RNA molecules lighting up under the microscope

Histochemistry and Cell Biology

Volumn 106, Issue 2, 1996, Pages 151-166

  Dirks, Roeland W ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

CONFERENCE PAPER; FLUORESCENCE MICROSCOPY; HUMAN; IN SITU HYBRIDIZATION; METHODOLOGY; NONHUMAN; PRIORITY JOURNAL; RNA TRANSCRIPTION;

EID: 0029785989     PISSN: 09486143     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02484398     Document Type: Conference Paper

References (105)

1. Adams JC (1992) Biotin amplification of biotin and horseradish peroxidase signals in histochemical stains. J Histochem Cytochem 40:1457-1463
2. Aitchison JD, Blobel G, Rout MP (1995) Nup 120p: a yeast nucleoporin required for NPC distribution and mRNA transport. J Cell Biol 131:1659-1675
3. + RNA in sea urchin eggs and embryos by quantitative in situ hybridization. Nucleic Acids Res 9:2819-2840
4. Angerer LM, Angerer RC (1991) Localization of mRNAs by in situ hybridization. Methods Cell Biol 35:37-71
5. Artero RD, Akam M, Pérez-Alonso M (1992) Oligonucleotide probes detect splicing variants in situ in Drosophila embryos. Nucleic Acids Res 20:5687-5690
6. Asan E, Kugler P (1995) Qualitative and quantitative detection of alkaline phosphatase coupled to an oligonucleotide probe for somatostatin mRNA after in situ hybridization using unfixed rat brain tissue. Histochemistry 103:463-471
7. Baldino F, Ruth JL, Davis LG (1989) Nonradioactive detection of vasopressin mRNA with in situ hybridization histochemistry. Exp Neurol 104:200-207
8. Burns J, Graham AK, Frank C, Fleming KA, Evans MF, McGee JOD (1987) Detection of low copy human papilloma virus DNA and mRNA in routine paraffin sections of cervix by non-isotopic in situ hybridization. J Clin Pathol 40:858-864
9. Carmo-Fonseca M, Pepperkok R, Sproat BS, Ansorge W, Swanson MS, Lamond AI (1991) In vivo detection of snRNP-rich organelles in the nuclei of mammalian cells. EMBO J 10:1863-1873
10. 35S-labeled riboprobes. In: Celis JE (ed) Cell biology; a laboratory handbook. Academic Press, San Diego, pp 466-476
11. Carter KC, Taneja KL, Lawrence JB (1991) Discrete nuclear domains of poly (A) RNA and their relationship to the functional organization of the nucleus. J Cell Biol 115:1191-1202
12. Cox KH, DeLeon DV, Angerer LM, Angerer RC (1984) Detection of mRNAs in sea urchin embryos by in situ hybridization using asymmetric RNA probes. Dev Biol 101:485-502
13. Cremer T, Kurz A, Zirbel R, Dietzel S, Rinke B, Schröck E, Speicher MR, Mathieu U, Jauch A, Emmerlich P, Scherthan H, Ried T, Cremer C, Lichter P (1993) Role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harbor Symp Quant Biol 58:777-792
14. Cunningham DA, Pattison JR, Craig RK (1988) Detection of parvovirus DNA in human serum using biotinylated RNA hybridization probes. J Virol Methods 19:279-288
15. Danscher G (1981) Localization of gold in biological tissue. A photochemical method for light and electron microscopy. Histochemistry 71:81-88
16. Dårgerlind A, Friberg K, Bean AJ, Hökfelt (1992) Sensitive mRNA detection using unfixed tissue: combined radioactive and non-radioactive in situ hybridization histochemistry 98:39-49
17. DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1363
18. Dirks RW, Raap AK (1995) Cell-cycle-dependent gene expression studied by two-colour fluorescent detection of a mRNA and histone mRNA. Histochem Cell Biol 104:391-395
19. Dirks RW, Raap AK, Van Minnen J, Vreugdenhil E, Smit AB, Van der Ploeg (1989) Detection of mRNA molecules coding for neuropeptide hormones of the pond snail Lymnaea stagnalis by radioactive and non-radioactive in situ hybridization: a model system for mRNA detection. J Histochem Cytochem 37:7-14
20. Dirks RW, Van Gijlswijk RPM, Tullis RH, Smit AB, Van der Ploeg M, Raap AK (1990) Simultaneous detection of different mRNA sequences coding for neuropeptide hormones by double in situ hybridization using FITC- and biotin-labeled oligonucleotides. J Histochem Cytochem 38:467-473
