21.Forney JD, Blackburn EH. Developmentally Controlled Telomere Addition in Wild-Type and Mutant Paramecia. Mol Cell Biol. 1988;8(1):251-8. 22.Ammermann D, Steinbruck G, von Berger L, Hennig W. The Development of the Macronucleus in the Ciliated Protozoan Stylonychia Mytilus. Chromosoma. 1974;45(4):401-29. 23.Meyer GF, Lipps HJ. Chromatin Elimination in the Hypotrichous Ciliate Stylonychia Mytilus. Chromosoma. 1980;77(3):285-97. 24.Meyer GF, Lipps HJ. The Formation of Polytene Chromosomes During Macronuclear Development of the Hypotrichous Ciliate Stylonychia Mytilus. Chromosoma. 1981;82(2):309-14. 25.Baird SE, Klobutcher LA. Characterization of Chromosome Fragmentation in Two Protozoans and Identification of a Candidate Fragmentation Sequence in Euplotes Crassus. Genes Dev. 1989;3(5):585-97. 26.Herrick G, Hunter D, Williams K, Kotter K. Alternative Processing During Development of a Macronuclear Chromosome Family in Oxytricha Fallax. Genes Dev. 1987;1(10):1047-58. 27.Gall JG. The Molecular Biology of Ciliated Protozoa. Academic Press, INC. 1986. 28.Yao MC, Chao JL. Rna-Guided DNA Deletion in Tetrahymena: An Rnai-Based Mechanism for Programmed Genome Rearrangements. Annu Rev Genet. 2005;39:537-59. 29.Hamilton EP, Kapusta A, Huvos PE, Bidwell SL, Zafar N, Tang H, et al. Structure of the Germline Genome of Tetrahymena Thermophila and Relationship to the Massively Rearranged Somatic Genome. Elife. 2016;5. 30.Chalker DL, Yao MC. Nongenic, Bidirectional Transcription Precedes and May Promote Developmental DNA Deletion in Tetrahymena Thermophila. Genes Dev. 2001;15(10):1287-98. 31.Malone CD, Hannon GJ. Small Rnas as Guardians of the Genome. Cell. 2009;136(4):656-68. 32.Chalker DL, Fuller P, Yao MC. Communication between Parental and Developing Genomes During Tetrahymena Nuclear Differentiation Is Likely Mediated by Homologous Rnas. Genetics. 2005;169(1):149-60. 33.Yifan L, Sean DT, Tara LM, Jeffrey S, Donald FH, C. David A. Rnai-Dependent H3k27 Methylation Is Required for Heterochromatin Formation and DNA Elimination in Tetrahymena. Genes Dev. 2007;21:1530-45. 34.Madireddi MT, Coyne RS, Smothers JF, Mickey KM, Yao MC, Allis CD. Pdd1p, a Novel Chromodomain-Containing Protein, Links Heterochromatin Assembly and DNA Elimination in Tetrahymena. Cell. 1996;87(1):75-84. 35.Taverna SD, Coyne RS, Allis CD. Methylation of Histone H3 at Lysine 9 Targets Programmed DNA Elimination in Tetrahymena. Cell. 2002;110(6):701-11. 36.Liu Y, Taverna SD, Muratore TL, Shabanowitz J, Hunt DF, Allis CD. Rnai-Dependent H3k27 Methylation Is Required for Heterochromatin Formation and DNA Elimination in Tetrahymena. Genes Dev. 2007;21(12):1530-45. 37.Cheng CY, Vogt A, Mochizuki K, Yao MC. A Domesticated Piggybac Transposase Plays Key Roles in Heterochromatin Dynamics and DNA Cleavage During Programmed DNA Deletion in Tetrahymena Thermophila. Mol Biol Cell.21(10):1753-62. 38.Austerberry CF, Snyder RO, Yao MC. Sequence Microheterogeneity Is Generated at Junctions of Programmed DNA Deletions in Tetrahymena Thermophila. Nucleic Acids Res. 1989;17(18):7263-72. 39.Saveliev SV, Cox MM. Developmentally Programmed DNA Deletion in Tetrahymena Thermophila by a Transposition-Like Reaction Pathway. EMBO J. 1996;15(11):2858-69. 40.Lin IT, Chao JL, Yao MC. An Essential Role for the DNA Breakage-Repair Protein Ku80 in Programmed DNA Rearrangements in Tetrahymena Thermophila. Mol Biol Cell. 2012;23(11):2213-25. 