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For: Jin Y, Tam OH, Paniagua E, Hammell M. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics 2015. [PMID: 26206304 DOI: 10.1093/bioinformatics/btv422] [Citation(s) in RCA: 405] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
301
Ipsaro JJ, O'Brien PA, Bhattacharya S, Palmer AG, Joshua-Tor L. Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons. Cell Rep 2021;34:108914. [PMID: 33789107 DOI: 10.1016/j.celrep.2021.108914] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/15/2021] [Accepted: 03/05/2021] [Indexed: 02/05/2023]  Open
302
Jönsson ME, Garza R, Sharma Y, Petri R, Södersten E, Johansson JG, Johansson PA, Atacho DA, Pircs K, Madsen S, Yudovich D, Ramakrishnan R, Holmberg J, Larsson J, Jern P, Jakobsson J. Activation of endogenous retroviruses during brain development causes an inflammatory response. EMBO J 2021;40:e106423. [PMID: 33644903 PMCID: PMC8090857 DOI: 10.15252/embj.2020106423] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 01/09/2023]  Open
303
The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity. Nature 2021;591:322-326. [PMID: 33658714 DOI: 10.1038/s41586-021-03313-9] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023]
304
Yin Y, Liu XZ, He X, Zhou LQ. Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human Cells. Front Cell Infect Microbiol 2021;11:609160. [PMID: 33732659 PMCID: PMC7959850 DOI: 10.3389/fcimb.2021.609160] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/18/2021] [Indexed: 01/08/2023]  Open
305
Ma X, Liu C, Kong X, Liu J, Zhang S, Liang S, Luan W, Cao X. Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants. SCIENCE CHINA-LIFE SCIENCES 2021;64:495-511. [DOI: 10.1007/s11427-020-1891-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/19/2021] [Indexed: 12/13/2022]
306
Tsai SY, Huang F. Acetyltransferase Enok regulates transposon silencing and piRNA cluster transcription. PLoS Genet 2021;17:e1009349. [PMID: 33524038 PMCID: PMC7877743 DOI: 10.1371/journal.pgen.1009349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/11/2021] [Accepted: 01/07/2021] [Indexed: 11/19/2022]  Open
307
Sun D, Layman TS, Jeong H, Chatterjee P, Grogan K, Merritt JR, Maney DL, Yi SV. Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows. Mol Ecol 2021;30:3453-3467. [PMID: 33421223 PMCID: PMC8359194 DOI: 10.1111/mec.15793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/25/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022]
308
Kaur D, Agrahari M, Singh SS, Mandal PK, Bhattacharya A, Bhattacharya S. Transcriptomic analysis of Entamoeba histolytica reveals domain-specific sense strand expression of LINE-encoded ORFs with massive antisense expression of RT domain. Plasmid 2021;114:102560. [PMID: 33482228 DOI: 10.1016/j.plasmid.2021.102560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 11/29/2022]
309
Cambier L, Stachelek K, Triska M, Jubran R, Huang M, Li W, Zhang J, Li J, Cobrinik D. Extracellular vesicle-associated repetitive element DNAs as candidate osteosarcoma biomarkers. Sci Rep 2021;11:94. [PMID: 33420117 PMCID: PMC7794510 DOI: 10.1038/s41598-020-77398-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]  Open
310
Shao W, Wang T. Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data. Genome Res 2021;31:88-100. [PMID: 33355230 PMCID: PMC7849386 DOI: 10.1101/gr.265173.120] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/24/2020] [Indexed: 12/28/2022]
311
Lee YS, Maple R, Dürr J, Dawson A, Tamim S, Del Genio C, Papareddy R, Luo A, Lamb JC, Amantia S, Sylvester AW, Birchler JA, Meyers BC, Nodine MD, Rouster J, Gutierrez-Marcos J. A transposon surveillance mechanism that safeguards plant male fertility during stress. NATURE PLANTS 2021;7:34-41. [PMID: 33398155 DOI: 10.1038/s41477-020-00818-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
312
Tsusaka T, Fukuda K, Shimura C, Kato M, Shinkai Y. The fibronectin type-III (FNIII) domain of ATF7IP contributes to efficient transcriptional silencing mediated by the SETDB1 complex. Epigenetics Chromatin 2020;13:52. [PMID: 33256805 PMCID: PMC7706265 DOI: 10.1186/s13072-020-00374-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/13/2020] [Indexed: 01/04/2023]  Open
313
