Ongoing endeavors to detect mobilization of transposable elements

키워드

참고문헌 (150)

1. Mc CB, "The origin and behavior of mutable loci in maize", Proc Natl Acad Sci U S A, 36, pp.344~355 (1950)
2. Kazazian HH Jr, "Mobile DNA in health and disease", N Engl J Med, 377, pp.361~370 (2017)
3. Richardson SR, "The Influence of LINE-1 and SINE retrotransposons on mammalian genomes", Microbiol Spectr, 3, pp.MDNA3-0061~ (2015)
4. Cordaux R, "The impact of retrotransposons on human genome evolution", Nat Rev Genet, 10, pp.691~703 (2009)
5. Hancks DC, "Roles for retrotransposon insertions in human disease", Mob DNA, 7, pp.9~ (2016)
6. Ostertag EM, "Biology of mammalian L1 retrotransposons", Annu Rev Genet, 35, pp.501~538 (2001)
7. Ewing AD, "High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes", Genome Res, 20, pp.1262~1270 (2010)
8. Mager DL, "Mammalian endogenous retroviruses", Microbiol Spectr, 3, pp.MDNA3-0009~ (2015)
9. Tarlinton RE, "Retroviral invasion of the koala genome", Nature, 442, pp.79~81 (2006)
10. Lander ES, "Initial sequencing and analysis of the human genome", Nature, 409, pp.860~921 (2001)
11. Clark JB, "A phylogenetic perspective on P transposable element evolution in Drosophila", Proc Natl Acad Sci U S A, 94, pp.11428~11433 (1997)
12. Khurana JS, "Adaptation to P element transposon invasion in Drosophila melanogaster", Cell, 147, pp.1551~1563 (2011)
13. Moon S, "A robust transposon-endogenizing response from germline stem cells", Dev Cell, 47, pp.660~671 (2018)
14. Kofler R, "Molecular dissection of a natural transposable element invasion", Genome Res, 28, pp.824~835 (2018)
15. Kofler R, "The recent invasion of natural Drosophila simulans populations by the P-element", Proc Natl Acad Sci U S A, 112, pp.6659~6663 (2015)
16. Hill T, "Hybrid dysgenesis in Drosophila simulans associated with a rapid invasion of the P-element", PLoS Genet, 12, pp.e1005920~ (2016)
17. Bellen HJ, "The Drosophila gene disruption project : progress using transposons with distinctive site specificities", Genetics, 188, pp.731~743 (2011)
18. Spradling AC, "Drosophila P elements preferentially transpose to replication origins", Proc Natl Acad Sci U S A, 108, pp.15948~15953 (2011)
19. Eickbush TH, "Integration, regulation, and long-term stability of R2 retrotransposons", Microbiol Spectr, 3, pp.MDNA3-0011~ (2015)
20. Huang CR, "Active transposition in genomes", Annu Rev Genet, 46, pp.651~675 (2012)
21. Sotero-Caio CG, "Evolution and diversity of transposable elements in vertebrate genomes", Genome Biol Evol, 9, pp.161~177 (2017)
22. Kissinger JC, "Genome cartography : charting the apicomplexan genome", Trends Parasitol, 27, pp.345~354 (2011)
23. Van’t Hof AE, "The industrial melanism mutation in British peppered moths is a transposable element", Nature, 534, pp.102~105 (2016)
24. Lisch D, "How important are transposons for plant evolution?", Nat Rev Genet, 14, pp.49~61 (2013)
25. Studer A, "Identification of a functional transposon insertion in the maize domestication gene tb1", Nat Genet, 43, pp.1160~1163 (2011)
26. Rebollo R, "C-GATE-catalogue of genes affected by transposable elements", Mob DNA, 3, pp.9~ (2012)
27. de Souza FS, "Exaptation of transposable elements into novel cis-regulatory elements : is the evidence always strong?", Mol Biol Evol, 30, pp.1239~1251 (2013)
28. Sundaram V, "Widespread contribution of transposable elements to the innovation of gene regulatory networks", Genome Res, 24, pp.1963~1976 (2014)
29. Notwell JH, "A family of transposable elements co-opted into developmental enhancers in the mouse neocortex", Nat Commun, 6, pp.6644~ (2015)
30. Lynch VJ, "Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals", Nat Genet, 43, pp.1154~1159 (2011)
31. Kapitonov VV, "RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons", PLoS Biol, 3, pp.e181~ (2005)
32. Huang S, "Discovery of an active RAG transposon illuminates the origins of V(D)J recombination", Cell, 166, pp.102~114 (2016)
