Dissecting noncoding and pathogen RNA-protein interactomes

RNA

Volumn 21, Issue 1, 2015, Pages 135-143

  Flynn, Ryan A ^a   Martin, Lance ^a,b   Spitale, Robert C ^c   Do, Brian T ^a   Sagan, Selena M ^d   Zarnegar, Brian ^a   Qu, Kun ^a   Khavari, Paul A ^a   Quake, Stephen R ^b,e   Sarnow, Peter ^a   Chang, Howard Y ^a,e  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Stanford University   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d MCGILL UNIVERSITY   (Canada)

^e STANFORD UNIVERSITY   (United States)

Author keywords

Genomics; Noncoding rna; RNA protein interactions; Virology

Indexed keywords

LONG UNTRANSLATED RNA; MESSENGER RNA; POLYCYTIDYLIC ACID; RNA; UNTRANSLATED RNA; VIRUS RNA; PROTEIN BINDING; RNA BINDING PROTEIN; TRANSCRIPTOME;

ARTICLE; BIOCHEMISTRY; CROSS LINKING; HEPATITIS C; IMMUNOPRECIPITATION; NONHUMAN; PROTEIN INTERACTION; CONSENSUS SEQUENCE; GENE EXPRESSION PROFILING; HEPACIVIRUS; HOST PATHOGEN INTERACTION; HUMAN; METABOLISM; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; TUMOR CELL LINE;

HEPATITIS C VIRUS;

BASE SEQUENCE; CELL LINE, TUMOR; CONSENSUS SEQUENCE; GENE EXPRESSION PROFILING; HEPACIVIRUS; HOST-PATHOGEN INTERACTIONS; HUMANS; IMMUNOPRECIPITATION; PROTEIN BINDING; RNA, MESSENGER; RNA, UNTRANSLATED; RNA, VIRAL; RNA-BINDING PROTEINS; TRANSCRIPTOME;

EID: 84920507947     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.047803.114     Document Type: Article

References (42)

1. Choi HS, Hwang CK, Song KY, Law PY, Wei LN, Loh HH. 2009. Poly (C)-binding proteins as transcriptional regulators of gene expression. Biochem Biophys Res Commun 380: 431-436.
2. Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U. 2011. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol 12: R79.
3. Du Z, Lee JK, Tjhen R, Li S, Pan H, Stroud RM, James TL. 2005. Crystal structure of the firstKH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.7 Å. J Biol Chem 280: 38823-38830.
4. Eiring AM, Harb JG, Neviani P, Garton C, Oaks JJ, Spizzo R, Liu S, Schwind S, Santhanam R, Hickey CJ, et al. 2010. miR-328 functions as an RNA decoy to modulate hnRNP E2 regulation of mRNA translation in leukemic blasts. Cell 140: 652-665.
5. Fraser CS, Doudna JA. 2006. Structural and mechanistic insights into hepatitis C viral translation initiation. Nat Rev Microbiol 5: 29-38.
6. Gamarnik AV, Andino R. 2000. Interactions of viral protein 3CD and poly (rC) binding protein with the 5' untranslated region of the poliovirus genome. J Virol 74: 2219-2226.
7. Guttman M, Rinn JL. 2012. Modular regulatory principles of large noncoding RNAs. Nature 482: 339-346.
8. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, et al. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129-141.
9. Han W, Xin Z, Zhao Z, Bao W, Lin X, Yin B, Zhao J, Yuan J, Qiang B, Peng X. 2013. RNA-binding protein PCBP2 modulates glioma growth by regulating FHL3. J Clin Invest 123: 2103-2118.
10. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. 2010. Simple combinations of line-age-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38: 576-589.
11. Herold J, Andino R. 2001. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol Cell 7: 581-591.
12. Huang DW, Sherman BT, Lempicki RA. 2009. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.
13. Huppertz I, Attig J, D'Ambrogio A, Easton LE, Sibley CR, Sugimoto Y, Tajnik M, König J, Ule J. 2014. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 65: 274-287.
14. König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. 2010. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17: 909-915.
15. König J, Zarnack K, Luscombe NM, Ule J. 2012. Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet 13: 77-83.
16. Li Y, Masaki T, Lemon SM. 2013a. miR-122 and the Hepatitis C RNA genome: more than just stability. RNA Biol 10: 919-923.
17. Li Y, Masaki T, Yamane D, McGivern DR, Lemon SM. 2013b. Competing and noncompeting activities of miR-122 and the 5? exonuclease Xrn1 in regulation of hepatitis C virus replication. Proc Natl Acad Sci 110: 1881-1886.
18. Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark TJ, Gehman LT, Hoon S, et al. 2013. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol 20: 1434-1442.
19. Lunde BM, Moore C, Varani G. 2007. RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol 8: 479-490.
20. Luo G. 1999. Cellular proteins bind to the poly (U) tract of the 3? untranslated region of hepatitis C virus RNA genome. Virology 256: 105-118.
21. Machlin ES, Sarnow P, Sagan SM. 2011. Masking the 5? terminal nucleotides of the hepatitis C virus genome by an unconventional microRNA-target RNA complex. Proc Natl Acad Sci 108: 3193-3198.
22. Martin L, Meier M, Lyons SM, Sit RV, Marzluff WF, Quake SR, ChangHY. 2012. Systematic reconstruction ofRNAfunctional motifs with high-throughput microfluidics. Nature Methods 9: 1192-1194.
23. Miyamoto M, Kato T, Date T, Mizokami M, Wakita T. 2006. Comparison between subgenomic replicons of hepatitis C virus genotypes 2a (JFH-1) and 1b (Con1 NK5.1). Intervirology 49: 37-43.
24. Papenfort K, Vogel J. 2010. Regulatory RNA in bacterial pathogens. Cell Host Microbe 8: 116-127.
25. Perreault J, Perreault JP, Boire G. 2007. Ro-associated Y RNAs in metazoans: evolution and diversification. Mol Biol Evol 24: 1678-1689.
26. Rapicavoli NA, Qu K, Zhang J, Mikhail M, Laberge RM, Chang HY. 2013. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. Elife 2: e00762-e00762.
27. Rinn JL, Chang HY. 2012. Genome regulation by long noncoding RNAs. Annu Rev Biochem 81: 145-166.
28. Rinn JL, Ule J. 2014. 'Oming in on RNA-protein interactions. Genome Biol 15: 401.
29. Shetty S, Stefanovic S, Mihailescu MR. 2013. Hepatitis C virus RNA: molecular switches mediated by long-range RNA-RNA interactions? Nucleic Acids Res 41: 2526-2540.
30. Song Y, Friebe P, Tzima E, Junemann C, Bartenschlager R, Niepmann M. 2006. The hepatitis C virus RNA 3? -untranslated region strongly enhances translation directed by the internal ribosome entry site. J Virol 80: 11579-11588.
31. Steinmann E, Pietschmann T. 2013. Cell culture systems for hepatitis C virus. Curr Top Microbiol Immunol 369: 17-48.
32. Tellinghuisen TL, Evans MJ, von Hahn T, You S, Rice CM. 2007. Studying hepatitis C virus: making the best of a bad virus. J Virol 81: 8853-8867.
33. Vanharanta S, Marney CB, Shu W, Valiente M, Zou Y, Mele A, Darnell RB, Massague J. 2014. Loss of the multifunctional RNAbinding protein RBM47 as a source of selectable metastatic traits in breast cancer. Elife 3: e02734-e02734.
34. Verhagen AP, Pruijn GJ. 2011. Are the Ro RNP-associated Y RNAs concealing microRNAs? Y RNA-derived miRNAs may be involved in autoimmunity. Bioessays 33: 674-682.
35. Waggoner SA, Liebhaber SA. 2003. Identification of mRNAs associated with α CP2-containing RNP complexes. Mol Cell Biol 23: 7055-7067.
36. Wakita T, Pietschmann T, Kato T, Date T, Miyamoto M, Zhao Z, Murthy K, Habermann A, Kräusslich HG, Mizokami M, et al. 2005. Production of infectious hepatitis C virus in tissue culture from a cloned viral genome. Nat Med 11: 791-796.
37. Walter BL, Parsley TB, Ehrenfeld E, Semler BL. 2002. Distinct poly(rC) binding protein KH domain determinants for poliovirus translation initiation and viral RNA replication. J Virol 76: 12008-12022.
38. Wang L, Jeng KS, Lai MM. 2011. Poly(C)-binding protein 2 interacts with sequences required for viral replication in the hepatitis C virus (HCV) 5? untranslated region and directs HCV RNA replication through circularizing the viral genome. J Virol 85: 7954-7964.
39. Weiss IM, Liebhaber SA. 1995. Erythroid cell-specific mRNA stability elements in the α2-globin 3' nontranslated region. Mol Cell Biol 15: 2457-2465.
40. Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, Xue C, Herre M, Silver PA, Zhang MQ, et al. 2014. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep 6: 1139-1152.
41. Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe NM, Ule J. 2013. Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 152: 453-466.
42. Zhang C, Darnell RB. 2011. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 29: 607-614.