Greve G, Schüler J, Grüning BA, Berberich B, Stomper J, Zimmer D, Gutenkunst L, Bönisch U, Meier R, Blagitko-Dorfs N, Grishina O, Pfeifer D, Weichenhan D, Plass C, Lübbert M. Decitabine Induces Gene Derepression on Monosomic Chromosomes: In Vitro and In Vivo Effects in Adverse-Risk Cytogenetics AML. Cancer Res 2020;81:834-846. [PMID: 33203699 DOI: 10.1158/0008-5472.can-20-1430] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/21/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022]
314
Apoptosis in the fetal testis eliminates developmentally defective germ cell clones. Nat Cell Biol 2020;22:1423-1435. [DOI: 10.1038/s41556-020-00603-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 10/12/2020] [Indexed: 01/22/2023]
315
Bloom JC, Schimenti JC. Sexually dimorphic DNA damage responses and mutation avoidance in the mouse germline. Genes Dev 2020;34:1637-1649. [PMID: 33184219 PMCID: PMC7706705 DOI: 10.1101/gad.341602.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
316
Tunbak H, Enriquez-Gasca R, Tie CHC, Gould PA, Mlcochova P, Gupta RK, Fernandes L, Holt J, van der Veen AG, Giampazolias E, Burns KH, Maillard PV, Rowe HM. The HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s. Nat Commun 2020;11:5387. [PMID: 33144593 PMCID: PMC7609715 DOI: 10.1038/s41467-020-19170-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/28/2020] [Indexed: 12/20/2022]  Open
317
Lefkopoulos S, Polyzou A, Derecka M, Bergo V, Clapes T, Cauchy P, Jerez-Longres C, Onishi-Seebacher M, Yin N, Martagon-Calderón NA, Potts KS, Klaeylé L, Liu F, Bowman TV, Jenuwein T, Mione MC, Trompouki E. Repetitive Elements Trigger RIG-I-like Receptor Signaling that Regulates the Emergence of Hematopoietic Stem and Progenitor Cells. Immunity 2020;53:934-951.e9. [DOI: 10.1016/j.immuni.2020.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 06/23/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
318
Linker SB, Randolph-Moore L, Kottilil K, Qiu F, Jaeger BN, Barron J, Gage FH. Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus. Genome Res 2020;30:1643-1654. [PMID: 33122305 PMCID: PMC7605253 DOI: 10.1101/gr.262196.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022]
319
Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4. Proc Natl Acad Sci U S A 2020;117:26520-26530. [PMID: 33020268 DOI: 10.1073/pnas.2005237117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
320
OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data. Genes (Basel) 2020;11:genes11101165. [PMID: 33023248 PMCID: PMC7650687 DOI: 10.3390/genes11101165] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 01/21/2023]  Open
321
Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly. Viruses 2020;12:v12101089. [PMID: 32993145 PMCID: PMC7650545 DOI: 10.3390/v12101089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]  Open
322
Shadle SC, Bennett SR, Wong CJ, Karreman NA, Campbell AE, van der Maarel SM, Bass BL, Tapscott SJ. DUX4-induced bidirectional HSATII satellite repeat transcripts form intranuclear double-stranded RNA foci in human cell models of FSHD. Hum Mol Genet 2020;28:3997-4011. [PMID: 31630170 DOI: 10.1093/hmg/ddz242] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/19/2019] [Accepted: 10/03/2019] [Indexed: 12/29/2022]  Open
323
GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data. PLoS One 2020;15:e0232994. [PMID: 32866155 PMCID: PMC7458328 DOI: 10.1371/journal.pone.0232994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/02/2020] [Indexed: 11/19/2022]  Open
324
Panda K, Slotkin RK. Long-Read cDNA Sequencing Enables a "Gene-Like" Transcript Annotation of Transposable Elements. THE PLANT CELL 2020;32:2687-2698. [PMID: 32647069 PMCID: PMC7474280 DOI: 10.1105/tpc.20.00115] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/11/2020] [Accepted: 06/25/2020] [Indexed: 05/05/2023]
325
Gutzat R, Rembart K, Nussbaumer T, Hofmann F, Pisupati R, Bradamante G, Daubel N, Gaidora A, Lettner N, Donà M, Nordborg M, Nodine M, Mittelsten Scheid O. Arabidopsis shoot stem cells display dynamic transcription and DNA methylation patterns. EMBO J 2020;39:e103667. [PMID: 32815560 PMCID: PMC7560203 DOI: 10.15252/embj.2019103667] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022]  Open
