Endogenous non-retroviral RNA virus elements evidence a novel type of antiviral immunity

Mobile Genetic Elements

Volumn 6, Issue 3, 2016, Pages

  Honda, Tomoyuki ^a   Tomonaga, Keizo ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Antiviral immunity; Endogenous viral element; Interference; LINE 1; Noncoding RNA; PiRNA; RNA virus; Transcript reversion

Indexed keywords

ENDOGENOUS BORNAVIRUS LIKE NUCLEOPROTEIN; NUCLEOPROTEIN; PIWI INTERACTING RNA; UNCLASSIFIED DRUG;

HUMAN; ICTIDOMYS TRIDECEMLINEATUS; IMMUNOMODULATION; MUS MUSCULUS; NONHUMAN; NOTE; PROTEIN EXPRESSION; PROTEIN FUNCTION; REVERTANT; SCIURIDAE;

EID: 85029737884     PISSN: 21592543     EISSN: 2159256X     Source Type: Journal    
DOI: 10.1080/2159256X.2016.1165785     Document Type: Note

References (33)

1. Horie M, Honda T, Suzuki Y, Kobayashi Y, Daito T, Oshida T, Ikuta K, Jern P, Gojobori T, Coffin JM, et al. Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 2010; 463:84-7; PMID:20054395; http://dx.doi.org/10.1038/nature08695
2. Belyi VA, Levine AJ, Skalka AM. Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes. PLoS Pathog 2010; 6:e1001030; PMID:20686665; http://dx.doi.org/10.1371/journal.ppat.1001030
3. Katzourakis A, Gifford RJ. Endogenous viral elements in animal genomes. PLoS Genet 2010; 6:e1001191; PMID: 21124940; http://dx.doi.org/10.1371/journal.pgen.1001191
4. Fujino K, Horie M, Honda T, Merriman DK, Tomonaga K. Inhibition of Borna disease virus replication by an endogenous bornavirus-like element in the ground squirrel genome. Proc Natl Acad Sci U S A 2014; 111:13175-80; PMID: 25157155; http://dx.doi.org/10.1073/pnas.1407046111
5. Stoye JP. Fv1, the mouse retrovirus resistance gene. Rev Sci Tech 1998; 17:269-77; PMID:9638816
6. Mura M, Murcia P, Caporale M, Spencer TE, Nagashima K, Rein A, Palmarini M. Late viral interference induced by transdominant Gag of an endogenous retrovirus. Proc Natl Acad Sci U S A 2004; 101:11117-22; PMID: 15263098; http://dx.doi.org/10.1073/pnas.0402877101
7. Aswad A, Katzourakis A. Paleovirology and virally derived immunity. Trends Ecol Evol 2012; 27:627-36; PMID: 22901901; http://dx.doi.org/10.1016/j.tree.2012.07.007
8. Hilditch L, Matadeen R, Goldstone DC, Rosenthal PB, Taylor IA, Stoye JP. Ordered assembly of murine leukemia virus capsid protein on lipid nanotubes directs specific binding by the restriction factor, Fv1. Proc Natl Acad Sci U S A 2011; 108:5771-6; PMID:21436027; http://dx.doi.org/10.1073/pnas.1100118108
9. Kobayashi Y, Horie M, Tomonaga K, Suzuki Y. No evidence for natural selection on endogenous borna-like nucleoprotein elements after the divergence of Old World and New World monkeys. PLoS One 2011; 6: e24403; PMID:21912690; http://dx.doi.org/10.1371/journal. pone.0024403
10. Sofuku K, Parrish NF, Honda T, Tomonaga K. Transcription Profiling Demonstrates Epigenetic Control of Nonretroviral RNA Virus-Derived Elements in the Human Genome. Cell Rep 2015; 12:1548-54; PMID:26321645; http://dx.doi.org/10.1016/j.celrep.2015.08.007
11. Harrison PM, Zheng D, Zhang Z, Carriero N, Gerstein M. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res 2005; 33:2374-83; PMID:15860774; http://dx.doi.org/10.1093/nar/gki531
12. Parrish NF, Fujino K, Shiromoto Y, Iwasaki YW, Ha H, Xing J, Makino A, Kuramochi-Miyagawa S, Nakano T, Siomi H, et al. piRNAs derived from ancient viral processed pseudogenes as transgenerational sequence-specific immune memory in mammals. RNA 2015; 21:1691-703; PMID:26283688; http://dx.doi.org/10.1261/rna.052092.115
13. Ishizu H, Siomi H, Siomi MC. Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines. Genes Dev 2012; 26:2361-73; PMID:23124062; http://dx.doi.org/10.1101/gad.203786.112
14. Karginov FV, Hannon GJ. The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol Cell 2010; 37:7-19; PMID:20129051; http://dx.doi.org/10.1016/j. molcel.2009.12.033
15. Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012; 482:331-8; PMID:22337052; http://dx.doi.org/10.1038/nature10886
16. Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel DP, Kingston RE. Characterization of the piRNA complex from rat testes. Science 2006; 313:363-7; PMID:16778019; http://dx.doi.org/10.1126/science.1130164
17. Girard A, Sachidanandam R, Hannon GJ, Carmell MA. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 2006; 442:199-202; PMID:16751776
18. Hirano T, Iwasaki YW, Lin ZY-C, Imamura M, Seki NM, Sasaki E, Saito K, Okano H, Siomi MC, Siomi H. Small RNA profiling and characterization of piRNA clusters in the adult testes of the common marmoset, a model primate. RNA 2014; 20:1223-37; PMID:24914035; http://dx.doi.org/10.1261/rna.045310.114
19. An W, Han JS, Wheelan SJ, Davis ES, Coombes CE, Ye P, Triplett C, Boeke JD. Active retrotransposition by a synthetic L1 element in mice. Proc Natl Acad Sci U S A 2006; 103:18662-7; PMID:17124176; http://dx.doi.org/10.1073/pnas.0605300103
20. Berry C, Hannenhalli S, Leipzig J, Bushman FD. Selection of target sites for mobile DNA integration in the human genome. PLoS Comput Biol 2006; 2:e157; PMID:17166054; http://dx.doi.org/10.1371/journal.pcbi.0020157
21. Kim A, Terzian C, Santamaria P, Pélisson A, Purd’homme N, Bucheton A. Retroviruses in invertebrates: the gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster. Proc Natl Acad Sci U S A 1994; 91:1285-9; PMID:8108403; http://dx.doi.org/10.1073/pnas.91.4.1285
22. Yamamoto Y, Watanabe T, Hoki Y, Shirane K, Li Y, Ichiiyanagi K, Kuramochi-Miyagawa S, Toyoda A, Fujiyama A, Oginuma M, et al. Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus. Genome Res 2013; 23:292-9; PMID:23132912; http://dx.doi.org/10.1101/gr.137224.112
23. McClintock B. Controlling elements and the gene. Cold Spring Harb Symp Quant Biol 1956; 21:197-216; PMID:13433592; http://dx.doi.org/10.1101/SQB.1956. 021.01.017
24. Livak KJ. Detailed structure of the Drosophila melanogaster stellate genes and their transcripts. Genetics 1990; 124:303-16; PMID:1689686
25. Kalmykova AI, Dobritsa AA, Gvozdev VA. Su(Ste) diverged tandem repeats in a Y chromosome of Drosophila melanogaster are transcribed and variously processed. Genetics 1998; 148:243-9; PMID:9475736
26. Burstein E, Hoberg JE, Wilkinson AS, Rumble JM, Csomos RA, Komarck CM, Maine GN, Wilkinson JC, Mayo MW, Duckett CS. COMMD proteins, a novel family of structural and functional homologs of MURR1. J Biol Chem 2005; 280:22222-32; PMID:15799966; http://dx.doi.org/10.1074/jbc.M501928200
27. Geuking MB, Weber J, Dewannieux M, Gorelik E, Heidmann T, Hengartner H, Zinkernagel RM, Hangartner L. Recombination of retrotransposon and exogenous RNA virus results in nonretroviral cDNA integration. Science 2009; 323:393-6; PMID:19150848; http://dx.doi.org/10.1126/science.1167375
28. Shimizu A, Nakatani Y, Nakamura T, Jinno-Oue A, Ishikawa O, Boeke JD, Takeuchi Y, Hoshino H. Characterisation of cytoplasmic DNA complementary to nonretroviral RNA viruses in human cells. Sci Rep 2014; 4:5074; PMID:24875540
29. Liu H, Fu Y, Li B, Yu X, Xie J, Cheng J, Ghabrial SA, Li G, Yi X, Jiang D. Widespread horizontal gene transfer from circular single-stranded DNA viruses to eukaryotic genomes. BMC Evol Biol 2011; 11:276; PMID:21943216; http://dx.doi.org/10.1186/1471-2148-11-276
30. Liu H, Fu Y, Jiang D, Li G, Xie J, Cheng J, Peng Y, Ghabrial SA, Yi X. Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. J Virol 2010; 84:11876-87; PMID:20810725; http://dx.doi.org/10.1128/JVI.00955-10
31. Feschotte C, Gilbert C. Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet 2012; 13:283-96; PMID:22421730; http://dx.doi.org/10.1038/nrg3199
32. Zhdanov VM. Integration of viral genomes. Nature 1975; 256:471-3; PMID:51475; http://dx.doi.org/10.1038/256471a0
33. Goic B, Vodovar N, Mondotte JA, Monot C, Frangeul L, Blanc H, Gausson V, Vera-Otarola J, Cristofari G, Saleh M-C. RNA-mediated interference and reverse transcription control the persistence of RNA viruses in the insect model Drosophila. Nat Immunol 2013; 14:396-403; PMID:23435119; http://dx.doi.org/10.1038/ni.2542