41.Cheng CY, Young JM, Lin CG, Chao JL, Malik HS, Yao MC. The Piggybac Transposon-Derived Genes Tpb1 and Tpb6 Mediate Essential Transposon-Like Excision During the Developmental Rearrangement of Key Genes in Tetrahymena Thermophila. Genes Dev. 2016;30(24):2724-36. 42.Yao MC, Zheng K, Yao CH. A Conserved Nucleotide Sequence at the Sites of Developmentally Regulated Chromosomal Breakage in Tetrahymena. Cell. 1987;48(5):779-88. 43.Challoner PB, Blackburn EH. Conservation of Sequences Adjacent to the Telomeric C4a2 Repeats of Ciliate Macronuclear Ribosomal Rna Gene Molecules. Nucleic Acids Res. 1986;14(15):6299-311. 44.Yao MC, Yao CH, Monks B. The Controlling Sequence for Site-Specific Chromosome Breakage in Tetrahymena. Cell. 1990;63(4):763-72. 45.Fan Q, Yao M. New Telomere Formation Coupled with Site-Specific Chromosome Breakage in Tetrahymena Thermophila. Mol Cell Biol. 1996;16(3):1267-74. 46.Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, et al. Macronuclear Genome Sequence of the Ciliate Tetrahymena Thermophila, a Model Eukaryote. PLoS Biol. 2006;4(9):e286. 47.Yao MC, Gall JG. A Single Integrated Gene for Ribosomal Rna in a Eucaryote, Tetrahymena Pyriformis. Cell. 1977;12(1):121-32. 48.Yao MC, Kimmel AR, Gorovsky MA. A Small Number of Cistrons for Ribosomal Rna in the Germinal Nucleus of a Eukaryote, Tetrahymena Pyriformis. Proc Natl Acad Sci U S A. 1974;71(8):3082-6. 49.Engberg J, Christiansen G, Leick V. Autonomous Rdna Molecules Containing Single Copies of the Ribosomal Rna Genes in the Macronucleus of Tetrahymena Pyriformis. Biochem Biophys Res Commun. 1974;59(4):1356-65. 50.Gall JG. Free Ribosomal Rna Genes in the Macronucleus of Tetrahymena. Proc Natl Acad Sci U S A. 1974;71(8):3078-81. 51.Yao MC, Zhu SG, Yao CH. Gene Amplification in Tetrahymena Thermophila: Formation of Extrachromosomal Palindromic Genes Coding for Rrna. Mol Cell Biol. 1985;5(6):1260-7. 52.Coyne RS, Yao MC. Evolutionary Conservation of Sequences Directing Chromosome Breakage and Rdna Palindrome Formation in Tetrahymenine Ciliates. Genetics. 1996;144(4):1479-87. 53.Eileen P. Hamilton SW, Sandra Dunn, Virginia Merriam, Cindy Lin, Linh Vong, Jessica Russell-Colantonio, and Eduardo Orias. The Highly Conserved Family of Tetrahymena Thermophila Chromosome Breakage Elements Contains an Invariant 10-Base-Pair Core. Eukaryot Cell. 2006;5(4):9. 54.Yao MC, Gorovsky MA. Comparison of the Sequences of Macro- and Micronuclear DNA of Tetrahymena Pyriformis. Chromosoma. 1974;48(1):1-18. 55.Yao MC, Choi J, Yokoyama S, Austerberry CF, Yao CH. DNA Elimination in Tetrahymena: A Developmental Process Involving Extensive Breakage and Rejoining of DNA at Defined Sites. Cell. 1984;36(2):433-40. 56.Austerberry CF, Yao MC. Sequence Structures of Two Developmentally Regulated, Alternative DNA Deletion Junctions in Tetrahymena Thermophila. Mol Cell Biol. 1988;8(9):3947-50. 57.Godiska R, Yao MC. A Programmed Site-Specific DNA Rearrangement in Tetrahymena Thermophila Requires Flanking Polypurine Tracts. Cell. 1990;61(7):1237-46. 58.Godiska R, James C, Yao MC. A Distant 10-Bp Sequence Specifies the Boundaries of a Programmed DNA Deletion in Tetrahymena. Genes Dev. 1993;7(12A):2357-65. 59.Carle CM, Zaher HS, Chalker DL. A Parallel G Quadruplex-Binding Protein Regulates the Boundaries of DNA Elimination Events of Tetrahymena Thermophila. PLoS Genet. 