The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster
暂无分享,去创建一个
A. Clark | S. Luo | Jian Lu | Xinmin Yao | Y. Duan | Hong Zhang | A. Clark | A. Clark
[1] G. Hannon,et al. piRNA-Guided Genome Defense: From Biogenesis to Silencing. , 2018, Annual review of genetics.
[2] R. Kofler. Dynamics of Transposable Element Invasions with piRNA Clusters , 2018, bioRxiv.
[3] Deniz M. Ozata,et al. PIWI-interacting RNAs: small RNAs with big functions , 2018, Nature Reviews Genetics.
[4] J. Flowers,et al. Origins and geographic diversification of African rice (Oryza glaberrima) , 2018, bioRxiv.
[5] J. Jensen,et al. The Demographic History of African Drosophila melanogaster , 2018, bioRxiv.
[6] C. Schlötterer,et al. Molecular dissection of a natural transposable element invasion , 2018, Genome research.
[7] A. Aravin,et al. piRNA Biogenesis in Drosophila melanogaster. , 2017, Trends in genetics : TIG.
[8] J. Brennecke,et al. A heterochromatin-dependent transcription machinery drives piRNA expression , 2017, Nature.
[9] Jian Lu,et al. Silencing of Transposable Elements by piRNAs in Drosophila: An Evolutionary Perspective , 2017, Genom. Proteom. Bioinform..
[10] R. B. Azevedo,et al. The Evolution of Small-RNA-Mediated Silencing of an Invading Transposable Element , 2017, bioRxiv.
[11] Daniel R. Schrider,et al. Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster , 2017, Genome biology and evolution.
[12] S. Luo,et al. Adaptation of A-to-I RNA editing in Drosophila , 2017, PLoS genetics.
[13] J. Blumenstiel,et al. What Drives Positive Selection in the Drosophila piRNA Machinery? The Genomic Autoimmunity Hypothesis , 2016, The Yale journal of biology and medicine.
[14] Stefan L Ameres,et al. Genetic and mechanistic diversity of piRNA 3' end formation , 2016, Nature.
[15] Laurent Modolo,et al. TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes , 2016, Nucleic acids research.
[16] E. Kelleher. Reexamining the P-Element Invasion of Drosophila melanogaster Through the Lens of piRNA Silencing , 2016, Genetics.
[17] A. Buckling,et al. Evolutionary Ecology of Prokaryotic Immune Mechanisms , 2016, Microbiology and Molecular Reviews.
[18] Russell B. Corbett-Detig,et al. A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus , 2016, bioRxiv.
[19] G. Hannon,et al. One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing , 2016, Trends in biochemical sciences.
[20] A. Aravin,et al. Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila , 2016, Genes & development.
[21] B. Brembs,et al. Unique transposon landscapes are pervasive across Drosophila melanogaster genomes , 2015, Nucleic acids research.
[22] R. Sachidanandam,et al. piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire , 2015, Genes & development.
[23] O. Kohany,et al. Repbase Update, a database of repetitive elements in eukaryotic genomes , 2015, Mobile DNA.
[24] M. Siomi,et al. PIWI-Interacting RNA: Its Biogenesis and Functions. , 2015, Annual review of biochemistry.
[25] Y. C. G. Lee. The Role of piRNA-Mediated Epigenetic Silencing in the Population Dynamics of Transposable Elements in Drosophila melanogaster , 2015, PLoS genetics.
[26] Zhiping Weng,et al. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production , 2015, Science.
[27] Julius Brennecke,et al. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis , 2015, Science.
[28] A. Clark,et al. Global Diversity Lines–A Five-Continent Reference Panel of Sequenced Drosophila melanogaster Strains , 2015, G3: Genes, Genomes, Genetics.
[29] Russell B. Corbett-Detig,et al. The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population , 2015, Genetics.
