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Cited by 13Virus-based gene therapy researchRNA Interference and Gene DeliveryMicroRNA in disease regulation

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Comprehensive Small RNA-Seq of Adeno-Associated Virus (AAV)-Infected Human Cells Detects Patterns of Novel, Non-Coding AAV RNAs in the Absence of Cellular miRNA Regulation

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Stutika, Catrin, Mietzsch, Mario, Gogol-Döring, Andreas, Weger, Stefan, Sohn, Madlen, Chen, Wei, Heilbronn, Regine·2016·PLOS ONE
DOI 10.1371/journal.pone.0161454PMC PMC5017669
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Abstract

Most DNA viruses express small regulatory RNAs, which interfere with viral or cellular gene expression. For adeno-associated virus (AAV), a small ssDNA virus with a complex biphasic life cycle miRNAs or other small regulatory RNAs have not yet been described. This is the first comprehensive Illumina-based RNA-Seq analysis of small RNAs expressed by AAV alone or upon co-infection with helper adenovirus or HSV. Several hotspots of AAV-specific small RNAs were detected mostly close to or within the AAV-ITR and apparently transcribed from the newly identified anti-p5 promoter. An additional small RNA hotspot was located downstream of the p40 promoter, from where transcription of non-coding RNAs associated with the inhibition of adenovirus replication were recently described. Parallel detection of known Ad and HSV miRNAs indirectly validated the newly identified small AAV RNA species. The predominant small RNAs were analyzed on Northern blots and by human argonaute protein-mediated co-immunoprecipitation. None of the small AAV RNAs showed characteristics of bona fide miRNAs, but characteristics of alternative RNA processing indicative of differentially regulated AAV promoter-associated small RNAs. Furthermore, the AAV-induced regulation of cellular miRNA levels was analyzed at different time points post infection. In contrast to other virus groups AAV infection had virtually no effect on the expression of cellular miRNA, which underscores the long-established concept that wild-type AAV infection is apathogenic.

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  • Stutika et al. mapped small RNAs from the wild-type AAV2 genome in the presence and absence of adenovirus, and in both scenarios multiple small RNAs were present in the ITR regions with a hotspot within the RBE.

    “Stutika et al. were able to map small RNAs from the wild-type AAV2 genome in the presence and absence of adenovirus and it is intriguing to note that in both scenarios, multiple small RNAs were present in the ITR regions with a hotspot within the RBE.39”

    From Adeno-Associated Virus Serotype-Specific Inverted Terminal Repeat Sequence Role in Vector Transgene Expression (2020) · cites this paper as [39]

    The Results (‘Small RNA read mapping to the AAV2 (+) and (-) strand,’ page unavailable) say reads were mapped to the wild-type AAV2 genome and that profiles with and without Ad2 were comparable, though read counts differed about 200-fold. ‘Detailed mapping of AAV2-specific small RNAs’ identifies multiple ITR hotspots, but its nucleotide-level analysis used Ad2-co-infected cells. The copy does not establish an ITR hotspot within the RBE in both conditions; the RBE-overlapping small RNA it mentions is near the p5 promoter. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • In the absence of a helper virus when Rep78 is acting to auto-suppress transcription from the p5 promoter, the sequence reads from the ITR region were higher than those from p5.

    “In the absence of a helper virus when Rep78 is acting to auto-suppress transcription from the p5 promoter,40 the sequence reads from the ITR region were actually higher than those from p5,39”

    From Adeno-Associated Virus Serotype-Specific Inverted Terminal Repeat Sequence Role in Vector Transgene Expression (2020) · cites this paper as [39]

    The Results section, “Small RNA read mapping to the AAV2 (+) and (-) strand” (page unavailable), reports many ITR reads and says the small-RNA mapping profile was comparable with and without the Ad2 helper virus. It does not explicitly state that ITR reads exceeded p5 reads in helper-virus-free cells; the reported p5-region reads are described as mapping opposite the promoter (anti-p5). The Rep78 explanation is separately cited to source 40, not this paper. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 61

