Detection of two mRNA species at single-cell resolution by double-fluorescence in situ hybridization

Nature Protocols

Volumn 3, Issue 8, 2008, Pages 1370-1379

  Pinaud, Raphael ^a   Mello, Claudio V ^b   Velho, Tarciso A ^b   Wynne, Ryan D ^a   Tremere, Liisa A ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

^b OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTIN; DIGOXIGENIN; HAPTEN; ISOPROPAMIDE IODIDE; MESSENGER RNA; PEROXIDASE;

ANIMAL TISSUE; ARTICLE; BRAIN TISSUE; CHEMICAL LABELING; CONTROLLED STUDY; FINCH; FLUORESCENCE IN SITU HYBRIDIZATION; FROZEN SECTION; GENE CONTROL; IMMUNOHISTOCHEMISTRY; MOUSE; NEUROCHEMISTRY; NONHUMAN; PRECIPITATION; PRIORITY JOURNAL; RNA ANALYSIS; RNA PROBE; SENSORY NERVE CELL;

ACETYLATION; ANIMALS; BRAIN; FINCHES; GENE EXPRESSION REGULATION; GENOMICS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICROTOMY; NEURONS, AFFERENT; RNA PROBES; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA;

PASSERI;

EID: 50349095769     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2008.115     Document Type: Article

References (37)