326
Li Z, Hua X, Serra-Cardona A, Xu X, Gan S, Zhou H, Yang WS, Chen CL, Xu RM, Zhang Z. DNA polymerase α interacts with H3-H4 and facilitates the transfer of parental histones to lagging strands. SCIENCE ADVANCES 2020;6:eabb5820. [PMID: 32923642 PMCID: PMC7449674 DOI: 10.1126/sciadv.abb5820] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/14/2020] [Indexed: 05/03/2023]
327
Goodier JL, Soares AO, Pereira GC, DeVine LR, Sanchez L, Cole RN, García-Pérez JL. C9orf72-associated SMCR8 protein binds in the ubiquitin pathway and with proteins linked with neurological disease. Acta Neuropathol Commun 2020;8:110. [PMID: 32678027 PMCID: PMC7364817 DOI: 10.1186/s40478-020-00982-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/26/2020] [Indexed: 02/08/2023]  Open
328
LaRocca TJ, Cavalier AN, Wahl D. Repetitive elements as a transcriptomic marker of aging: Evidence in multiple datasets and models. Aging Cell 2020;19:e13167. [PMID: 32500641 PMCID: PMC7412685 DOI: 10.1111/acel.13167] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/21/2020] [Accepted: 05/05/2020] [Indexed: 12/27/2022]  Open
329
Lanciano S, Cristofari G. Measuring and interpreting transposable element expression. Nat Rev Genet 2020;21:721-736. [PMID: 32576954 DOI: 10.1038/s41576-020-0251-y] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/21/2022]
330
Bravo JI, Nozownik S, Danthi PS, Benayoun BA. Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation. Development 2020;147:dev175786. [PMID: 32527937 PMCID: PMC10680986 DOI: 10.1242/dev.175786] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
331
Pisano MP, Grandi N, Tramontano E. High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development. Viruses 2020;12:E633. [PMID: 32545287 PMCID: PMC7354619 DOI: 10.3390/v12060633] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 01/19/2023]  Open
332
de Cubas AA, Dunker W, Zaninovich A, Hongo RA, Bhatia A, Panda A, Beckermann KE, Bhanot G, Ganesan S, Karijolich J, Rathmell WK. DNA hypomethylation promotes transposable element expression and activation of immune signaling in renal cell cancer. JCI Insight 2020;5:137569. [PMID: 32493845 PMCID: PMC7308050 DOI: 10.1172/jci.insight.137569] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022]  Open
333
Yates-Stewart AD, Daron J, Wijeratne S, Shahid S, Edgington HA, Slotkin RK, Michel A. Soybean aphids adapted to host-plant resistance by down regulating putative effectors and up regulating transposable elements. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020;121:103363. [PMID: 32201218 DOI: 10.1016/j.ibmb.2020.103363] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 03/06/2020] [Accepted: 03/15/2020] [Indexed: 06/10/2023]
334
poly(UG)-tailed RNAs in genome protection and epigenetic inheritance. Nature 2020;582:283-288. [PMID: 32499657 PMCID: PMC8396162 DOI: 10.1038/s41586-020-2323-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/16/2020] [Indexed: 12/17/2022]
335
Lynch-Sutherland CF, Chatterjee A, Stockwell PA, Eccles MR, Macaulay EC. Reawakening the Developmental Origins of Cancer Through Transposable Elements. Front Oncol 2020;10:468. [PMID: 32432029 PMCID: PMC7214541 DOI: 10.3389/fonc.2020.00468] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/16/2020] [Indexed: 12/12/2022]  Open
336
Marasca F, Gasparotto E, Polimeni B, Vadalà R, Ranzani V, Bodega B. The Sophisticated Transcriptional Response Governed by Transposable Elements in Human Health and Disease. Int J Mol Sci 2020;21:ijms21093201. [PMID: 32366056 PMCID: PMC7247572 DOI: 10.3390/ijms21093201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 01/15/2023]  Open
337
Corrêa RL, Sanz-Carbonell A, Kogej Z, Müller SY, Ambrós S, López-Gomollón S, Gómez G, Baulcombe DC, Elena SF. Viral Fitness Determines the Magnitude of Transcriptomic and Epigenomic Reprograming of Defense Responses in Plants. Mol Biol Evol 2020;37:1866-1881. [DOI: 10.1093/molbev/msaa091] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
338
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. Mob DNA 2020;11:13. [PMID: 32266012 PMCID: PMC7110667 DOI: 10.1186/s13100-020-00208-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/10/2020] [Indexed: 01/12/2023]  Open
339
