Tracking expression and subcellular localization of RNA and protein species using high-throughput single cell imaging flow cytometry

RNA

Volumn 18, Issue 8, 2012, Pages 1573-1579

  Borah, Sumit ^a   Nichols, Lisa A ^b   Hassman, Lynn M ^b   Kedes, Dean H ^b   Steitz, Joan A ^a  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF VIRGINIA   (United States)

Author keywords

FACS; High throughput; MIFC; Noncoding; RNA

Indexed keywords

NUCLEAR RNA; POLYADENYLATED NUCLEAR RNA; POLYADENYLATED RNA; POLYADENYLIC ACID BINDING PROTEIN; POLYADENYLIC ACID BINDING PROTEIN C1; PROTEIN; RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA; VIRUS PROTEIN; VIRUS RNA;

ARTICLE; CELL NUCLEUS; CELL POPULATION; CONFOCAL MICROSCOPY; CONTROLLED STUDY; CYTOPLASM; FLOW CYTOMETRY; GENE EXPRESSION; HERPES VIRUS INFECTION; HIGH THROUGHPUT SCREENING; HUMAN HERPESVIRUS 8; MOLECULAR IMAGING; MULTISPECTRAL IMAGING FLOW CYTOMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; VIRUS CELL INTERACTION;

CELL NUCLEUS; CYTOPLASM; FLOW CYTOMETRY; FLUORESCENT ANTIBODY TECHNIQUE; HERPESVIRIDAE INFECTIONS; HERPESVIRUS 8, HUMAN; HUMANS; IN SITU HYBRIDIZATION; POLY(A)-BINDING PROTEIN I; PROTEIN TRANSPORT; RNA, MESSENGER; RNA, NUCLEAR; RNA, UNTRANSLATED; RNA, VIRAL; SUBCELLULAR FRACTIONS; VIRAL PROTEINS; VIRUS REPLICATION;

HUMAN HERPESVIRUS 8;

EID: 84864063957     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.033126.112     Document Type: Article

References (34)

1. Adang LA, Parsons CH, Kedes DH. 2006. Asynchronous progression through the lytic cascade and variations in intracellular viral loads revealed by high-throughput single-cell analysis of Kaposi's sarcoma- associated herpesvirus infection. J Virol 80: 10073-10082. (Pubitemid 44522601)
2. Baerlocher GM, Vulto I, de Jong G, Lansdorp PM. 2006. Flow cytometry and FISH to measure the average length of telomeres (flow FISH). Nat Protoc 1: 2365-2376.
3. Basiji DA, Ortyn WE, Liang L, Venkatachalam V, Morrissey P. 2007. Cellular image analysis and imaging by flow cytometry. Clin Lab Med 27: 653-670 viii.
4. Borah S, Darricarrere N, Darnell A, Myoung J, Steitz JA. 2011. A viral nuclear noncoding RNA binds re-localized poly(A) binding protein and is required for late KSHV gene expression. PLoS Pathog 7: e1002300. doi: 10.1371/journal.ppat.1002300.
5. Boshoff C, Schulz TF, Kennedy MM, Graham AK, Fisher C, Thomas A, McGee JO, Weiss RA, O'Leary JJ. 1995. Kaposi's sarcoma-associated herpesvirus infects endothelial and spindle cells. Nat Med 1: 1274-1278.
6. Cai X, Lu S, Zhang Z, Gonzalez CM, Damania B, Cullen BR. 2005. Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proc Natl Acad Sci 102: 5570-5575. (Pubitemid 40530298)
7. Covarrubias S, Gaglia MM, Kumar GR, Wong W, Jackson AO, Glaunsinger BA. 2011. Coordinated destruction of cellular messages in translation complexes by the gammaherpesvirus host shutoff factor and the mammalian exonuclease Xrn1. PLoS Pathog 7: e1002339. doi: 10.1371/journal.ppat.1002339.
8. Crouch J, Leitenberg D, Smith BR, Howe JG. 1997. Epstein-Barr virus suspension cell assay using in situ hybridization and flow cytometry. Cytometry 29: 50-57. (Pubitemid 27397797)
9. Cullen BR. 2003. Nuclear RNA export. J Cell Sci 116: 587-597. (Pubitemid 36231297)
10. Daigle D, Megyola C, El-Guindy A, Gradoville L, Tuck D, Miller G, Bhaduri-McIntosh S. 2010. Upregulation of STAT3 marks Burkitt lymphoma cells refractory to Epstein-Barr virus lytic cycle induction by HDAC inhibitors. J Virol 84: 993-1004.
11. Dupin N, Fisher C, Kellam P, Ariad S, Tulliez M, Franck N, van Marck E, Salmon D, Gorin I, Escande JP, et al. 1999. Distribution of human herpesvirus-8 latently infected cells in Kaposi's sarcoma, multicentric Castleman's disease, and primary effusion lymphoma. Proc Natl Acad Sci 96: 4546-4551. (Pubitemid 29190373)
12. Ganem D. 2006. KSHV infection and the pathogenesis of Kaposi's sarcoma. Annu Rev Pathol 1: 273-296.
13. Glaunsinger B, Ganem D. 2004. Lytic KSHV infection inhibits host gene expression by accelerating global mRNA turnover. Mol Cell 13: 713-723. (Pubitemid 38368128)
14. Gorlach M, Burd CG, Dreyfuss G. 1994. The mRNA poly(A)-binding protein: localization, abundance, and RNA-binding specificity. Exp Cell Res 211: 400-407. (Pubitemid 124002450)
15. Grunwald D, Singer RH. 2010. In vivo imaging of labelled endogenous b-actin mRNA during nucleocytoplasmic transport. Nature 467: 604-607.
16. Hassman LM, Ellison TJ, Kedes DH. 2011. KSHV infects a subset of human tonsillar B cells, driving proliferation and plasmablast differentiation. J Clin Invest 121: 752-768.
17. Kimura H, Miyake K, Yamauchi Y, Nishiyama K, Iwata S, Iwatsuki K, Gotoh K, Kojima S, Ito Y, Nishiyama Y. 2009. Identification of Epstein-Barr virus (EBV)-infected lymphocyte subtypes by flow cytometric in situ hybridization in EBV-associated lymphoproliferative diseases. J Infect Dis 200: 1078-1087.
18. Kumar GR, Glaunsinger BA. 2010. Nuclear import of cytoplasmic poly(A) binding protein restricts gene expression via hyperadenylation and nuclear retention of mRNA. Mol Cell Biol 30: 4996-5008.
19. Kumar GR, Shum L, Glaunsinger BA. 2011. Importin a-mediated nuclear import of cytoplasmic poly(A) binding protein occurs as a direct consequence of cytoplasmic mRNA depletion. Mol Cell Biol 31: 3113-3125.
20. Lefort S, Flamand L. 2009. Kaposi's sarcoma-associated herpesvirus K-bZIP protein is necessary for lytic viral gene expression, DNA replication, and virion production in primary effusion lymphoma cell lines. J Virol 83: 5869-5880.
21. Li M, MacKey J, Czajak SC, Desrosiers RC, Lackner AA, Jung JU. 1999. Identification and characterization of Kaposi's sarcoma-associated herpesvirus K8.1 virion glycoprotein. J Virol 73: 1341-1349. (Pubitemid 29036789)
22. Mangus DA, Evans MC, Jacobson A. 2003. Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol 4: 223. doi: 10.1186/gb-2003-4-7-223.
23. Nakamura H, Lu M, Gwack Y, Souvlis J, Zeichner SL, Jung JU. 2003. Global changes in Kaposi's sarcoma-associated virus gene expression patterns following expression of a tetracycline-inducible Rta transactivator. J Virol 77: 4205-4220. (Pubitemid 36350959)
24. Ortyn WE, Perry DJ, Venkatachalam V, Liang L, Hall BE, Frost K, Basiji DA. 2007. Extended depth of field imaging for high speed cell analysis. Cytometry A 71: 215-231. (Pubitemid 46581283)
25. Paulose-Murphy M, Ha NK, Xiang C, Chen Y, Gillim L, Yarchoan R, Meltzer P, Bittner M, Trent J, Zeichner S. 2001. Transcription program of human herpesvirus 8 (Kaposi's sarcoma-associated herpesvirus). J Virol 75: 4843-4853. (Pubitemid 32381527)
26. Renne R, Blackbourn D, Whitby D, Levy J, Ganem D. 1998. Limited transmission of Kaposi's sarcoma-associated herpesvirus in cultured cells. J Virol 72: 5182-5188. (Pubitemid 28215700)
27. Robertson KL, Verhoeven AB, Thach DC, Chang EL. 2010. Monitoring viral RNA in infected cells with LNA flow-FISH. RNA 16: 1679-1685.
28. Rossetto CC, Pari G. 2012. KSHV PAN RNA associates with demethylases UTX and JMJD3 to activate lytic replication through a physical interaction with the virus genome. PLoS Pathog 8: e1002680. doi: 10.1371/journal.ppat.1002680.
29. Samols MA, Hu J, Skalsky RL, Renne R. 2005. Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. J Virol 79: 9301-9305. (Pubitemid 40934841)
30. Santarelli R, Farina A, Granato M, Gonnella R, Raffa S, Leone L, Bei R, Modesti A, Frati L, Torrisi MR, et al. 2008. Identification and characterization of the product encoded by ORF69 of Kaposi's sarcoma-associated herpesvirus. J Virol 82: 4562-4572. (Pubitemid 351563693)
31. Speel EJ, Hopman AH, Komminoth P. 2006. Tyramide signal amplification for DNA and mRNA in situ hybridization. Methods Mol Biol 326: 33-60.
32. Sun R, Lin SF, Gradoville L, Miller G. 1996. Polyadenylylated nuclear RNA encoded by Kaposi sarcoma-associated herpesvirus. Proc Natl Acad Sci 93: 11883-11888. (Pubitemid 26347218)
33. Zhong W, Ganem D. 1997. Characterization of ribonucleoprotein complexes containing an abundant polyadenylated nuclear RNA encoded by Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8). J Virol 71: 1207-1212. (Pubitemid 27030293)
34. Zhu FX, Chong JM, Wu L, Yuan Y. 2005. Virion proteins of Kaposi's sarcoma-associated herpesvirus. J Virol 79: 800-811. (Pubitemid 40053863)