1. Pinaud, R. Critical calcium-regulated biochemical and gene expression programs involved in experience-dependent plasticity. in Plasticity in the Visual System: From Genes to Circuits (eds. Pinaud, R., Tremere, L.A. & De Weerd, P.) 153-180 (Springer-Verlag, New York, 2005).
2. Pinaud, R. & Tremere, L.A. Immediate Early Genes in Sensory Processing, Cognitive Performance and Neurological Disorders (Springer-Verlag, New York, 2006).
3. Pinaud, R., Tremere, L.A. & De Weerd, P. Plasticity in the Visual System: From Genes to Circuits (Springer-Verlag, New York, 2005).
4. Hatten, M.E. & Heintz, N. Large-scale genomic approaches to brain development and circuitry. Annu. Rev. Neurosci. 28, 89-108 (2005).
5. Gustincich, S. et al. The complexity of the mammalian transcriptome. J. Physiol. 575, 321-332 (2006).
6. Hofmann, H.A. Functional genomics of neural and behavioral plasticity. J. Neurobiol. 54, 272-282 (2003).
7. Pascual-Leone, A., Amedi, A., Fregni, F. & Merabet, L.B. The plastic human brain cortex. Annu. Rev. Neurosci. 28, 377-401 (2005).
8. Hensch, T.K. Critical period regulation. Annu. Rev. Neurosci. 27, 549-579 (2004).
9. Buonomano, D.V. & Merzenich, M.M. Cortical plasticity: From synapses to maps. Annu. Rev. Neurosci. 21, 149-186 (1998).
10. Yao, H. & Dan, Y. Synaptic learning rules, cortical circuits, and visual function. Neuroscientist 11, 206-216 (2005).
11. Chklovskii, D.B., Mel, B.W. & Svoboda, K. Cortical rewiring and information storage. Nature 431, 782-788 (2004).
12. Sanes, J.N. & Donoghue, J.P. Plasticity and primary motor cortex. Annu. Rev. Neurosci. 23, 393-415 (2000).
13. Weinberger, N.M. Dynamic regulation of receptive fields and maps in the adult sensory cortex. Annu. Rev. Neurosci. 18, 129-158 (1995).
14. Singh, S.M., Treadwell, J., Kleiber, M.L., Harrison, M. & Uddin, R.K. Analysis of behavior using genetical genomics in mice as a model: From alcohol preferences to gene expression differences. Genome 50 877-897 (2007).
15. Chambers, D. & Fishell, G. Functional genomics of early cortex patterning. Genome Biol. 7, 202 (2006).
16. Clayton, D.F. Songbird genomics: Methods, mechanisms, opportunities, and pitfalls. Ann. NY Acad. Sci. 1016, 45-60 (2004).
17. Tribl, F. et al. Proteomics of the human brain: Sub-proteomes might hold the key to handle brain complexity. J. Neural. Transm. 113, 1041-1054 (2006).
18. Pinaud, R., Osorio, C. Alzate, O. & Jarvis, E.D. Profiling of experience-regulated proteins in the songbird auditory forebrain using quantitative proteomics. Eur. J. Neurosci. 27, 1409-1422 (2008).
19. Kee, N., Teixeira, C.M., Wang, A.H. & Frankland, P.W. Imaging activation of adult-generated granule cells in spatial memory. Nat. Protoc. 2, 3033-3044 (2007).
20. Guzowski, J.F. et al. Mapping behaviorally relevant neural circuits with immediate-early gene expression. Curr. Opin. Neurobiol. 15, 599-606 (2005).
21. Terleph, T.A. & Tremere, L.A. The use of immediate early genes as mapping tools for neuronal activation: Concepts and methods. in Immediate Early Genes in Sensory Processing, Cognitive Performance and Neurological Disorders (eds. Pinaud, R. & Tremere, L.A.) 1-10 (Springer-Verlag, New York, 2006).
22. Guzowski, J.F. Immediate early genes and the mapping of environmental representations in hippocampal networks. in Immediate Early Genes in Sensory Processing, Cognitive Performance and Neurological Disorders (eds. Pinaud, R. & Tremere, L.A.) 159-176 (Springer-Verlag, New York, 2006).
23. Owens, N.C., Hess, F.M. & Badoer, E. In situ hybridization using riboprobes on free-floating brain sections. Methods Mol. Biol. 326, 163-171 (2006).
24. Henderson, Z. In Situ Hybridization Techniques for the Brain (John Wiley & Sons, New York, 1996).
25. Schneider Gasser, E.M. et al. Immunofluorescence in brain sections: Simultaneous detection of presynaptic and postsynaptic proteins in identified neurons. Nat. Protoc. 1, 1887-1897 (2006).
26. Glynn, M.W. & McAllister, A.K. Immunocytochemistry and quantification of protein colocalization in cultured neurons. Nat. Protoc. 1, 1287-1296 (2006).
27. Wisden, W. & Morris, B.J. In Situ Hybridization Protocols for the Brain (Academic Press Inc., San Diego, 1994).
28. Zaidi, A.U., Enomoto, H., Milbrandt, J. & Roth, K.A. Dual fluorescent in situ hybridization and immunohistochemical detection with tyramide signal amplification. J. Histochem. Cytochem. 48, 1369-1375 (2000).
29. Guzowski, J.F., McNaughton, B.L., Barnes, C.A. & Worley, P.F. Environment-specific expression of the immediate-earLy gene Arc in hippocampal neuronal ensembles. Nat. Neurosci. 2, 1120-1124 (1999).
30. Breininger, J. F. & Baskin, D.G. Fluorescence in situ hybridization of scarce leptin receptor mRNA using the enzyme-labeled fluorescent substrate method and tyramide signal amplification. J. Histochem. Cytochem. 48, 1593-1599 (2000).
31. Velho, T.A., Pinaud, R., Rodrigues, P.V. & Mello, C.V. Co-induction of activity-dependent genes in songbirds. Eur J. Neurosci. 22, 1667-1678 (2005).
32. Pinaud, R. et al. GABAergic neurons participate in the brain's response to birdsong auditory stimulation. Eur. J. Neurasci. 20 1318-1330 (2004).
33. Pinaud, R., Penner, M.R., Robertson, H.A. & Currie, R.W. Upregulation of the immediate early gene arc in the brains of rats exposed to environmental enrichment: Implications for molecular plasticity. Brain Res. Mol. Brain Res. 91, 50-56 (2001).
34. Pinaud, R. et al. Complexity of sensory environment drives the expression of candidate-plasticity gene, nerve growth factor induced-A. Neuroscience 112, 573-582 (2002).
35. Pinaud, R., Saldanha, C.J., Wynne, R.D., Lovell, P.V. & Mello, C.V. The excitatory thalamo-'cortical' projection within the song control system of zebra finches is formed by calbindin-expressing neurons. J. Comp. Neurol. 504, 601-618 (2007).
36. Mello, C.V., Jarvis, E.D., Denisenko, N. & Rivas, M. Isolation of song-regulated genes in the brain of songbirds. Methods Mol. Biol. 85, 205-217 (1997).
37. Mello, C.V. & Clayton, D.F. Differential induction of the ZENK gene in the avian forebrain and song control circuit after metrazole-induced depolarization. J. Neurobiol. 26, 145-161 (1995).