• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (5078129)   Today's Articles (443)
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)
351
Zhang W, Chen F, Chen R, Xie D, Yang J, Zhao X, Guo R, Zhang Y, Shen Y, Göke J, Liu L, Lu X. Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes. Nucleic Acids Res 2019;47:8485-8501. [PMID: 31304534 PMCID: PMC7145578 DOI: 10.1093/nar/gkz594] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 01/09/2023]  Open
352
Chen Z, Yin Q, Inoue A, Zhang C, Zhang Y. Allelic H3K27me3 to allelic DNA methylation switch maintains noncanonical imprinting in extraembryonic cells. SCIENCE ADVANCES 2019;5:eaay7246. [PMID: 32064321 PMCID: PMC6989337 DOI: 10.1126/sciadv.aay7246] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/05/2019] [Indexed: 05/08/2023]
353
Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nat Commun 2019;10:5228. [PMID: 31745090 PMCID: PMC6864081 DOI: 10.1038/s41467-019-13035-2] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 10/15/2019] [Indexed: 12/19/2022]  Open
354
Tam OH, Rozhkov NV, Shaw R, Kim D, Hubbard I, Fennessey S, Propp N, Fagegaltier D, Harris BT, Ostrow LW, Phatnani H, Ravits J, Dubnau J, Gale Hammell M. Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia. Cell Rep 2019;29:1164-1177.e5. [PMID: 31665631 PMCID: PMC6866666 DOI: 10.1016/j.celrep.2019.09.066] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/03/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022]  Open
355
Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH. SQuIRE reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Res 2019;47:e27. [PMID: 30624635 PMCID: PMC6411935 DOI: 10.1093/nar/gky1301] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/18/2018] [Accepted: 01/03/2019] [Indexed: 12/13/2022]  Open
356
Transcriptomic analysis of human endogenous retroviruses in systemic lupus erythematosus. Proc Natl Acad Sci U S A 2019;116:21350-21351. [PMID: 31594853 PMCID: PMC6815141 DOI: 10.1073/pnas.1907705116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]  Open
357
McKerrow W, Fenyö D. L1EM: a tool for accurate locus specific LINE-1 RNA quantification. Bioinformatics 2019;36:1167-1173. [PMID: 31584629 PMCID: PMC8215917 DOI: 10.1093/bioinformatics/btz724] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/31/2019] [Accepted: 09/25/2019] [Indexed: 01/31/2023]  Open
358
Transposable elements in human genetic disease. Nat Rev Genet 2019;20:760-772. [DOI: 10.1038/s41576-019-0165-8] [Citation(s) in RCA: 206] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
359
Chung N, Jonaid GM, Quinton S, Ross A, Sexton CE, Alberto A, Clymer C, Churchill D, Navarro Leija O, Han MV. Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements. Mob DNA 2019;10:39. [PMID: 31497073 PMCID: PMC6720085 DOI: 10.1186/s13100-019-0180-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 08/14/2019] [Indexed: 12/12/2022]  Open
360
Bendall ML, de Mulder M, Iñiguez LP, Lecanda-Sánchez A, Pérez-Losada M, Ostrowski MA, Jones RB, Mulder LCF, Reyes-Terán G, Crandall KA, Ormsby CE, Nixon DF. Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLoS Comput Biol 2019;15:e1006453. [PMID: 31568525 PMCID: PMC6786656 DOI: 10.1371/journal.pcbi.1006453] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/10/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022]  Open
361
Navarro FCP, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB. TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PLoS Comput Biol 2019;15:e1007293. [PMID: 31425522 PMCID: PMC6715295 DOI: 10.1371/journal.pcbi.1007293] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/29/2019] [Accepted: 07/26/2019] [Indexed: 11/19/2022]  Open
362
Guffanti G, Bartlett A, Klengel T, Klengel C, Hunter R, Glinsky G, Macciardi F. Novel Bioinformatics Approach Identifies Transcriptional Profiles of Lineage-Specific Transposable Elements at Distinct Loci in the Human Dorsolateral Prefrontal Cortex. Mol Biol Evol 2019;35:2435-2453. [PMID: 30053206 PMCID: PMC6188555 DOI: 10.1093/molbev/msy143] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
363