[30] Brian T. Lee,et al. The UCSC Genome Browser database: 2015 update , 2014, Nucleic Acids Research.
[31] Maite G. Barrón,et al. Population genomics of transposable elements in Drosophila. , 2014, Annual review of genetics.
[32] Kevin R. Thornton,et al. Gene Expression Variation in Drosophila melanogaster Due to Rare Transposable Element Insertion Alleles of Large Effect , 2014, Genetics.
[33] Kevin C. Chen,et al. Variation in piRNA and Transposable Element Content in Strains of Drosophila melanogaster , 2014, Genome biology and evolution.
[34] Paul Theodor Pyl,et al. HTSeq – A Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[35] Josefa González,et al. A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila , 2014, PLoS genetics.
[36] R. Sachidanandam,et al. Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing , 2014, Genes & development.
[37] R. Gibbs,et al. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines , 2014, Genome research.
[38] A. Siepel,et al. Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines , 2014, Genome research.
[39] Fabio Mohn,et al. The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila , 2014, Cell.
[40] Z. Weng,et al. The HP1 Homolog Rhino Anchors a Nuclear Complex that Suppresses piRNA Precursor Splicing , 2014, Cell.
[41] Zhiping Weng,et al. TEMP: a computational method for analyzing transposable element polymorphism in populations , 2014, Nucleic acids research.
[42] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[43] I. Olovnikov,et al. Euchromatic Transposon Insertions Trigger Production of Novel Pi- and Endo-siRNAs at the Target Sites in the Drosophila Germline , 2014, PLoS genetics.
[44] W. Rice. Nothing in Genetics Makes Sense Except in Light of Genomic Conflict , 2013 .
[45] Matthias Zytnicki,et al. Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters , 2013, Proceedings of the National Academy of Sciences.
[46] D. Barbash,et al. Analysis of piRNA-mediated silencing of active TEs in Drosophila melanogaster suggests limits on the evolution of host genome defense. , 2013, Molecular biology and evolution.
[47] Kevin R. Thornton,et al. Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources , 2013, Molecular biology and evolution.
[48] Nikolaos S. Alachiotis,et al. SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes , 2013, Molecular biology and evolution.
[49] S. Pfaff,et al. Transposable elements as genetic regulatory substrates in early development. , 2013, Trends in cell biology.
[50] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[51] C. Vaury,et al. De novo piRNA cluster formation in the Drosophila germ line triggered by transgenes containing a transcribed transposon fragment , 2013, Nucleic acids research.
[52] J. Dubnau,et al. Activation of transposable elements during aging and neuronal decline in Drosophila , 2013, Nature Neuroscience.
[53] Georgi K Marinov,et al. Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. , 2013, Genes & development.
[54] E. Zelentsova,et al. Evolution and dynamics of small RNA response to a retroelement invasion in Drosophila. , 2013, Molecular biology and evolution.
[55] C. Langley,et al. Long-Term and Short-Term Evolutionary Impacts of Transposable Elements on Drosophila , 2012, Genetics.
[56] Julius Brennecke,et al. Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression , 2012, Cell.
[57] D. Mager,et al. Transposable elements: an abundant and natural source of regulatory sequences for host genes. , 2012, Annual review of genetics.
[58] S. Elgin,et al. Ectopic assembly of heterochromatin in Drosophila melanogaster triggered by transposable elements , 2012, Proceedings of the National Academy of Sciences.
[59] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[60] Kevin R. Thornton,et al. The Drosophila melanogaster Genetic Reference Panel , 2012, Nature.
[61] Robert Kofler,et al. Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster , 2012, PLoS genetics.
[62] Zhiping Weng,et al. Adaptation to P Element Transposon Invasion in Drosophila melanogaster , 2011, Cell.
[63] Celina E. Juliano,et al. Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms. , 2011, Annual review of genetics.
[64] A. Spradling,et al. Drosophila P elements preferentially transpose to replication origins , 2011, Proceedings of the National Academy of Sciences.
