Six RNA Viruses and Forty-One Hosts: Viral Small RNAs and Modulation of Small RNA Repertoires in Vertebrate and Invertebrate Systems

被引:213
作者
Parameswaran, Poornima [1 ]
Sklan, Ella [2 ]
Wilkins, Courtney [3 ]
Burgon, Trever [1 ]
Samuel, Melanie A. [4 ]
Lu, Rui [5 ]
Ansel, K. Mark [6 ,7 ]
Heissmeyer, Vigo [8 ]
Einav, Shirit [2 ]
Jackson, William [1 ]
Doukas, Tammy [1 ]
Paranjape, Suman [9 ]
Polacek, Charlotta [9 ]
dos Santos, Flavia Barreto [9 ]
Jalili, Roxana [10 ]
Babrzadeh, Farbod [10 ]
Gharizadeh, Baback [10 ]
Grimm, Dirk [11 ,12 ]
Kay, Mark [11 ,12 ]
Koike, Satoshi [13 ]
Sarnow, Peter [1 ]
Ronaghi, Mostafa [10 ]
Ding, Shou-Wei [5 ]
Harris, Eva [9 ]
Chow, Marie [3 ]
Diamond, Michael S. [4 ,14 ,15 ]
Kirkegaard, Karla [1 ]
Glenn, Jeffrey S. [2 ]
Fire, Andrew Z. [12 ,16 ]
机构
[1] Stanford Univ, Sch Med, Dept Microbiol & Immunol, Stanford, CA 94305 USA
[2] Stanford Univ, Sch Med, Dept Gastroenterol & Hepatol, Stanford, CA 94305 USA
[3] Univ Arkansas Med Sci, Dept Microbiol & Immunol, Little Rock, AR 72205 USA
[4] Washington Univ, Sch Med, Dept Mol Microbiol, St Louis, MO 63110 USA
[5] Univ Calif Riverside, Dept Plant Pathol & Microbiol, Riverside, CA 92521 USA
[6] Univ Calif San Francisco, Dept Microbiol & Immunol, San Francisco, CA 94143 USA
[7] Univ Calif San Francisco, Strateg Asthma Basic Res Ctr, San Francisco, CA 94143 USA
[8] German Res Ctr Environm Hlth, Helmholtz Ctr Munich, Inst Mol Immunol, Munich, Germany
[9] Univ Calif Berkeley, Sch Publ Hlth, Div Infect Dis & Vaccinol, Berkeley, CA 94720 USA
[10] Stanford Univ, Sch Med, Stanford Genome Technol Ctr, Stanford, CA 94305 USA
[11] Stanford Univ, Sch Med, Dept Pediat, Stanford, CA 94305 USA
[12] Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA
[13] Tokyo Metropolitan Inst Med Sci, Tokyo Metropolitan Org Med Res, Tokyo 113, Japan
[14] Washington Univ, Sch Med, Dept Med, St Louis, MO 63110 USA
[15] Washington Univ, Sch Med, Dept Pathol & Immunol, St Louis, MO 63110 USA
[16] Stanford Univ, Sch Med, Dept Pathol, Stanford, CA 94305 USA
关键词
DOUBLE-STRANDED-RNA; HEPATITIS-C VIRUS; VESICULAR STOMATITIS-VIRUS; INDUCED SILENCING COMPLEX; ANTIVIRAL IMMUNITY; CELLULAR MICRORNAS; CORE PROTEIN; DENGUE VIRUS; NS1; PROTEIN; LEADER RNA;
D O I
10.1371/journal.ppat.1000764
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
We have used multiplexed high-throughput sequencing to characterize changes in small RNA populations that occur during viral infection in animal cells. Small RNA-based mechanisms such as RNA interference (RNAi) have been shown in plant and invertebrate systems to play a key role in host responses to viral infection. Although homologs of the key RNAi effector pathways are present in mammalian cells, and can launch an RNAi-mediated degradation of experimentally targeted mRNAs, any role for such responses in mammalian host-virus interactions remains to be characterized. Six different viruses were examined in 41 experimentally susceptible and resistant host systems. We identified virus-derived small RNAs (vsRNAs) from all six viruses, with total abundance varying from "vanishingly rare'' (less than 0.1% of cellular small RNA) to highly abundant (comparable to abundant micro-RNAs "miRNAs''). In addition to the appearance of vsRNAs during infection, we saw a number of specific changes in host miRNA profiles. For several infection models investigated in more detail, the RNAi and Interferon pathways modulated the abundance of vsRNAs. We also found evidence for populations of vsRNAs that exist as duplexed siRNAs with zero to three nucleotide 39 overhangs. Using populations of cells carrying a Hepatitis C replicon, we observed strand-selective loading of siRNAs onto Argonaute complexes. These experiments define vsRNAs as one possible component of the interplay between animal viruses and their hosts.
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页数:21
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