33. Traverse KL, "A spontaneously opened ring chromosome of Drosophila melanogaster has acquired He-T DNA sequences at both new telomeres", Proc Natl Acad Sci U S A, 85, pp.8116~8120 (1988)
34. Levis RW, "Transposons in place of telomeric repeats at a Drosophila telomere", Cell, 75, pp.1083~1093 (1993)
35. Abad JP, "TAHRE, a novel telomeric retrotransposon from Drosophila melanogaster, reveals the origin of Drosophila telomeres", Mol Biol Evol, 21, pp.1620~1624 (2004)
36. Villasante A, "Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase", Genome Res, 17, pp.1909~1918 (2007)
37. Agudo M, "Centromeres from telomeres? The centromeric region of the Y chromosome of Drosophila melanogaster contains a tandem array of telomeric HeT-Aand TART-related sequences", Nucleic Acids Res, 27, pp.3318~3324 (1999)
38. Chang CH, "Islands of retroelements are major components of Drosophila centromeres", PLoS Biol, 17, pp.e3000241~ (2019)
39. Neumann P, "Plant centromeric retrotransposons : a structural and cytogenetic perspective", Mob DNA, 2, pp.4~ (2011)
40. Glockner G, "Centromere sequence and dynamics in Dictyostelium discoideum", Nucleic Acids Res, 37, pp.1809~1816 (2009)
41. Ferreri GC, "Recent amplification of the kangaroo endogenous retrovirus, KERV, limited to the centromere", J Virol, 85, pp.4761~4771 (2011)
42. Rad R, "PiggyBac transposon mutagenesis : a tool for cancer gene discovery in mice", Science, 330, pp.1104~1107 (2010)
43. Dupuy AJ, "Mammalian mutagenesis using a highly mobile somatic Sleeping Beauty transposon system", Nature, 436, pp.221~226 (2005)
44. Lee E, "Landscape of somatic retrotransposition in human cancers", Science, 337, pp.967~971 (2012)
45. Babaian A, "Endogenous retroviral promoter exaptation in human cancer", Mob DNA, 7, pp.24~ (2016)
46. Shukla R, "Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma", Cell, 153, pp.101~111 (2013)
47. Bailey JA, "An Alu transposition model for the origin and expansion of human segmental duplications", Am J Hum Genet, 73, pp.823~834 (2003)
48. Montgomery EA, "Chromosome rearrangement by ectopic recombination in Drosophila melanogaster : genome structure and evolution", Genetics, 129, pp.1085~1098 (1991)
49. Deininger PL, "Alu repeats and human disease", Mol Genet Metab, 67, pp.183~193 (1999)
50. Deniz O, "Regulation of transposable elements by DNA modifications", Nat Rev Genet, 20, pp.417~431 (2019)
51. Ozata DM, "PIWI-interacting RNAs : small RNAs with big functions", Nat Rev Genet, 20, pp.89~108 (2019)
52. Yang P, "The role of KRAB-ZFPs in transposable element repression and mammalian evolution", Trends Genet, 33, pp.871~881 (2017)
53. Wang L, "Hijacking oogenesis enables massive propagation of LINE and retroviral transposons", Cell, 174, pp.1082~1094 (2018)
54. Nagirnaja L, "Variant PNLDC1, defective piRNA processing, and azoospermia", N Engl J Med, 385, pp.707~719 (2021)
55. Houwing S, "A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish", Cell, 129, pp.69~82 (2007)
56. Carmell MA, "MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline", Dev Cell, 12, pp.503~514 (2007)
57. Bourc’his D, "Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L", Nature, 431, pp.96~99 (2004)
58. Siudeja K, "Unraveling the features of somatic transposition in the Drosophila intestine", EMBO J, 40, pp.e106388~ (2021)
59. Brouha B, "Hot L1s account for the bulk of retrotransposition in the human population", Proc Natl Acad Sci U S A, 100, pp.5280~5285 (2003)
60. Beck CR, "LINE-1retrotransposition activity in human genomes", Cell, 141, pp.1159~1170 (2010)
61. Hancks DC, "Retrotransposition of marked SVA elements by human L1s in cultured cells", Hum Mol Genet, 20, pp.3386~3400 (2011)
62. Raiz J, "The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery", Nucleic Acids Res, 40, pp.1666~1683 (2012)
63. Boeke JD, "Ty elements transpose through an RNA intermediate", Cell, 40, pp.491~500 (1985)