[65] J. V. Moran,et al. Dynamic interactions between transposable elements and their hosts , 2011, Nature Reviews Genetics.
[66] J. Werren. Selfish genetic elements, genetic conflict, and evolutionary innovation , 2011, Proceedings of the National Academy of Sciences.
[67] Gonçalo R. Abecasis,et al. The variant call format and VCFtools , 2011, Bioinform..
[68] Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .
[69] D. Petrov,et al. Population genomics of transposable elements in Drosophila melanogaster. , 2011, Molecular biology and evolution.
[70] A. Aravin,et al. PIWI-interacting small RNAs: the vanguard of genome defence , 2011, Nature Reviews Molecular Cell Biology.
[71] K. Senti,et al. The piRNA pathway: a fly's perspective on the guardian of the genome. , 2010, Trends in genetics : TIG.
[72] B. Loppin,et al. Drosophila I-R hybrid dysgenesis is associated with catastrophic meiosis and abnormal zygote formation , 2010, Journal of Cell Science.
[73] W. Stephan,et al. Searching for Footprints of Positive Selection in Whole-Genome SNP Data From Nonequilibrium Populations , 2010, Genetics.
[74] C. Langley,et al. Transposable elements in natural populations of Drosophila melanogaster , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.
[75] A. Clark,et al. Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. , 2010, Genome research.
[76] Dawn H. Nagel,et al. The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.
[77] Haifan Lin,et al. The biogenesis and function of PIWI proteins and piRNAs: progress and prospect. , 2009, Annual review of cell and developmental biology.
[78] Jeffrey C Barrett,et al. Haploview: Visualization and analysis of SNP genotype data. , 2009, Cold Spring Harbor protocols.
[79] Julius Brennecke,et al. Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary , 2009, Cell.
[80] Z. Weng,et al. Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies , 2009, Cell.
[81] B. Charlesworth. Effective population size and patterns of molecular evolution and variation , 2009, Nature Reviews Genetics.
[82] R. Sachidanandam,et al. An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing , 2008, Science.
[83] F. Jiggins,et al. The evolution of RNAi as a defence against viruses and transposable elements , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.
[84] Josefa González,et al. High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster , 2008, PLoS biology.
[85] C. Brun,et al. piRNA-mediated nuclear accumulation of retrotransposon transcripts in the Drosophila female germline , 2008, Proceedings of the National Academy of Sciences.
[86] B. Charlesworth,et al. The Effects of Recombination Rate on the Distribution and Abundance of Transposable Elements , 2008, Genetics.
[87] J. Bennetzen,et al. A unified classification system for eukaryotic transposable elements , 2007, Nature Reviews Genetics.
[88] W. Theurkauf,et al. Biogenesis and germline functions of piRNAs , 2007, Development.
[89] Haifan Lin,et al. An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster , 2007, Nature.
[90] Melanie A. Huntley,et al. Evolution of genes and genomes on the Drosophila phylogeny , 2007, Nature.
[91] Kuniaki Saito,et al. Gene silencing mechanisms mediated by Aubergine piRNA complexes in Drosophila male gonad. , 2007, RNA.
[92] Christina A. Cuomo,et al. The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization , 2007, Science.
[93] C. Bergman,et al. Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster , 2007, Proceedings of the National Academy of Sciences.
[94] C. Mungall,et al. The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin , 2007, Science.
[95] Eugene Berezikov,et al. A Role for Piwi and piRNAs in Germ Cell Maintenance and Transposon Silencing in Zebrafish , 2007, Cell.
[96] R. Martienssen,et al. Transposable elements and the epigenetic regulation of the genome , 2007, Nature Reviews Genetics.
[97] Manolis Kellis,et al. Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila , 2007, Cell.
[98] Kuniaki Saito,et al. A Slicer-Mediated Mechanism for Repeat-Associated siRNA 5' End Formation in Drosophila , 2007, Science.