  1. RM Kotin, 1990, Site-specific integration by adeno-associated virus, Proc Natl Acad Sci U S A, 87, 2211, 10.1073/pnas.87.6.2211 · DOI
  2. D Hüser, 2014, Adeno-associated virus type 2 wild-type and vector-mediated genomic integration profiles of human diploid fibroblasts analyzed by third-generation PacBio DNA sequencing, J Virol, 88, 11253, 10.1128/JVI.01356-14 · DOI
  3. J Yang, 1999, Concatamerization of adeno-associated virus circular genomes occurs through intermolecular recombination, J Virol, 73, 9468, 10.1128/JVI.73.11.9468-9477.1999 · DOI
  4. NR Blacklow, 1967, Isolation of adenovirus-associated viruses from man, Proc Natl Acad Sci U S A, 58, 1410, 10.1073/pnas.58.4.1410 · DOI
  5. RM Buller, 1981, Herpes simplex virus types 1 and 2 completely help adenovirus-associated virus replication, J Virol, 40, 241, 10.1128/JVI.40.1.241-247.1981 · DOI
  6. B Georg-Fries, 1984, Analysis of proteins, helper dependence, and seroepidemiology of a new human parvovirus, Virology, 134, 64, 10.1016/0042-6822(84)90272-1 · DOI
  7. RA McPherson, 1985, Human cytomegalovirus completely helps adeno-associated virus replication, Virology, 147, 217, 10.1016/0042-6822(85)90243-0 · DOI
  8. BJ Thomson, 1994, Human herpesvirus 6 (HHV6) is a helper virus for adeno-associated virus type 2 (AAV2) and the rep gene homologue in HHV6 can mediate AAV-2 DNA replication and regulate gene expression, Virology, 204, 304, 10.1006/viro.1994.1535 · DOI
  9. A Srivastava, 1983, Nucleotide sequence and organization of the adeno-associated virus 2 genome, J Virol, 45, 555, 10.1128/JVI.45.2.555-564.1983 · DOI · Paper page
  10. F Sonntag, 2010, A viral assembly factor promotes AAV2 capsid formation in the nucleolus, Proc Natl Acad Sci U S A, 107, 10220, 10.1073/pnas.1001673107 · DOI · Paper page
  11. C Stutika, 2015, A Comprehensive RNA-Seq Analysis of the Adeno-Associated Virus type 2 Transcriptome Reveals Novel AAV Transcripts, Splice Variants, and Derived Proteins, J Virol
  12. S Weger, 2016, A regulatory element near the 3' -end of the AAV rep gene inhibits adenovirus replication in cis by means of p40 promoter-associated short transcripts, J Virol
  13. DP Bartel, 2004, MicroRNAs: genomics, biogenesis, mechanism, and function, Cell, 116, 281, 10.1016/S0092-8674(04)00045-5 · DOI
  14. VN Kim, 2005, MicroRNA biogenesis: coordinated cropping and dicing, Nat Rev Mol Cell Biol, 6, 376, 10.1038/nrm1644 · DOI · Paper page
  15. RW Carthew, 2009, Origins and Mechanisms of miRNAs and siRNAs, Cell, 136, 642, 10.1016/j.cell.2009.01.035 · DOI
  16. DP Bartel, 2009, MicroRNAs: target recognition and regulatory functions, Cell, 136, 215, 10.1016/j.cell.2009.01.002 · DOI · Paper page
  17. SP Keam, 2015, tRNA-Derived Fragments (tRFs): Emerging New Roles for an Ancient RNA in the Regulation of Gene Expression, Life, 5, 1638, 10.3390/life5041638 · DOI
  18. D Langenberger, 2009, Evidence for human microRNA-offset RNAs in small RNA sequencing data, Bioinformatics, 25, 2298, 10.1093/bioinformatics/btp419 · DOI
  19. BX Yan, 2012, Promoter-associated RNAs and promoter-targeted RNAs, Cell Mol Life Sci, 69, 2833, 10.1007/s00018-012-0953-1 · DOI
  20. RP Kincaid, 2012, Virus-encoded microRNAs: an overview and a look to the future, PLoS Pathog, 8, e1003018, 10.1371/journal.ppat.1003018 · DOI
  21. KT Tycowski, 2015, Viral noncoding RNAs: more surprises, Genes Dev, 29, 567, 10.1101/gad.259077.115 · DOI
  22. MG Andersson, 2005, Suppression of RNA interference by adenovirus virus-associated RNA, J Virol, 79, 9556, 10.1128/JVI.79.15.9556-9565.2005 · DOI
  23. F Bellutti, 2015, Identification of RISC-associated adenoviral microRNAs, a subset of their direct targets, and global changes in the targetome upon lytic adenovirus 5 infection, J Virol, 89, 1608, 10.1128/JVI.02336-14 · DOI
  24. O Aparicio, 2010, Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair, Nucleic Acids Res, 38, 750, 10.1093/nar/gkp1028 · DOI
  25. JL Umbach, 2008, MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs, Nature, 454, 780, 10.1038/nature07103 · DOI
  26. O Flores, 2013, Mutational inactivation of herpes simplex virus 1 microRNAs identifies viral mRNA targets and reveals phenotypic effects in culture, J Virol, 87, 6589, 10.1128/JVI.00504-13 · DOI
  27. I Jurak, 2010, Numerous conserved and divergent microRNAs expressed by herpes simplex viruses 1 and 2, J Virol, 84, 4659, 10.1128/JVI.02725-09 · DOI
  28. MK Meshesha, 2012, The microRNA Transcriptome of Human Cytomegalovirus (HCMV), Open Virol J, 6, 38, 10.2174/1874357901206010038 · DOI
  29. K Winter, 2012, Roles of E4orf6 and VA I RNA in adenovirus-mediated stimulation of human parvovirus B19 DNA replication and structural gene expression, J Virol, 86, 5099, 10.1128/JVI.06991-11 · DOI
  30. R Heilbronn, 1990, The adeno-associated virus rep gene suppresses herpes simplex virus-induced DNA-amplification, J Virol, 64, 3012, 10.1128/JVI.64.6.3012-3018.1990 · DOI
  31. M Mietzsch, 2014, Differential adeno-associated virus serotype-specific interaction patterns with synthetic heparins and other glycans, J Virol, 88, 2991, 10.1128/JVI.03371-13 · DOI