21. Dirks RW, Van Gijlswijk RPM, Vooijs MA, Smit AB, Bogerg J, Van Minnen J, Raap AK, Van der Ploeg M (1991) 3′-End fluorochromized and haptenized oligonucleotides as in situ hybridization probes for multiple, simultaneous RNA detection. Exp Cell Res 194:310-315
22. Dirks RW, Raap AK, Van der Ploeg M (1992a) Principles and applications of nonradioactive labeling methods for in situ hybridization. In: Calas A, Bloch B, Fournier JG, Trembleau A (eds) Hybridation in situ: méthodes pratiques. SFME, Paris, pp 17-28
23. Dirks RW, Van Dorp AGM, Van Minnen J, Fransen JAM, Van der Ploeg M, Raap AK (1992b) Electron microscopic detection of RNA sequences by non-radioactive in situ hybridization in the mollusc Lymnaea stagnalis. J Histochem Cytochem 40:1647-1657
24. Dirks RW, Van Dorp AGM, Van Minnen J, Fransen JAM, Van der Ploeg M, Raap AK (1993a) Ultrastructural evidence for the axonal localization of caudodorsal cell hormone mRNA in the central nervous system of the mollusc Lymnaea stagnalis. Microsc Res Techn 25:12-18
25. Dirks RW, Van de Rijke FM, Fujishita S, Van der Ploeg M, Raap AK (1993b) Methodologies for specific intron and exon localization in cultured cells by haptenized and fluorochromized probes. J Cell Sci 104:1187-1197
26. Dirks RW, Van de Rijke FM, Raap AK (1994) In situ hybridization applicable to abundantly expressed mRNA species. In: Celis JE (ed) Cell biology: a laboratory handbook. Academic Press, San Diego, pp 459-465
27. Dirks RW, Daniël KC, Raap AK (1995) RNAs radiate from gene to cytoplasm as revealed by fluorescence in situ hybridization. J Cell Sci 108:2565-2572
28. Egger D, Troxler M, Bienz K (1994) Light and electron microscopic in situ hybridization: non-radioactive labelling and detection, double hybridization, and combined hybridization-immunocytochemistry. J Histochem Cytochem 42:815-822
29. Egholm M, Buchardt O, Christensen L, Behrens C, Freier S, Driver DA, Berg RH, Kim SK, Norden D, Nielsen PE (1993) PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen bonding rules. Nature 365:566-568
30. Fahre E, Boelens WC, Wimmer C, Mattaj IW, Hurt EC (1994) Nup 145p is required for nuclear export of mRNA and binds homopolymeric RNA in vitro via a novel conserved motif. Cell 78:275-289
31. Florijn RJ, Slats J, Tanke HJ, Raap AK (1995) Analysis of antifading reagents for fluorescence microscopy. Cytometry 19:177-182
32. Francis-Lang H, Davis I, Ish-Horowicz D (1996) Asymmetric localization of Drosophila pair-rule transcripts from displaced nuclei: evidence for directional nuclear export. EMBO J 15:640-649
33. Harrison PR, Conkie D, Paul J, Jones K (1973) Localization of cellular globin messenger RNA by in situ hybridization to complementary DNA. FEBS Lett 32:109-112
34. Harrison PR, Conkie D, Affara N, Paul J (1974) In situ localization of globin messenger RNA formation. I. During mouse fetal liver development. J Cell Biol 63:401-413
35. + RNA associated with mutation of the Saccharmoyces cerevisiae RAT2/NUP120 gene. J Cell Biol 131:1677-1697
36. Hölkte HJ, Kessler C (1990) Non-radioactive labeling of RNA transcripts in vitro with the hapten digoxigenin (DIG): hybridization and ELISA-based detection. Nuclei Acids Res 18:5843-5851
37. Jarmolowski A, Boelens WC, Izaurralde E, Mattaj IW (1994) Nuclear export of different classes of RNA is mediated by specific factors. J Cell Biol 124:627-635
38. Julbert AR, Burrel CJ, Growans EJ, Rowland R (1986) Histological aspects of in situ hybridization. Detection of poly(A) nucleotide sequences in mouse liver sections as a model system. Histochemistry 85:505-514
39. Jirikowski GF, Sanna PP, Bloom FE (1990) mRNA coding for oxytocin is present in axons of the hypothalamo-neurohypophysial tract. Proc Natl Acad Sci USA 87:7400-7404
40. Kalle WHJ, Macville MVF, Van de Corpot MPC, De Grooth BG, Tanke HJ, Raap AK (1996) Imaging of RNA in situ hybridization by atomic force microscopy. J Microsc 182:192-199