Chen Z, Zhang Y. Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development. Nat Genet 2019;51:947-951. [PMID: 31133747 PMCID: PMC6545155 DOI: 10.1038/s41588-019-0418-7] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/11/2019] [Indexed: 11/09/2022]
364
Kaul T, Morales ME, Smither E, Baddoo M, Belancio VP, Deininger P. RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level. J Vis Exp 2019. [PMID: 31157783 DOI: 10.3791/59771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]  Open
365
Babarinde IA, Li Y, Hutchins AP. Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts. Comput Struct Biotechnol J 2019;17:628-637. [PMID: 31193391 PMCID: PMC6526290 DOI: 10.1016/j.csbj.2019.04.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022]  Open
366
Choi J, Strickler SR, Richards EJ. Loss of CRWN Nuclear Proteins Induces Cell Death and Salicylic Acid Defense Signaling. PLANT PHYSIOLOGY 2019;179:1315-1329. [PMID: 30696746 PMCID: PMC6446779 DOI: 10.1104/pp.18.01020] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/18/2019] [Indexed: 05/09/2023]
367
Benayoun BA, Pollina EA, Singh PP, Mahmoudi S, Harel I, Casey KM, Dulken BW, Kundaje A, Brunet A. Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses. Genome Res 2019;29:697-709. [PMID: 30858345 PMCID: PMC6442391 DOI: 10.1101/gr.240093.118] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/25/2019] [Indexed: 12/20/2022]
368
Stein CB, Genzor P, Mitra S, Elchert AR, Ipsaro JJ, Benner L, Sobti S, Su Y, Hammell M, Joshua-Tor L, Haase AD. Decoding the 5' nucleotide bias of PIWI-interacting RNAs. Nat Commun 2019;10:828. [PMID: 30783109 PMCID: PMC6381166 DOI: 10.1038/s41467-019-08803-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/30/2019] [Indexed: 12/26/2022]  Open
369
Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells. Nat Commun 2019;10:34. [PMID: 30604769 PMCID: PMC6318327 DOI: 10.1038/s41467-018-08006-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/11/2018] [Indexed: 01/18/2023]  Open
370
Panzade G, Gangwar I, Awasthi S, Sharma N, Shankar R. Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019;2019:5650983. [PMID: 31796964 PMCID: PMC6891001 DOI: 10.1093/database/baz130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/20/2022]
371
Pereira GC, Sanchez L, Schaughency PM, Rubio-Roldán A, Choi JA, Planet E, Batra R, Turelli P, Trono D, Ostrow LW, Ravits J, Kazazian HH, Wheelan SJ, Heras SR, Mayer J, García-Pérez JL, Goodier JL. Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis. Mob DNA 2018;9:35. [PMID: 30564290 PMCID: PMC6295051 DOI: 10.1186/s13100-018-0138-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023]  Open
372
Lai YS, Zhang W, Zhang X, Shen D, Wang H, Qiu Y, Song J, Li X. Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression. G3 (BETHESDA, MD.) 2018;8:3981-3991. [PMID: 30377155 PMCID: PMC6288824 DOI: 10.1534/g3.118.200755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/29/2018] [Indexed: 12/31/2022]
373
Lai YS, Shen D, Zhang W, Zhang X, Qiu Y, Wang H, Dou X, Li S, Wu Y, Song J, Ji G, Li X. Temperature and photoperiod changes affect cucumber sex expression by different epigenetic regulations. BMC PLANT BIOLOGY 2018;18:268. [PMID: 30400867 PMCID: PMC6220452 DOI: 10.1186/s12870-018-1490-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 10/19/2018] [Indexed: 05/25/2023]
374
Göbel U, Arce AL, He F, Rico A, Schmitz G, de Meaux J. Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids. Genome Biol Evol 2018;10:1403-1415. [PMID: 29788048 PMCID: PMC6007786 DOI: 10.1093/gbe/evy095] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 12/23/2022]  Open
375
Guo J, Grow EJ, Mlcochova H, Maher GJ, Lindskog C, Nie X, Guo Y, Takei Y, Yun J, Cai L, Kim R, Carrell DT, Goriely A, Hotaling JM, Cairns BR. The adult human testis transcriptional cell atlas. Cell Res 2018;28:1141-1157. [PMID: 30315278 PMCID: PMC6274646 DOI: 10.1038/s41422-018-0099-2] [Citation(s) in RCA: 437] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/07/2018] [Accepted: 09/19/2018] [Indexed: 11/09/2022]  Open
376
Goerner-Potvin P, Bourque G. Computational tools to unmask transposable elements. Nat Rev Genet 2018;19:688-704. [DOI: 10.1038/s41576-018-0050-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