O'Neill K, Brocks D, Hammell MG. Mobile genomics: tools and techniques for tackling transposons. Philos Trans R Soc Lond B Biol Sci 2020;375:20190345. [PMID: 32075565 PMCID: PMC7061981 DOI: 10.1098/rstb.2019.0345] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2019] [Indexed: 12/22/2022]  Open
340
Venkei ZG, Choi CP, Feng S, Chen C, Jacobsen SE, Kim JK, Yamashita YM. A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage. PLoS Genet 2020;16:e1008648. [PMID: 32168327 PMCID: PMC7094869 DOI: 10.1371/journal.pgen.1008648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/25/2020] [Accepted: 02/03/2020] [Indexed: 12/26/2022]  Open
341
Sybirna A, Tang WWC, Pierson Smela M, Dietmann S, Gruhn WH, Brosh R, Surani MA. A critical role of PRDM14 in human primordial germ cell fate revealed by inducible degrons. Nat Commun 2020;11:1282. [PMID: 32152282 PMCID: PMC7062732 DOI: 10.1038/s41467-020-15042-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 12/31/2019] [Indexed: 11/09/2022]  Open
342
Ovejero T, Sadones O, Sánchez-Fito T, Almenar-Pérez E, Espejo JA, Martín-Martínez E, Nathanson L, Oltra E. Activation of Transposable Elements in Immune Cells of Fibromyalgia Patients. Int J Mol Sci 2020;21:1366. [PMID: 32085571 PMCID: PMC7072917 DOI: 10.3390/ijms21041366] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/06/2020] [Accepted: 02/14/2020] [Indexed: 02/07/2023]  Open
343
A role for the rare endogenous retrovirus β4 in development of Japanese fancy mice. Commun Biol 2020;3:53. [PMID: 32020010 PMCID: PMC7000388 DOI: 10.1038/s42003-020-0781-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 11/18/2022]  Open
344
Fouché S, Badet T, Oggenfuss U, Plissonneau C, Francisco CS, Croll D. Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen. Mol Biol Evol 2020;37:221-239. [PMID: 31553475 DOI: 10.1093/molbev/msz216] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
345
Macchietto MG, Langlois RA, Shen SS. Virus-induced transposable element expression up-regulation in human and mouse host cells. Life Sci Alliance 2020;3:3/2/e201900536. [PMID: 31964680 PMCID: PMC6977392 DOI: 10.26508/lsa.201900536] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/18/2022]  Open
346
Neou M, Villa C, Armignacco R, Jouinot A, Raffin-Sanson ML, Septier A, Letourneur F, Diry S, Diedisheim M, Izac B, Gaspar C, Perlemoine K, Verjus V, Bernier M, Boulin A, Emile JF, Bertagna X, Jaffrezic F, Laloe D, Baussart B, Bertherat J, Gaillard S, Assié G. Pangenomic Classification of Pituitary Neuroendocrine Tumors. Cancer Cell 2020;37:123-134.e5. [PMID: 31883967 DOI: 10.1016/j.ccell.2019.11.002] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/07/2019] [Accepted: 11/21/2019] [Indexed: 12/14/2022]
347
Kaul T, Morales ME, Sartor AO, Belancio VP, Deininger P. Comparative analysis on the expression of L1 loci using various RNA-Seq preparations. Mob DNA 2020;11:2. [PMID: 31921361 PMCID: PMC6945437 DOI: 10.1186/s13100-019-0194-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023]  Open
348
Vendrell-Mir P, López-Obando M, Nogué F, Casacuberta JM. Different Families of Retrotransposons and DNA Transposons Are Actively Transcribed and May Have Transposed Recently in Physcomitrium (Physcomitrella) patens. FRONTIERS IN PLANT SCIENCE 2020;11:1274. [PMID: 32973835 PMCID: PMC7466625 DOI: 10.3389/fpls.2020.01274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/05/2020] [Indexed: 05/07/2023]
349
Teissandier A, Servant N, Barillot E, Bourc'his D. Tools and best practices for retrotransposon analysis using high-throughput sequencing data. Mob DNA 2019;10:52. [PMID: 31890048 PMCID: PMC6935493 DOI: 10.1186/s13100-019-0192-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/04/2019] [Indexed: 12/26/2022]  Open
350
Bhargava V, Goldstein CD, Russell L, Xu L, Ahmed M, Li W, Casey A, Servage K, Kollipara R, Picciarelli Z, Kittler R, Yatsenko A, Carmell M, Orth K, Amatruda JF, Yanowitz JL, Buszczak M. GCNA Preserves Genome Integrity and Fertility Across Species. Dev Cell 2019;52:38-52.e10. [PMID: 31839537 DOI: 10.1016/j.devcel.2019.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 08/07/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022]
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