41. Kerstens HMJ, Poddighe PJ, Hanselaar AGJM (1995) A novel in situ hybridization signal amplification method, based on the deposition of biotinylated tyramine. J Histochem Cytochem 43:347-352
42. Kislauskis EH, Singer RH (1992) Determinants of RNA localization. Curr Opin Cell Biol 4:975-978
43. Kislauskis EH, Zhu X, Singer RH (1994) Sequences responsible for intracellular localizalion of β-acin messenger RNA also affect cell phenotype. J Cell Biol 127:441-451
44. Kiyama H, Emson PC, Ruth J, Morgan C (1990) Sensitive non-radioistopic in situ hybridization histochemistry: demonstration of tyrosine hydroxylase gene expression in rat brain and adrenal. Mol Brain Res 7:213-219
45. 35S- and digoxigenin-labeled RNA and oligonucleotide probes for in situ hybridization. Histochemistry 98:217-228
46. Lansdorp PM, Verwoerd NP, Van de Rijke FM, Dragowska V, Little M-T, Dirks RW, Raap AK, Tanke HJ (1996) Heterogeneity in telomere length of human chromosomes. Hum Mol Genet 5:685-691
47. Larsson L-I, Hougaard DM (1990) Optimization of non-radioactive in situ hybridization: image analysis of varying pretreatment, hybridization and probe labelling conditions. Histochemistry 93:347-354
48. Larsson L-I, Christensen T, Dalboge H (1988) Detection of proopiomelanocortin mRNA by in situ hybridization using a biotinylated oligonucleotide probe and avidin-alkaline phosphatase histochemistry. Histochemistry 89:109-116
49. Lawrence JB, Singer RH (1985) Quantitative analysis of in situ hybridization methods for the detection of actin gene expression. Nucleic Acids Res 13:1777-1799
50. Lawrence JB, Singer RH (1986) Intracellular localization of messenger RNAs for cytoskeletal proteins. Cell 45:407-415
51. Lawrence JB, Singer RH, Marselle LM (1989) Highly localized tracks of specific transcripts within interphase nuclei visualized by in situ hybridization. Cell 57:493-502
52. Le Beau MM (1996) One FISH, two FISH, red FISH, blue FISH. Nut Genet 12:341-344
53. Macville MVE, Van Dorp AGM, Wiesmeijer KC, Dirks RW, Fransen JAM, Raap AK (1995a) Monitoring morphology and signal during non-radioactive in situ hybridization procedures by reflection-contrast microscopy and transmission electron microscopy. J Histochem Cytochem 43:665-674
54. Macville MVE, Wiesmeijer KC, Dirks RW, Fransen JAM, Raap AK (1995b) Saponin pretreatment in pre-embedding electron microscopic in situ hybridization for detection of specific RNA sequences in cultured cells: a methodological study. J Histochem Cytochem 43:1005-1018
55. Macville MVE, Wiesmeijer KC, Fransen JAM, Dirks RW, Raap AK (1995c) Detection of specific messenger RNA by electron microscopic in situ hybridization: implications for nucleocytoplasmic transport. Eur J Cell Biol 68:470-474
56. Macville MVE, Van Dorp AGM, Dirks RW, Fransen JAM, Raap AK (1996) Evaluation of pepsin treatment for electron microscopic RNA in situ hybridization on ultra-thin cryosections of cultured cells. Histochem Cell Biol 105:139-145
57. Matera AG, Frey MR, Margelot K, Wolin SL (1995) A perinucleolar compartment contains several RNA polymerase III transcripts as well as the polypyrimidine tract-binding protein. hnRNPI. J Cell Biol 129:1181-1193
58. Mattaj IW (1994) Splicing in space. Nature 372:727-728
59. Meester I, Ramkema MD, Van Minnen J, Boer HH (1992) Differential expression of four genes encoding molluscan insulin-reluted peptides in the central nervous system of the pond snail Lymnaea stagnalis. Cell Tissue Res 269:183-188
60. Melton DA, Krieg PA, Rebagliati MR, Maniatis T, Zinn K, Green MR (1984) Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucl Acids Res 12:7035-7056
61. Mohr E, Fehr S, Richter D (1991) Axonal transport of neuropeptide encoding mRNAs within the hypothalamo-hypophyseal tract of rats. EMBO J 10:2419-2424
62. Mohr E, Morris JF, Richter D (1995) Differential subcellular mRNA targeting: deletion of a single nucleotide prevents the transport of axons but not to dendrites of rat hypothalamic magnocellular neurons. Proc Natl Acad Sci USA 92:4377-4381