64. Moran JV, "High frequency retrotrans-position in cultured mammalian cells", Cell, 87, pp.917~927 (1996)
65. Ostertag EM, "Determination of L1 retrotransposition kinetics in cultured cells", Nucleic Acids Res, 28, pp.1418~1423 (2000)
66. Xie Y, "Characterization of L1 retrotransposition with highthroughput dual-luciferase assays", Nucleic Acids Res, 39, pp.e16~ (2011)
67. Kannan M, "Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration", Mob DNA, 8, pp.8~ (2017)
68. Kopera HC, "LINE-1 cultured cell retrotransposition assay", Methods Mol Biol, 1400, pp.139~156 (2016)
69. Wei W, "A transient assay reveals that cultured human cells can accommodate multiple LINE-1 retrotransposition events", Anal Biochem, 284, pp.435~438 (2000)
70. Morrish TA, "DNA repair mediated by endonuclease-independent LINE-1 retrotransposition", Nat Genet, 31, pp.159~165 (2002)
71. Feng Q, "Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition", Cell, 87, pp.905~916 (1996)
72. An W, "Active retrotransposition by a synthetic L1 element in mice", Proc Natl Acad Sci U S A, 103, pp.18662~18667 (2006)
73. Muotri AR, "Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition", Nature, 435, pp.903~910 (2005)
74. Newkirk SJ, "Intact piRNA pathway prevents L1 mobilization in male meiosis", Proc Natl Acad Sci U S A, 114, pp.E5635~ (2017)
75. Jensen S, "An indicator gene for detection of germline retrotransposition in transgenic Drosophila demonstrates RNA-mediated transposition of the LINE I element", EMBO J, 10, pp.1927~1937 (1991)
76. Sultana T, "The landscape of L1 retrotransposons in the human genome is shaped by pre-insertion sequence biases and post-insertion selection", Mol Cell, 74, pp.555~570 (2019)
77. Flasch DA, "Genomewide de novo L1 retrotransposition connects endonuclease activity with replication", Cell, 177, pp.837~851 (2019)
78. Marlor RL, "The Drosophila melanogaster gypsy transposable element encodes putative gene products homologous to retroviral proteins", Mol Cell Biol, 6, pp.1129~1134 (1986)
79. Kim A, "Retroviruses in invertebrates : the gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster", Proc Natl Acad Sci U S A, 91, pp.1285~1289 (1994)
80. Song SU, "An env-like protein encoded by a Drosophila retroelement : evidence that gypsy is an infectious retrovirus", Genes Dev, 8, pp.2046~2057 (1994)
81. Mevel-Ninio M, "Mobilization of the gypsy and copia retrotransposons in Drosophila melanogaster induces reversion of the ovo dominant female-sterile mutations : molecular analysis of revertant alleles", EMBO J, 8, pp.1549~1558 (1989)
82. Dej KJ, "A hotspot for the Drosophila gypsy retroelement in the ovo locus", Nucleic Acids Res, 26, pp.4019~4025 (1998)
83. Labrador M, "Insulator and Ovo proteins determine the frequency and specificity of insertion of the gypsy retrotransposon in Drosophila melanogaster", Genetics, 180, pp.1367~1378 (2008)
84. Li W, "Activation of transposable elements during aging and neuronal decline in Drosophila", Nat Neurosci, 16, pp.529~531 (2013)
85. Duffy JB, "GAL4 system in Drosophila : a fly geneticist’s Swiss army knife", Genesis, 34, pp.1~15 (2002)
86. Jones BC, "A somatic piRNA pathway in the Drosophila fat body ensures metabolic homeostasis and normal lifespan", Nat Commun, 7, pp.13856~ (2016)
87. Wood JG, "Chromatinmodifying genetic interventions suppress age-associated transposable element activation and extend life span in Drosophila", Proc Natl Acad Sci U S A, 113, pp.11277~11282 (2016)
88. Sousa-Victor P, "Piwi is required to limit exhaustion of aging somatic stem cells", Cell Rep, 20, pp.2527~2537 (2017)
89. Sun W, "Pathogenic tau-induced piRNA depletion promotes neuronal death through transposable element dysregulation in neurodegenerative tauopathies", Nat Neurosci, 21, pp.1038~1048 (2018)
90. Fort-Aznar L, "Retrovirus reactivation in CHMP2BIntron5 models of frontotemporal dementia", Hum Mol Genet, 29, pp.2637~2646 (2020)