377
Attig J, Agostini F, Gooding C, Chakrabarti AM, Singh A, Haberman N, Zagalak JA, Emmett W, Smith CWJ, Luscombe NM, Ule J. Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing. Cell 2018;174:1067-1081.e17. [PMID: 30078707 PMCID: PMC6108849 DOI: 10.1016/j.cell.2018.07.001] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 04/23/2018] [Accepted: 07/01/2018] [Indexed: 12/30/2022]
378
Warkocki Z, Krawczyk PS, Adamska D, Bijata K, Garcia-Perez JL, Dziembowski A. Uridylation by TUT4/7 Restricts Retrotransposition of Human LINE-1s. Cell 2018;174:1537-1548.e29. [PMID: 30122351 PMCID: PMC6191937 DOI: 10.1016/j.cell.2018.07.022] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 05/27/2018] [Accepted: 07/18/2018] [Indexed: 12/19/2022]
379
Yao B, Li Y, Wang Z, Chen L, Poidevin M, Zhang C, Lin L, Wang F, Bao H, Jiao B, Lim J, Cheng Y, Huang L, Phillips BL, Xu T, Duan R, Moberg KH, Wu H, Jin P. Active N6-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons. Mol Cell 2018;71:848-857.e6. [PMID: 30078725 DOI: 10.1016/j.molcel.2018.07.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 06/05/2018] [Accepted: 07/03/2018] [Indexed: 12/22/2022]
380
Kenchanmane Raju SK, Shao M, Wamboldt Y, Mackenzie S. Epigenomic plasticity of Arabidopsis msh1 mutants under prolonged cold stress. PLANT DIRECT 2018;2:e00079. [PMID: 31245744 PMCID: PMC6508824 DOI: 10.1002/pld3.79] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/20/2018] [Accepted: 07/05/2018] [Indexed: 05/05/2023]
381
Jung H, Choi JK, Lee EA. Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers. Genome Res 2018;28:1136-1146. [PMID: 29970450 PMCID: PMC6071633 DOI: 10.1101/gr.231837.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 06/29/2018] [Indexed: 12/15/2022]
382
Slotkin RK. The case for not masking away repetitive DNA. Mob DNA 2018;9:15. [PMID: 29743957 PMCID: PMC5930866 DOI: 10.1186/s13100-018-0120-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/23/2018] [Indexed: 11/11/2022]  Open
383
Jiao W, Yuan J, Jiang S, Liu Y, Wang L, Liu M, Zheng D, Ye W, Wang X, Chen ZJ. Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018;93:828-842. [PMID: 29265531 DOI: 10.1111/tpj.13805] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/04/2017] [Indexed: 05/26/2023]
384
Mangul S, Yang HT, Strauli N, Gruhl F, Porath HT, Hsieh K, Chen L, Daley T, Christenson S, Wesolowska-Andersen A, Spreafico R, Rios C, Eng C, Smith AD, Hernandez RD, Ophoff RA, Santana JR, Levanon EY, Woodruff PG, Burchard E, Seibold MA, Shifman S, Eskin E, Zaitlen N. ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. Genome Biol 2018;19:36. [PMID: 29548336 PMCID: PMC5857127 DOI: 10.1186/s13059-018-1403-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/02/2018] [Indexed: 11/22/2022]  Open
385
Jankovics F, Bence M, Sinka R, Faragó A, Bodai L, Pettkó-Szandtner A, Ibrahim K, Takács Z, Szarka-Kovács AB, Erdélyi M. Drosophila small ovary gene is required for transposon silencing and heterochromatin organisation and ensures germline stem cell maintenance and differentiation. Development 2018;145:dev.170639. [DOI: 10.1242/dev.170639] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/29/2018] [Indexed: 12/17/2022]
386
Analysis of RNA-Seq Data Using TEtranscripts. Methods Mol Biol 2018;1751:153-167. [PMID: 29508296 DOI: 10.1007/978-1-4939-7710-9_11] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
387
Yao B, Cheng Y, Wang Z, Li Y, Chen L, Huang L, Zhang W, Chen D, Wu H, Tang B, Jin P. DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress. Nat Commun 2017;8:1122. [PMID: 29066820 PMCID: PMC5654764 DOI: 10.1038/s41467-017-01195-y] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/25/2017] [Indexed: 12/13/2022]  Open
388
Fast I, Hewel C, Wester L, Schumacher J, Gebert D, Zischler H, Berger C, Rosenkranz D. Temperature-responsive miRNAs in Drosophila orchestrate adaptation to different ambient temperatures. RNA (NEW YORK, N.Y.) 2017;23:1352-1364. [PMID: 28630141 PMCID: PMC5558905 DOI: 10.1261/rna.061119.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/06/2017] [Indexed: 06/14/2023]
389