63. Moorman AFM, De Boer PAJ, Vermeulen JLM, Lamers WH (1993) Practical aspects of radio-isotopic in situ hybridization on RNA. Histochem J 25:251-266
64. Nakane PK, Wilson B (1975) Cytochemical localization of polyadenylic acid (poly A). J Cell Biol 67:302
65. Nielsen PE, Egholm M, Berg RH, Buchardt O (1991) Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254:1497-1500
66. Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP, Landegren U (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265:2085-2088
67. Perrone Capano C, Guiditta A, Castigli E, Kaplan B (1987) Occurrence and sequence complexity of polyadenylated RNA in squid axoplasm. J Neurochem 49:698-704
68. Pinkel D, Straume T, Gray JW (1986) Cytogenetic analysis using quantitative, high sensitivity, fluorescence hybridization. Proc Natl Acad Sci 83:2934-2938
69. Pringle HJ, Primrose L, Kind CN, Talbot IC, Lauder I (1989) In situ hybridization demonstration of polyadenylated RNA sequences in formalin-fixed paraffin sections using a biotinylated oligonucleotide poly d(T) probe. J Pathol 158:279-286
70. Raap AK, Dirks RW, Jiwa NM, Nederlof PM, Van der Ploeg M (1990) In situ hybridization with hapten-modified probes. In: Racz P, Haase AT, Gluckman JC (eds) Modern pathology of AIDS and other retroviral infections. Karger, Basel, pp 17-28
71. Raap AK, Van de Rijke FM, Dirks RW, Sol CJ, Boom R, Van der Ploeg M (1991) Bicolar fluorescence in situ hybridization to intron and exon mRNA sequences. Exp Cell Res 197:319-322
72. Raap AK, Van der Corput MPC, Vervenne RAW, Van Gijlswijk RPM, Tanke HJ, Raap AK (1995) Ultra-sensitive FISH using peroxidase-mediated deposition of biotin or fluorochrome tyramides. Hum Mol Genet 4:529-534
73. Shotton DM (1995) Electronic light microscopy: present capabilities and future prospects. Histochem Cell Biol 104:97-138
74. Sibon OCM, Humbel BM, De Graaf A, Verkleij AJ, Cremers FFM (1994) Ultrastructural localization of epidermal growth factor (EGF)-receptor in the cell nucleus using pre-embedding in situ hybridization in combination with ultra-small gold probes and silver-enhancement. Histochemistry 101:223-232
75. Sibon OCM, Cremers FFM, Humbel BM, Boonstra J, Verkleij AJ (1995) Localization of nuclear RNA by pre- and post-embedding in situ hybridization using different gold probes. Histochem J 27:35-45
76. Singer RH, Lawrence JB, Villnave CA (1986) Optimization of in situ hybridization using isotopic and non-isotopic detection methods. Biotechniques 4:230-250
77. Singer RH, Lawrence JB, Langevin GL, Rashtchian RN, Villnave CA, Cremer T, Tesin D, Manuelidis L, Ward DC (1987) Double labeling in situ hybridization using non-isotopic and isotopic detection. Acta Histochem Cytochem 20:589-599
78. Skutella T, Probst JC, Blanco E, Jirikowski GF (1994) Localization of tyrosine hydroxylase mRNA in the axons of the hypothalamo-neurohypophysial system. Mol Brain Res 23:179-184
79. Smit AB, Vreugdenhil E, Ebberink RHM, Graerts WPM, Klootwijk J, Joosse J (1988) Growth-controlling molluscan neurons produce the precursor of an insulin-related peptide. Nature 331:535-538
80. Smit AB, Jimenez CR, Dirks RW, Croll RP, Geraerts WPM (1992) Characterization of a cDNA clone encoding multiple copies of the neuropeptide APGWamide in the mollusc Lymnaea stagnalis. J Neurosci 12:1709-1715
81. Steward O, Banker GA (1992) Getting the message from the gene to the synapse: sorting and intracellular transport of RNA in neurons. TINS 15:180-186
82. St Johnston D (1995) The intracellular localization of messenger RNAs. Cell 81:161-170
83. Taneja K, Singer R (1987) Use of oligodeoxynucleotide probes for quantitative in situ hybridization to actin mRNA. Anal Biochem 166:389-398
84. + RNA in heat-shocked yeast cells: implication of nucleolar involvement in mRNA transport. Mol Biol Cell 7:173-192
85. Tanke HJ, Florijn RJ, Wiegant J, Raap AK, Vrolijk J (1995) CCD microscopy and image analysis of cells and chromosomes stained by fluorescence in situ hybridization. Histochem J 27:4-14