91. Penke TJ, "Direct interrogation of the role of H3K9 in metazoan heterochromatin function", Genes Dev, 30, pp.1866~1880 (2016)
92. Chang YH, "Cellular labeling of endogenous retrovirus replication(CLEVR)reveals de novo insertions of the gypsy retrotransposable element in cell culture and in both neurons and glial cells of aging fruit flies", PLoS Biol, 17, pp.e3000278~ (2019)
93. Keegan RM, "Intercellular viral spread and intracellular transposition of Drosophila gypsy", PLoS Genet, 17, pp.e1009535~ (2021)
94. Song SU, "Infection of the germ line by retroviral particles produced in the follicle cells : a possible mechanism for the mobilization of the gypsy retroelement of Drosophila", Development, 124, pp.2789~2798 (1997)
95. Chang YH, "The gypsy endogenous retrovirus drives non-cell-autonomous propagation in a Drosophila TDP-43 model of neurodegeneration", Curr Biol, 29, pp.3135~3152 (2019)
96. Wensink PC, "The clustered and scrambled arrangement of moderately repetitive elements in Drosophila DNA", Cell, 18, pp.1231~1246 (1979)
97. Potter S, "Eucaryotic transposable genetic elements with inverted terminal repeats", Cell, 20, pp.639~647 (1980)
98. Biemont C, "Localization of P elements, copy number regulation, and cytotype determination in Drosophila melanogaster", Genet Res, 56, pp.3~14 (1990)
99. Badge RM, "ATLAS : a system to selectively identify human-specific L1 insertions", Am J Hum Genet, 72, pp.823~838 (2003)
100. Sheen FM, "Reading between the LINEs : human genomic variation induced by LINE-1 retrotransposition", Genome Res, 10, pp.1496~1508 (2000)
101. Pornthanakasem W, "LINE-1insertion dimorphisms identification by PCR", Biotechniques, 37, pp.750~ (2004)
102. Kim EY, "Determination of TE insertion positions using transposon display", Methods Mol Biol, 2250, pp.115~121 (2021)
103. Goerner-Potvin P, "Computational tools to unmask transposable elements", Nat Rev Genet, 19, pp.688~704 (2018)
104. Tubio JMC, "Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes", Science, 345, pp.1251343~ (2014)
105. Treiber CD, "Resolving the prevalence of somatic transposition in Drosophila", Elife, 6, pp.e28297~ (2017)
106. Kim J, "Patientcustomized oligonucleotide therapy for a rare genetic disease", N Engl J Med, 381, pp.1644~1652 (2019)
107. van Dijk EL, "The third revolution in sequencing technology", Trends Genet, 34, pp.666~681 (2018)
108. Wang Y, "Nanopore sequencing technology, bioinformatics and applications", Nat Biotechnol, 39, pp.1348~1365 (2021)
109. Logsdon GA, "Long-read human genome sequencing and its applications", Nat Rev Genet, 21, pp.597~614 (2020)
110. Kasianowicz JJ, "Characterization of individual polynucleotide molecules using a membrane channel", Proc Natl Acad Sci U S A, 93, pp.13770~13773 (1996)
111. Song L, "Structure of staphylococcal alphahemolysin, a heptameric transmembrane pore", Science, 274, pp.1859~1866 (1996)
112. Jain M, "The Oxford Nanopore MinION : delivery of nanopore sequencing to the genomics community", Genome Biol, 17, pp.239~ (2016)
113. Manrao EA, "Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase", Nat Biotechnol, 30, pp.349~353 (2012)
114. Cherf GM, "Automated forward and reverse ratcheting of DNA in a nanopore at 5-A precision", Nat Biotechnol, 30, pp.344~348 (2012)
115. Amarasinghe SL, "longread-tools.org: an interactive catalogue of analysis methods for long-read sequencing data", Gigascience, 10, pp.giab003~ (2021)
116. Gong L, "Picky comprehensively detects high-resolution structural variants in nanopore long reads", Nat Methods, 15, pp.455~460 (2018)
117. Goodwin S, "Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome", Genome Res, 25, pp.1750~1756 (2015)
118. David M, "Nanocall : an open source basecaller for Oxford Nanopore sequencing data", Bioinformatics, 33, pp.49~55 (2017)
119. Boza V, "DeepNano : deep recurrent neural networks for base calling in MinION nanopore reads", PLoS One, 12, pp.e0178751~ (2017)