2016;12(3):e1005842. 60.Austerberry CF, Yao MC. Nucleotide Sequence Structure and Consistency of a Developmentally Regulated DNA Deletion in Tetrahymena Thermophila. Mol Cell Biol. 1987;7(1):435-43. 61.Chalker DL, La Terza A, Wilson A, Kroenke CD, Yao MC. Flanking Regulatory Sequences of the Tetrahymena R Deletion Element Determine the Boundaries of DNA Rearrangement. Mol Cell Biol. 1999;19(8):5631-41. 62.Wells JM, Ellingson JL, Catt DM, Berger PJ, Karrer KM. A Small Family of Elements with Long Inverted Repeats Is Located near Sites of Developmentally Regulated DNA Rearrangement in Tetrahymena Thermophila. Mol Cell Biol. 1994;14(9):5939-49. 63.Patil NS, Hempen PM, Udani RA, Karrer KM. Alternate Junctions and Microheterogeneity of Tlr1, a Developmentally Regulated DNA Rearrangement in Tetrahymena Thermophila. J Eukaryot Microbiol. 1997;44(5):518-22. 64.Patil NS, Karrer KM. A Developmentally Regulated Deletion Element with Long Terminal Repeats Has Cis-Acting Sequences in the Flanking DNA. Nucleic Acids Res. 2000;28(6):1465-72. 65.Fillingham JS, Bruno D, Pearlman RE. Cis-Acting Requirements in Flanking DNA for the Programmed Elimination of Mse2.9: A Common Mechanism for Deletion of Internal Eliminated Sequences from the Developing Macronucleus of Tetrahymena Thermophila. Nucleic Acids Res. 2001;29(2):488-98. 66.Fan X, Abbott TE, Larson D, Chen K. Breakdancer: Identification of Genomic Structural Variation from Paired-End Read Mapping. Curr Protoc Bioinformatics. 2014;45:15 6 1-1. 67.Collins K, Gorovsky MA. Tetrahymena Thermophila. Curr Biol. 2005;15(9):R317-8. 68.Cheng CY, Vogt A, Mochizuki K, Yao MC. A Domesticated Piggybac Transposase Plays Key Roles in Heterochromatin Dynamics and DNA Cleavage During Programmed DNA Deletion in Tetrahymena Thermophila. Mol Biol Cell. 2010;21(10):1753-62. 69.Xu HF, Xia QY, Liu C, Cheng TC, Zhao P, Duan J, et al. Identification and Characterization of Piggybac-Like Elements in the Genome of Domesticated Silkworm, Bombyx Mori. Mol Genet Genomics. 2006;276(1):31-40. 70.Cary LC, Goebel M, Corsaro BG, Wang HG, Rosen E, Fraser MJ. Transposon Mutagenesis of Baculoviruses: Analysis of Trichoplusia Ni Transposon Ifp2 Insertions within the Fp-Locus of Nuclear Polyhedrosis Viruses. Virology. 1989;172(1):156-69. 71.Wang J, Du Y, Wang S, Brown SJ, Park Y. Large Diversity of the Piggybac-Like Elements in the Genome of Tribolium Castaneum. Insect Biochem Mol Biol. 2008;38(4):490-8. 72.Baudry C, Malinsky S, Restituito M, Kapusta A, Rosa S, Meyer E, et al. Piggymac, a Domesticated Piggybac Transposase Involved in Programmed Genome Rearrangements in the Ciliate Paramecium Tetraurelia. Genes Dev. 2009;23(21):2478-83. 73.Austerberry CF, Allis CD, Yao MC. Specific DNA Rearrangements in Synchronously Developing Nuclei of Tetrahymena. Proc Natl Acad Sci U S A. 1984;81(23):7383-7. 74.Gros J, Rosu F, Amrane S, De Cian A, Gabelica V, Lacroix L, et al. Guanines Are a Quartet''s Best Friend: Impact of Base Substitutions on the Kinetics and Stability of Tetramolecular Quadruplexes. Nucleic Acids Res. 2007;35(9):3064-75. 75.Cassidy-Hanley D, Bisharyan Y, Fridman V, Gerber J, Lin C, Orias E, et al. Genome-Wide Characterization of Tetrahymena Thermophila Chromosome Breakage Sites. Ii. Physical and Genetic Mapping. Genetics. 