86. Torre ER, Steward O (1992) Demonstration of local protein synthesis within dendrites using a new cell culture system that permits the isolation of living axons and dendrites from their cell bodies. J Neurosci 12:762-772
87. Trembleau A, Bloom FE (1995) Enhanced sensitivity for light and electron microscopic in situ hybridization with multiple simultaneous non-radioactive oligodeoxynucleotide probes. J Histochem Cytochem 43:829-841
88. Van Gijlswijk RPM, Wiegant J, Raap AK, Tanke HJ (1996) Improved localization of fluroescent tyramides for fluorescence in situ hybridization using dextran sulfate and polyvinyl alcohol. J Histochem Cytochem 44:389-392
89. Van Kesteren RE, Smit AB, Dirks RW, De With ND, Geraerts WPM, Joosse J (1992) Evolution of the vasopressin/oxytocin superfamily: characterization of a cDNA encoding a vasopressin-related precursor, preproconopressin, from the mollusc Lymnaea stagnalis. Proc Natl Acad Sci 89:4593-4597
90. Van Minnen J (1994a) RNA in the axonal domain: a new dimension in neuronal functioning? Histochem J 26:377-391
91. Van Minnen J (1994b) Axonal localization of neuropeptide-encoding mRNA in identified neurons of the snail Lymnaea stagnalis. Cell Tissue Res 276:155-161
92. Van Minnen J, Van der Haar C, Raap AK, Vreugdenhil E (1988) Localization of ovulation hormone-like neuropeptide in the central nervous system of the snail Lymnaea stagnalis by means of immunocytochemistry and in situ hybridization. Cell Tissue Res 251:477-484
93. Van Minnen J, Dirks RW, Vreugdenhil E, Van Diepen J (1989) Expression of the egg-laying hormone genes in peripheral neurons of exocrine cells in the reproductive tract of the mollusc Lymnaea stagnalis. Neuroscience 33:35-46
94. Vervenne RAW, Dirks RW, Ramesar J, Waters AP, Janse CJ (1994) Differential expression in blood stages of the gene coding for the 21-kilodalton surface protein of ookinetes of Plamsodium berghei as detected by RNA in situ hybridization. Mol Biochem Parasitol 68:259-266
95. Visa N, Izaurralde E, Ferreira J, Daneholt B, Mattaj IW (1996a) A nuclear cap-binding complex binds Balbiani ring pre-mRNA cotranscriptionally and accompanies the ribonucleoprotein particle during nuclear export. J Cell Biol 133:5-14
96. Visa N, Alzhanova-Ericsson AT, Sun X, Kiseleva E, Björkroth B, Wurtz T, Daneholt B (1996b) A pre-mRNA-binding protein accompanies the RNA from the gene through the nuclear pores into polysomes. Cell 84:253-264
97. Wiegant J, Ried T, Nederlof PM, Van der Ploeg M, Tanke HJ, Raap AK (1991) In situ hybridization with fluoresceinated DNA. Nucleic Acids Res 19:3237-3241
98. Wiegant J, Verwoerd N, Mascheretti S, Bolk M, Tanke HJ, Raap AK (1996) An evaluation of a new series of fluorescent dUTPs for fluorescence in situ hybridization. J Histochem Cytochem 44:525-529
99. Xing Y, Lawrence JB (1993) Nuclear RNA tracks: structural basis for transcription and splicing? Trends Cell Biol 3:346-353
100. Xing Y, Johnson CV, Dobner PR, Lawrence JB (1993) Higher level organization of individual gene transcription and RNA splicing. Science 259:1326-1330
101. Xing Y, Johnson CV, Moen PT, McNeil JA, Lawrence JB (1995) Nonrandom gene organization: structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains. J Cell Biol 131:1635-1647
102. Young WS (1989) Simultaneous use of digoxigenin- and radiolabeled oligodeoxyribonucleotide probes for hybridization histochemistry. Neuropeptides 13:271-275
103. Yu H, Ernst L, Wagner M, Waggoner A (1992) Sensitive detection of RNAs in single cells by flow cytometry. Nucleic Acids Res 20:83-88
104. Zachar Z, Kramer J, Mims IP, Bingham PM (1993) Evidence for channeled diffusion of pre-mRNAs during nuclear RNA transport in metazoans. J Cell Biol 121:729-742
105. Zirbel RM, Mathieu UR, Kurz A, Cremer T, Lichter P (1993) Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries. Chromosome Res 1:93-106