Jakšić AM, Kofler R, Schlötterer C. Regulation of transposable elements: Interplay between TE-encoded regulatory sequences and host-specific trans-acting factors in Drosophila melanogaster. Mol Ecol 2017;26:5149-5159. [PMID: 28742942 DOI: 10.1111/mec.14259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 12/18/2022]
390
Ludwig AK, Zhang P, Hastert FD, Meyer S, Rausch C, Herce HD, Müller U, Lehmkuhl A, Hellmann I, Trummer C, Storm C, Leonhardt H, Cardoso MC. Binding of MBD proteins to DNA blocks Tet1 function thereby modulating transcriptional noise. Nucleic Acids Res 2017;45:2438-2457. [PMID: 27923996 PMCID: PMC5389475 DOI: 10.1093/nar/gkw1197] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/20/2016] [Indexed: 12/18/2022]  Open
391
Jain D, Meydan C, Lange J, Claeys Bouuaert C, Lailler N, Mason CE, Anderson KV, Keeney S. rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline. PLoS Genet 2017;13:e1006964. [PMID: 28854222 PMCID: PMC5607212 DOI: 10.1371/journal.pgen.1006964] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/20/2017] [Accepted: 08/07/2017] [Indexed: 12/30/2022]  Open
392
Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses. PLoS Genet 2017;13:e1006883. [PMID: 28700586 PMCID: PMC5529029 DOI: 10.1371/journal.pgen.1006883] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 07/26/2017] [Accepted: 06/21/2017] [Indexed: 12/26/2022]  Open
393
McKerrow WH, Savva YA, Rezaei A, Reenan RA, Lawrence CE. Predicting RNA hyper-editing with a novel tool when unambiguous alignment is impossible. BMC Genomics 2017;18:522. [PMID: 28693467 PMCID: PMC5502491 DOI: 10.1186/s12864-017-3898-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/22/2017] [Indexed: 12/13/2022]  Open
394
Zhang P, Ludwig AK, Hastert FD, Rausch C, Lehmkuhl A, Hellmann I, Smets M, Leonhardt H, Cardoso MC. L1 retrotransposition is activated by Ten-eleven-translocation protein 1 and repressed by methyl-CpG binding proteins. Nucleus 2017;8:548-562. [PMID: 28524723 PMCID: PMC5703239 DOI: 10.1080/19491034.2017.1330238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
395
Krug L, Chatterjee N, Borges-Monroy R, Hearn S, Liao WW, Morrill K, Prazak L, Rozhkov N, Theodorou D, Hammell M, Dubnau J. Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS. PLoS Genet 2017;13:e1006635. [PMID: 28301478 PMCID: PMC5354250 DOI: 10.1371/journal.pgen.1006635] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/14/2017] [Indexed: 12/11/2022]  Open
396
Ge SX. Exploratory bioinformatics investigation reveals importance of "junk" DNA in early embryo development. BMC Genomics 2017;18:200. [PMID: 28231763 PMCID: PMC5324221 DOI: 10.1186/s12864-017-3566-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/07/2017] [Indexed: 11/10/2022]  Open
397
Shao MR, Kumar Kenchanmane Raju S, Laurie JD, Sanchez R, Mackenzie SA. Stress-responsive pathways and small RNA changes distinguish variable developmental phenotypes caused by MSH1 loss. BMC PLANT BIOLOGY 2017;17:47. [PMID: 28219335 PMCID: PMC5319189 DOI: 10.1186/s12870-017-0996-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/08/2017] [Indexed: 05/03/2023]
398
Bodak M, Cirera-Salinas D, Yu J, Ngondo RP, Ciaudo C. Dicer, a new regulator of pluripotency exit and LINE-1 elements in mouse embryonic stem cells. FEBS Open Bio 2017;7:204-220. [PMID: 28174687 PMCID: PMC5292673 DOI: 10.1002/2211-5463.12174] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/18/2016] [Accepted: 12/05/2016] [Indexed: 12/18/2022]  Open
399
De S, Gorospe M. Bioinformatic tools for analysis of CLIP ribonucleoprotein data. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016;8. [PMID: 28008714 DOI: 10.1002/wrna.1404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/26/2016] [Accepted: 10/07/2016] [Indexed: 12/15/2022]
400
Clayton EA, Wang L, Rishishwar L, Wang J, McDonald JF, Jordan IK. Patterns of Transposable Element Expression and Insertion in Cancer. Front Mol Biosci 2016;3:76. [PMID: 27900322 PMCID: PMC5110550 DOI: 10.3389/fmolb.2016.00076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/31/2016] [Indexed: 11/20/2022]  Open
PrevPage 8 of 9 1256789Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA