Probes for intracellular RNA imaging in live cells

Methods in Enzymology

Volumn 505, Issue , 2012, Pages 383-399

  Santangelo, Philip J ^a   Alonas, Eric ^a   Jung, Jeenah ^a   Lifland, Aaron W ^a   Zurla, Chiara ^a  

^a Emory University   (United States)

Author keywords

fluorescence; gene expression; live cell imaging; localization; microscopy; nanotechnology; RNA; single molecule imaging

Indexed keywords

BETA ACTIN; MESSENGER RNA; RNA; RNA BINDING PROTEIN;

ARTICLE; CELL CYCLE; DRUG TARGETING; GENE EXPRESSION; HUMAN; IMAGING SYSTEM; INTRACELLULAR SIGNALING; MOLECULAR BEACON; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; PROTEIN LOCALIZATION; RNA VIRUS; SINGLE CELL ANALYSIS;

RNA VIRUSES;

EID: 84856466028     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-388448-0.00028-0     Document Type: Chapter

References (62)

1. A. Agrawal, and R. Deo Nanometer-scale mapping and single-molecule detection with color-coded nanoparticle probes Proc. Natl. Acad. Sci. USA 105 9 2008 3298 3303 (Pubitemid 351723547)
2. P. Anderson, and N. Kedersha RNA granules J. Cell Biol. 172 6 2006 803 808
3. P. Anderson, and N. Kedersha Stress granules: The Tao of RNA triage Trends Biochem. Sci. 33 3 2008 141 150
4. P. Anderson, and N. Kedersha RNA granules: Post-transcriptional and epigenetic modulators of gene expression Nat. Rev. Mol. Cell Biol. 10 6 2009 430 436
5. P. Anderson, and N. Kedersha Stress granules Curr. Biol. 19 10 2009 R397 R398
6. G. Bao, and A. Tsourkas Engineering nanostructured probes for sensitive intracellular gene detection Mech. Chem. Biosyst. 1 1 2004 23 36
7. E.L. Barry, and F.A. Gesek Introduction of antisense oligonucleotides into cells by permeabilization with streptolysin O Biotechniques 15 6 1993 1016 1018 1020
8. M. Bengtsson, and M. Hemberg Quantification of mRNA in single cells and modelling of RT-qPCR induced noise BMC Mol. Biol. 9 2008 63
9. D.P. Bratu, and B.J. Cha Visualizing the distribution and transport of mRNAs in living cells Proc. Natl. Acad. Sci. USA 100 23 2003 13308 13313 (Pubitemid 37444738)
10. A.S. Brodsky, and P.A. Silver Identifying proteins that affect mRNA localization in living cells Methods 26 2 2002 151 155 (Pubitemid 34969576)
11. J.R. Buchan, and R. Parker Eukaryotic stress granules: The ins and outs of translation Mol. Cell 36 6 2009 932 941
12. A.K. Chen, and M.A. Behlke Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells Nucleic Acids Res. 35 16 2007 e105
13. A.K. Chen, and M.A. Behlke Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA Nucleic Acids Res. 36 12 2008 e69
14. R.E. Clark, and J. Grzybowski Clinical use of streptolysin-O to facilitate antisense oligodeoxyribonucleotide delivery for purging autografts in chronic myeloid leukaemia Bone Marrow Transplant. 23 12 1999 1303 1308 (Pubitemid 29312940)
15. N. Daigle, and J. Ellenberg LambdaN-GFP: An RNA reporter system for live-cell imaging Nat. Methods 4 8 2007 633 636 (Pubitemid 47202473)
16. I.L. de Silanes, and M.P. Quesada Aberrant regulation of messenger RNA 3′-untranslated region in human cancer Cell. Oncol. 29 2007 1 17
17. A. Diercks, and H. Kostner Resolving cell population heterogeneity: Real-time PCR for simultaneous multiplexed gene detection in multiple single-cell samples PLoS One 4 7 2009 e6326
18. A.M. Femino, and F.S. Fay Visualization of single RNA transcripts in situ Science 280 5363 1998 585 590 (Pubitemid 28227761)
19. D. Fusco, and N. Accornero Single mRNA molecules demonstrate probabilistic movement in living mammalian cells Curr. Biol. 13 2 2003 161 167 (Pubitemid 36154346)
20. R.V. Giles, and D.G. Spiller Selecting optimal oligonucleotide composition for maximal antisense effect following streptolysin O-mediated delivery into human leukaemia cells Nucleic Acids Res. 26 7 1998 1567 1575 (Pubitemid 28291789)
21. C. Giorgi, and M. Moore The nuclear nurture and cytoplasmic nature of localized mRNPs Semin. Cell Dev. Biol. 18 2007 186 193 (Pubitemid 46756360)
22. D. Grunwald, and R.H. Singer In vivo imaging of labelled endogenous beta-actin mRNA during nucleocytoplasmic transport Nature 467 7315 2010 604 607
23. D. Grunwald, and R.H. Singer Cell biology of mRNA decay Methods Enzymol. 448 2008 553 577
24. S. Itzkovitz, and A. van Oudenaarden Validating transcripts with probes and imaging technology Nat. Methods 8 4 Suppl. 2011 S12 S19
25. A. Jambhekar, and J.L. Derisi Cis-acting determinants of asymmetric, cytoplasmic RNA transport RNA 13 5 2007 625 642 (Pubitemid 46641521)
26. J. Kanno, and K. Aisaki "Per cell" normalization method for mRNA measurement by quantitative PCR and microarrays BMC Genomics 7 2006 64
27. N. Kedersha, and P. Anderson Mammalian stress granules and processing bodies Methods Enzymol. 431 2007 61 81
28. N. Kedersha, and G. Stoecklin Stress granules and processing bodies are dynamically linked sites of mRNP remodeling J. Cell Biol. 169 6 2005 871 884 (Pubitemid 41002864)
29. N. Kedersha, and S. Tisdale Real-time and quantitative imaging of mammalian stress granules and processing bodies Methods Enzymol. 448 2008 521 552
30. A.W. Lifland, and C. Zurla Single molecule sensitive multivalent polyethylene glycol probes for RNA imaging Bioconjug. Chem. 21 3 2010 483 488
31. A.W. Lifland, and C. Zurla Dynamics of native β-actin mRNA transport in the cytoplasm Traffic 12 8 2011 1000 1011 10.1111/j.1600-0854.2011.01209.x
32. W.J. Lin, and A. Duffy Localization of AU-rich element-containing mRNA in cytoplasmic granules containing exosome subunits J. Biol. Chem. 282 27 2007 19958 19968 (Pubitemid 47100060)
33. M.E. Lindquist, and A.W. Lifland Respiratory syncytial virus induces host RNA stress granules to facilitate viral replication J. Virol. 84 23 2010 12274 12284
34. T. Lionnet, and K. Czaplinski A transgenic mouse for in vivo detection of endogenous labeled mRNA Nat. Methods 8 2 2011 165 170
35. M.M. Mhlanga, and D.Y. Vargas tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells Nucleic Acids Res. 33 6 2005 1902 1912 (Pubitemid 41748335)
36. C. Molenaar, and S.A. Marras Linear 2′ O-methyl RNA probes for the visualization of RNA in living cells Nucleic Acids Res. 29 17 2001 E89
37. C. Molenaar, and A. Abdulle Poly(A)+ RNAs roam the cell nucleus and pass through speckle domains in transcriptionally active and inactive cells J. Cell Biol. 165 2 2004 191 202 (Pubitemid 38544522)
38. N. Nitin, and P.J. Santangelo Peptide-linked molecular beacons for efficient delivery and rapid mRNA detection in living cells Nucleic Acids Res. 32 6 2004 e58
39. T. Ozawa, and Y. Natori Imaging dynamics of endogenous mitochondrial RNA in single living cells Nat. Methods 4 5 2007 413 419 (Pubitemid 46901275)
40. S. Paillasson, and M. Van De Corput In situ hybridization in living cells: Detection of RNA molecules Exp. Cell Res. 231 1 1997 226 233 (Pubitemid 27187532)