[99] Christopher M. Player,et al. Large-Scale Sequencing Reveals 21U-RNAs and Additional MicroRNAs and Endogenous siRNAs in C. elegans , 2006, Cell.
[100] Michael Ashburner,et al. Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome , 2006, Genome Biology.
[101] W. Stephan,et al. Inferring the Demographic History and Rate of Adaptive Substitution in Drosophila , 2006, PLoS genetics.
[102] Kuniaki Saito,et al. Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. , 2006, Genes & development.
[103] N. Lau,et al. Characterization of the piRNA Complex from Rat Testes , 2006, Science.
[104] Vladimir Gvozdev,et al. A Distinct Small RNA Pathway Silences Selfish Genetic Elements in the Germline , 2006, Science.
[105] Ravi Sachidanandam,et al. A germline-specific class of small RNAs binds mammalian Piwi proteins , 2006, Nature.
[106] Haifan Lin,et al. A novel class of small RNAs in mouse spermatogenic cells. , 2006, Genes & development.
[107] Carlos Bustamante,et al. Genomic scans for selective sweeps using SNP data. , 2005, Genome research.
[108] W. Stephan,et al. Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation. , 2005, Molecular biology and evolution.
[109] D. Petrov,et al. References and Notes Materials and Methods Tables S1 and S2 References and Notes Pesticide Resistance via Transposition-mediated Adaptive Gene Truncation in Drosophila , 2022 .
[110] Casey M. Bergman,et al. Combined Evidence Annotation of Transposable Elements in Genome Sequences , 2005, PLoS Comput. Biol..
[111] Kevin R. Thornton,et al. Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. , 2005, Genome research.
[112] M. Cáceres,et al. Silencing of a gene adjacent to the breakpoint of a widespread Drosophila inversion by a transposon-induced antisense RNA , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[113] W. Stephan,et al. Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach. , 2003, Genetics.
[114] D. Marks,et al. The small RNA profile during Drosophila melanogaster development. , 2003, Developmental cell.
[115] A. E. Hirsh,et al. Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila. , 2003, Molecular biology and evolution.
[116] J. Jurka,et al. Molecular paleontology of transposable elements in the Drosophila melanogaster genome , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[117] M. Ashburner,et al. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective , 2002, Genome Biology.
[118] W. J. Kent,et al. BLAT--the BLAST-like alignment tool. , 2002, Genome research.
[119] W. Stephan,et al. Detecting a local signature of genetic hitchhiking along a recombining chromosome. , 2002, Genetics.
[120] A. Aravin,et al. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline , 2001, Current Biology.
[121] Justin C. Fay,et al. Hitchhiking under positive Darwinian selection. , 2000, Genetics.
[122] Stephen M. Mount,et al. The genome sequence of Drosophila melanogaster. , 2000, Science.
[123] M. G. Kidwell,et al. Transposable elements and host genome evolution. , 2000, Trends in ecology & evolution.
[124] M. G. Kidwell,et al. A phylogenetic perspective on P transposable element evolution in Drosophila. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[125] L. Hurst,et al. Genetic Conflicts , 1996, The Quarterly Review of Biology.
[126] C. Caggese,et al. Transposable elements are stable structural components of Drosophila melanogaster heterochromatin. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[127] Wolfgang Stephan,et al. The evolutionary dynamics of repetitive DNA in eukaryotes , 1994, Nature.
[128] J. Brookfield. Models of repression of transposition in P-M hybrid dysgenesis by P cytotype and by zygotically encoded repressor proteins. , 1991, Genetics.
[129] W. Engels,et al. High-frequency P element loss in Drosophila is homolog dependent , 1990, Cell.
[130] F. Tajima. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.
[131] R. Hudson,et al. On the role of unequal exchange in the containment of transposable element copy number. , 1988, Genetical research.