  32. FW Weindler, 1991, A subset of herpes simplex virus replication genes provides helper functions for productive adeno-associated virus replication, J Virol, 65, 2476, 10.1128/JVI.65.5.2476-2483.1991 · DOI
  33. CJ Harris, 2015, FDF-PAGE: a powerful technique revealing previously undetected small RNAs sequestered by complementary transcripts, Nucleic Acids Res, 43, 7590, 10.1093/nar/gkv604 · DOI
  34. K Damm, 2015, Improved Northern Blot Detection of Small RNAs Using EDC Crosslinking and DNA/LNA Probes, Methods Mol Biol, 1296, 41, 10.1007/978-1-4939-2547-6_5 · DOI
  35. SW Kim, 2010, A sensitive non-radioactive northern blot method to detect small RNAs, Nucleic Acids Res, 38, e98, 10.1093/nar/gkp1235 · DOI
  36. A Kozomara, 2014, miRBase: annotating high confidence microRNAs using deep sequencing data, Nucleic Acids Res, 42, D68, 10.1093/nar/gkt1181 · DOI · Paper page
  37. B Langmead, 2010, Aligning short sequencing reads with Bowtie, Curr Protoc Bioinformatics, 10.1002/0471250953.bi1107s32 · DOI
  38. XJ Jing, 2001, Inhibition of adenovirus cytotoxicity, replication, and E2a gene expression by adeno-associated virus, Virology, 291, 140, 10.1006/viro.2001.1192 · DOI
  39. JM Timpe, 2006, Effects of adeno-associated virus on adenovirus replication and gene expression during coinfection, J Virol, 80, 7807, 10.1128/JVI.00198-06 · DOI
  40. H Zhao, 2015, Fluctuating expression of microRNAs in adenovirus infected cells, Virology, 478, 99, 10.1016/j.virol.2015.01.033 · DOI
  41. O Aparicio, 2006, Adenovirus virus-associated RNA is processed to functional interfering RNAs involved in virus production, J Virol, 80, 1376, 10.1128/JVI.80.3.1376-1384.2006 · DOI
  42. Y Furuse, 2013, Persistently adenovirus-infected lymphoid cells express microRNAs derived from the viral VAI and especially VAII RNA, Virology, 447, 140, 10.1016/j.virol.2013.08.024 · DOI
  43. DJ Munson, 2012, A novel miRNA produced during lytic HSV-1 infection is important for efficient replication in tissue culture, Arch Virol, 157, 1677, 10.1007/s00705-012-1345-4 · DOI
  44. S Griffiths-Jones, 2006, miRBase: the microRNA sequence database, Methods Mol Biol, 342, 129
  45. V Agarwal, 2015, Predicting effective microRNA target sites in mammalian mRNAs, Elife, 4, 10.7554/eLife.05005 · DOI · Paper page
  46. JL Stilwell, 2004, Role of viral vectors and virion shells in cellular gene expression, Mol Ther, 9, 337, 10.1016/j.ymthe.2003.11.007 · DOI
  47. L Wang, 2015, Productive life cycle of adeno-associated virus serotype 2 in the complete absence of a conventional polyadenylation signal, J Gen Virol, 96, 2780, 10.1099/jgv.0.000229 · DOI
  48. KN Son, 2015, Double-Stranded RNA Is Detected by Immunofluorescence Analysis in RNA and DNA Virus Infections, Including Those by Negative-Stranded RNA Viruses, J Virol, 89, 9383, 10.1128/JVI.01299-15 · DOI
  49. TR Flotte, 1993, Expression of the cystic fibrosis transmembrane conductance regulator from a novel adeno-associated virus promoter, J Biol Chem, 268, 3781, 10.1016/S0021-9258(18)53762-5 · DOI
  50. J Qiu, 2002, Characterization of the transcription profile of adeno-associated virus type 5 reveals a number of unique features compared to previously characterized adeno-associated viruses, J Virol, 76, 12435, 10.1128/JVI.76.24.12435-12447.2002 · DOI
  51. S Rother, 2011, Small RNAs derived from longer non-coding RNAs, Biochimie, 93, 1905, 10.1016/j.biochi.2011.07.032 · DOI
  52. JR Brister, 1999, Rep-mediated nicking of the adeno-associated virus origin requires two biochemical activities, DNA helicase activity and transesterification, J Virol, 73, 9325, 10.1128/JVI.73.11.9325-9336.1999 · DOI
  53. JR Brister, 2000, Mechanism of Rep-mediated adeno-associated virus origin nicking, J Virol, 74, 7762, 10.1128/JVI.74.17.7762-7771.2000 · DOI
  54. DJ Pereira, 1997, The adeno-associated virus (AAV) Rep protein acts as both a repressor and an activator to regulate AAV transcription during a productive infection, J Virol, 71, 1079, 10.1128/JVI.71.2.1079-1088.1997 · DOI
  55. S He, 2008, The properties and functions of virus encoded microRNA, siRNA, and other small noncoding RNAs, Crit Rev Microbiol, 34, 175, 10.1080/10408410802482008 · DOI
  56. YT Lin, 2010, Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs, RNA, 16, 1540, 10.1261/rna.1967910 · DOI
  57. L Tuddenham, 2012, Small RNA deep sequencing identifies microRNAs and other small noncoding RNAs from human herpesvirus 6B, J Virol, 86, 1638, 10.1128/JVI.05911-11 · DOI
  58. WW Hauswirth, 1977, Origin and termination of adeno-associated virus DNA replication, Virology, 78, 488, 10.1016/0042-6822(77)90125-8 · DOI
  59. JA King, 2001, DNA helicase-mediated packaging of adeno-associated virus type 2 genomes into preformed capsids, Embo J, 20, 3282, 10.1093/emboj/20.12.3282 · DOI · Paper page
  60. AC Seila, 2008, Divergent transcription from active promoters, Science, 322, 1849, 10.1126/science.1162253 · DOI
  61. RJ Taft, 2009, Tiny RNAs associated with transcription start sites in animals, Nat Genet, 41, 572, 10.1038/ng.312 · DOI