41. A. Raj, and C.S. Peskin Stochastic mRNA synthesis in mammalian cells PLoS Biol. 4 10 2006 e309
42. A. Raj, and P. van den Bogaard Imaging individual mRNA molecules using multiple singly labeled probes Nat. Methods 5 10 2008 877 879
43. J.B. Randolph, and A.S. Waggoner Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes Nucleic Acids Res. 25 14 1997 2923 2929 (Pubitemid 27299812)
44. W.J. Rhee, and P.J. Santangelo Target accessibility and signal specificity in live-cell detection of BMP-4 mRNA using molecular beacons Nucleic Acids Res. 36 5 2008 e30
45. P.J. Santangelo Molecular beacons and related probes for intracellular RNA imaging Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 2 1 2010 11 19
46. P.J. Santangelo, and G. Bao Dynamics of filamentous viral RNPs prior to egress Nucleic Acids Res. 35 11 2007 3602 3611 (Pubitemid 47244655)
47. P.J. Santangelo, and N. Nitin Direct visualization of mRNA colocalization with mitochondria in living cells using molecular beacons J. Biomed. Opt. 10 4 2005 44025
48. P. Santangelo, and N. Nitin Live-cell characterization and analysis of a clinical isolate of bovine respiratory syncytial virus, using molecular beacons J. Virol. 80 2 2006 682 688 (Pubitemid 43062881)
49. P.J. Santangelo, and A.W. Lifland Single molecule-sensitive probes for imaging RNA in live cells Nat. Methods 6 5 2009 347 349
50. B. Schwanhausser, and D. Busse Global quantification of mammalian gene expression control Nature 473 7347 2011 337 342
51. Y. Shav-Tal, and X. Darzacq Dynamics of single mRNPs in nuclei of living cells Science 304 5678 2004 1797 1800 (Pubitemid 38787895)
52. D.G. Spiller, and R.V. Giles Improving the intracellular delivery and molecular efficacy of antisense oligonucleotides in chronic myeloid leukemia cells: A comparison of streptolysin-O permeabilization, electroporation, and lipophilic conjugation Blood 91 12 1998 4738 4746 (Pubitemid 28270324)
53. K. Taniguchi, and T. Kajiyama Quantitative analysis of gene expression in a single cell by qPCR Nat. Methods 6 7 2009 503 506
54. R. Tomecki, and A. Dziembowski Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism RNA 16 9 2010 1692 1724
55. R. Tomecki, and K. Drazkowska Mechanisms of RNA degradation by the eukaryotic exosome Chembiochem 11 7 2010 938 945
56. S. Tyagi, and O. Alsmadi Imaging native beta-actin mRNA in motile fibroblasts Biophys. J. 87 6 2004 4153 4162 (Pubitemid 39602919)
57. T.J. Utley, and N.A. Ducharme Respiratory syncytial virus uses a Vps4-independent budding mechanism controlled by Rab11-FIP2 Proc. Natl. Acad. Sci. USA 105 29 2008 10209 10214
58. D.Y. Vargas, and A. Raj Mechanism of mRNA transport in the nucleus Proc. Natl. Acad. Sci. USA 102 47 2005 17008 17013 (Pubitemid 41692674)
59. V.E. Velculescu, and S.L. Madden Analysis of human transcriptomes Nat. Genet. 23 4 1999 387 388
60. I. Walev, and S.C. Bhakdi Delivery of proteins into living cells by reversible membrane permeabilization with streptolysin-O Proc. Natl. Acad. Sci. USA 98 6 2001 3185 3190 (Pubitemid 32220820)
61. T. Yamada, and H. Yoshimura Visualization of non-engineered single mRNAs in living cells using genetically encoded fluorescent probes Anal. Chem. 83 14 2011 5708 5714
62. C. Zurla, and A.W. Lifland Characterizing mRNA interactions with RNA granules during translation initiation inhibition PLoS One 6 5 2011 e19727