2005;170(4):1623-31. 76.Stover NA, Krieger CJ, Binkley G, Dong Q, Fisk DG, Nash R, et al. Tetrahymena Genome Database (Tgd): A New Genomic Resource for Tetrahymena Thermophila Research. Nucleic Acids Res. 2006;34(Database issue):D500-3. 77.Tetrahymena thermophila SB210 wgssp, http://www.ncbi.nlm.nih.gov/nuccore/AFSS00000000.2/. 78.Coyne RS, Nikiforov MA, Smothers JF, Allis CD, Yao MC. Parental Expression of the Chromodomain Protein Pdd1p Is Required for Completion of Programmed DNA Elimination and Nuclear Differentiation. Mol Cell. 1999;4(5):865-72. 79.Kataoka K, Mochizuki K. Phosphorylation of an Hp1-Like Protein Regulates Heterochromatin Body Assembly for DNA Elimination. Dev Cell. 2015;35(6):775-88. 80.Xiong J, Lu X, Zhou Z, Chang Y, Yuan D, Tian M, et al. Transcriptome Analysis of the Model Protozoan, Tetrahymena Thermophila, Using Deep Rna Sequencing. PLoS One. 2012;7(2):e30630. 81.Tetrahymena Comparative Sequencing Project BIoHaM, https://www.ncbi.nlm.nih.gov/bioproject/?term=Tetrahymena%20broad%20institute. 82.Karamysheva Z, Wang L, Shrode T, Bednenko J, Hurley LA, Shippen DE. Developmentally Programmed Gene Elimination in Euplotes Crassus Facilitates a Switch in the Telomerase Catalytic Subunit. Cell. 2003;113(5):565-76. 83.Gorovsky MA, Yao MC, Keevert JB, Pleger GL. Isolation of Micro- and Macronuclei of Tetrahymena Pyriformis. Methods Cell Biol. 1975;9(0):311-27. 84.Liu Y, Schroder J, Schmidt B. Musket: A Multistage K-Mer Spectrum-Based Error Corrector for Illumina Sequence Data. Bioinformatics. 2013;29(3):308-15. 85.Li H, Durbin R. Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform. Bioinformatics. 2009;25(14):1754-60. 86.Langmead B, Salzberg SL. Fast Gapped-Read Alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9. 87.Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map Format and Samtools. Bioinformatics. 2009;25(16):2078-9. 88.Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (Igv): High-Performance Genomics Data Visualization and Exploration. Brief Bioinform. 2013;14(2):178-92. 89.Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential Gene and Transcript Expression Analysis of Rna-Seq Experiments with Tophat and Cufflinks. Nat Protoc. 2012;7(3):562-78. 90.Saitou N, Nei M. The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Mol Biol Evol. 1987;4(4):406-25. 91.Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. Mega5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol. 2011;28(10):2731-9. 92.Felsenstein J. Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution. 1985;39:783-91. 93.Zuckerkandl E, Pauling L. Evolutionary Divergence and Convergence in Proteins. Evolving genes and proteins. 1965:97-166. 94.Schwartz DC, Cantor CR. Separation of Yeast Chromosome-Sized Dnas by Pulsed Field Gradient Gel Electrophoresis. Cell. 1984;37(1):67-75. 95.Lukaszewicz A, Howard-Till RA, Novatchkova M, Mochizuki K, Loidl J. Mre11 and Com1/Sae2 Are Required for Double-Strand Break Repair and Efficient Chromosome Pairing During Meiosis of the Protist Tetrahymena. Chromosoma. 2010;119(5):505-18. 96.Yao MC, Fuller P, Xi X. Programmed DNA Deletion as an Rna-Guided System of Genome Defense. Science. 2003;300(5625):1581-4. 97.Crooks GE, Hon G, Chandonia JM, Brenner SE. Weblogo: A Sequence Logo Generator. Genome Res. 2004;14(6):1188-90.
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