120. Gong L, "Ultra-long read sequencing for whole genomic DNA analysis", J Vis Exp, 145, pp.e58954~ (2019)
121. Branton D, "Nanopore sequencing:an introduction" (2018), World Scientific
122. De Coster W, "Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome", Genome Res, 29, pp.1178~1187 (2019)
123. De Roeck A, "NanoSatellite : accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION", Genome Biol, 20, pp.239~ (2019)
124. Kim HS, "Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information", Gigascience, 8, pp.giz125~ (2019)
125. Nicholls SM, "Ultra-deep, long-read nanopore sequencing of mock microbial community standards", Gigascience, 8, pp.giz043~ (2019)
126. Payne A, "BulkVis : a graphical viewer for Oxford nanopore bulk FAST5 files", Bioinformatics, 35, pp.2193~2198 (2019)
127. Jain M, "Nanopore sequencing and assembly of a human genome with ultralong reads", Nat Biotechnol, 36, pp.338~345 (2018)
128. Solares EA, "Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing", G3 (Bethesda), 8, pp.3143~3154 (2018)
129. Tyson JR, "MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome", Genome Res, 28, pp.266~274 (2018)
130. Jain M, "Linear assembly of a human centromere on the Y chromosome", Nat Biotechnol, 36, pp.321~323 (2018)
131. Miga KH, "Telomere-to-telomere assembly of a complete human X chromosome", Nature, 585, pp.79~84 (2020)
132. Michael TP, "High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell", Nat Commun, 9, pp.541~ (2018)
133. Chernyavskaya Y, "Long-read sequencing of the zebrafish genome reorganizes genomic architecture", BMC Genomics, 23, pp.116~ (2022)
134. Garg S, "Chromosome-scale, haplotype-resolved assembly of human genomes", Nat Biotechnol, 39, pp.309~312 (2021)
135. Kirov I, "Transposons hidden in Arabidopsis thaliana genome assembly gaps and mobilization of non-autonomous LTR retrotransposons unravelled by nanotei pipeline", Plants(Basel), 10, pp.2681~ (2021)
136. Mohamed M, "A transposon story : from TE content to TE dynamic invasion of Drosophila genomes using the single-molecule sequencing technology from Oxford Nanopore", Cells, 9, pp.1776~ (2020)
137. Miller DE, "Highly contiguous genome assemblies of 15 Drosophila species generated using Nanopore sequencing", G3 (Bethesda), 8, pp.3131~3141 (2018)
138. Pradhan B, "Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing", Sci Rep, 7, pp.14521~ (2017)
139. Fujimoto A, "Wholegenome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer", Genome Med, 13, pp.65~ (2021)
140. Ellison CE, "Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster", Nucleic Acids Res, 48, pp.290~303 (2020)
141. Siudeja K, "Unraveling the features of somatic transposition in the Drosophila intestine", EMBO J, 40, pp.e106388~ (2021)
142. Frommer M, "A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands", Proc Natl Acad Sci U S A, 89, pp.1827~1831 (1992)
143. Ewing AD, "Nanopore sequencing enables comprehensive transposable element epigenomic profiling", Mol Cell, 80, pp.915~928 (2020)
144. Haggerty C, "Dnmt1 has de novo activity targeted to transposable elements", Nat Struct Mol Biol, 28, pp.594~603 (2021)
145. Jiang F, "Long-read direct RNA sequencing by 5’-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts", RNA Biol, 16, pp.950~959 (2019)
146. Kirov I, "Nanopore RNA sequencing revealed long non-coding and LTR retrotransposon-related RNAs expressed at early stages of triticale SEED development", Plants(Basel), 9, pp.1794~ (2020)
147. Lee SC, "Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA", Genome Res, 30, pp.576~588 (2020)
148. Panda K, "Long-read cDNA sequencing enables a"gene-like"transcript annotation of transposable elements", Plant Cell, 32, pp.2687~2698 (2020)
149. Berrens RV, "Locusspecific expression of transposable elements in single cells with CELLO-seq", Nat Biotechnol, 40, pp.546~554 (2021)
150. Maringer K, "Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti", BMC Genomics, 18, pp.101~ (2017)

관련 논문AI추천