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Metadata

Authors
Stutika, C., Mietzsch, M., Gogol-Döring, A., Weger, S., Sohn, M., Chen, W., & Heilbronn, R.
Affiliations
  • Charité – Universitätsmedizin Berlin (DE)
  • Max Delbrück Center (DE)
Corresponding author
Heilbronn, Regine
ORCID
Venue
PLOS ONE
Publisher
Public Library of Science (PLoS)
Published
2016-09-09
Volume
11
Issue
9
Pages
e0161454
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0161454
PMC
PMC5017669
OpenAlex
W2507266321
Cited by
13
References
4
Citations by year
2026: 1 · 2024: 1 · 2023: 1 · 2022: 2 · 2020: 2 · 2019: 3 · 2018: 1 · 2017: 2
FWCI
1.62
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
  • Refubium (Universitätsbibliothek der Freien Universität Berlin) (submittedVersion, cc-by)
  • Universitätsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver (cc-by)
Funders
  • Charité Universitätsmedizin Berlin
  • Sonnenfeld Stiftung
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
Keywords
adeno-associated virus, small regulatory RNAs, alternative RNA processing, Argonaute proteins, viral gene expression regulation
MeSH terms
Dependovirus, Cell Line, Gene Expression Regulation, Humans, Parvoviridae Infections, RNA, Viral, Gene Library, Gene Expression Regulation, Viral, Genome, Viral, Herpesvirus 1, Human, RNA, Untranslated, MicroRNAs, Host-Pathogen Interactions, High-Throughput Nucleotide Sequencing, Argonaute Proteins

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