[132] M. G. Kidwell. Hybrid dysgenesis in Drosophila melanogaster: nature and inheritance of P element regulation. , 1985, Genetics.
[133] G. Rubin,et al. Analysis of P transposable element functions in drosophila , 1984, Cell.
[134] Graham K. Rand,et al. Quantitative Applications in the Social Sciences , 1983 .
[135] B. Charlesworth,et al. The population dynamics of transposable elements , 1983 .
[136] G. Rubin,et al. Structures of P transposable elements and their sites of insertion and excision in the Drosophila melanogaster genome , 1983, Cell.
[137] C. Langley,et al. Transposable Elements in Mendelian Populations. II. Distribution of Three COPIA-like Elements in a Natural Population of DROSOPHILA MELANOGASTER. , 1983, Genetics.
[138] M. G. Kidwell. Evolution of hybrid dysgenesis determinants in Drosophila melanogaster. , 1983, Proceedings of the National Academy of Sciences of the United States of America.
[139] G. Rubin,et al. Genetic transformation of Drosophila with transposable element vectors. , 1982, Science.
[140] Jeffrey H. Miller,et al. Transposable elements , 1980, Cell.
[141] J. Krebs,et al. Arms races between and within species , 1979, Proceedings of the Royal Society of London. Series B. Biological Sciences.
[142] M. G. Kidwell,et al. Hybrid Dysgenesis in DROSOPHILA MELANOGASTER: A Syndrome of Aberrant Traits Including Mutation, Sterility and Male Recombination. , 1977, Genetics.
[143] A. Bucheton,et al. [A partially inheritable aging influence on a non-Mendelian female sterility in Drosophila melanogaster]. , 1975, Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D: Sciences naturelles.
[144] A. Bucheton. [Study of non Mendelian female sterility in Drosophila melanogaster. Hereditary transmission of the degree of efficacy of the reactor factor]. , 1973, Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D: Sciences naturelles.
[145] R. Britten,et al. Repeated Sequences in DNA , 1968 .
[146] M. Neiman,et al. Antagonistic Interspecific Coevolution , 2016 .
[147] Christophe Antoniewski,et al. Computing siRNA and piRNA overlap signatures. , 2014, Methods in molecular biology.
[148] Patrik Nosil,et al. Conflictual speciation: species formation via genomic conflict. , 2013, Trends in ecology & evolution.
[149] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[150] Robert C. Edgar,et al. Search and clustering orders of magnitude faster than BLAST , 2010 .
[151] Ira M. Hall,et al. BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..
[152] Claude-Alain H. Roten,et al. Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..
[153] M. Feder,et al. Location of P element insertions in the proximal promoter region of Hsp70A is consequential for gene expression and correlated with fecundity in Drosophila melanogaster , 2007, Cell Stress and Chaperones.
[154] Lilya V. Matyunina,et al. Ltr retrotransposons and the evolution of eukaryotic enhancers , 2004, Genetica.
[155] S. Nuzhdin. Sure facts, speculations, and open questions about the evolution of transposable element copy number , 2004, Genetica.
[156] E. Galun. Transposable Elements , 2003, Springer Netherlands.
[157] Hilde van der Togt,et al. Publisher's Note , 2003, J. Netw. Comput. Appl..
[158] C. Schlötterer,et al. Chromosomal patterns of microsatellite variability contrast sharply in African and non-African populations of Drosophila melanogaster. , 2002, Genetics.
[159] Michael Ashburner,et al. Drosophila: A laboratory handbook , 1990 .
[160] B. Charlesworth,et al. The population genetics of Drosophila transposable elements. , 1989, Annual review of genetics.
[161] D. Finnegan,et al. Eukaryotic transposable elements and genome evolution. , 1989, Trends in genetics : TIG.
[162] Michael Ashburner,et al. A Laboratory handbook , 1989 .
[163] L. V. Valen,et al. A new evolutionary law , 1973 .