Potato virus X (PVX) ................................. 158, 159, 163,
167, 168, 170, 171, 176, 182–188, 191
PP7...............................93, 123, 270, 374–376, 379, 382
Protein-RNA crosslinking ................................... 245, 284
Protoplast transfection.................................................. 423
Proximity biotinylation ....................................... 288, 290,
292, 300, 304
Proximity-CLIP .................................................... 283–305
Pseudomonas aeruginosa ............................................... 158
Q
Quantitative RT-PCR ................................................... 185
R
Radioactive labeling of RNA ............................... 259, 263
Recombination-mediated cassette exchange
(RMCE) .................................................... 374–376
Renilla luciferase......................................... 271, 440–442,
448, 449
Ribosomes .................................................. 35, 36, 38, 46,
47, 454, 455, 457, 461, 467
RNA affinity purifications .................................... 241–252
RNA-binding proteins (RBPs) ........................... 103, 104,
106, 241–252, 255, 269, 278, 284, 285
RNA extractions......................................... 185, 190, 191,
199, 203, 229, 231, 293, 391–395, 397, 406,
455, 461, 462
RNA fractionation by polyacrylamide gel
electrophoresis ................................................... 424
RNA immunoprecipitation.................................. 255–266
RNA interference ........................................ 216, 227, 387
RNA isolation...................................................... 190, 256,
260, 264, 309, 314
RNA labeling.............................................. 7, 9, 117, 150,
216, 220, 233
RNA mobility .............................182, 183, 187, 270, 271
RNA particles ....................................................... 274–277
RNase decontamination ................................................... 9
RNAseq................................................285, 457, 462, 463
RNA silencing .....................................182, 390, 431–449
RNA uptake.......................................................... 215–224
RNA virus ............................................................. 105, 309
RNP footprints..................................................... 294–299
S
Saccharomyces cerevisiae................................................. 107
SDS PAGE.................................................. 264, 266, 311,
312, 321, 436, 444, 445
Seeding cells .................................................................. 273
Seed sterilization .................................................. 415, 420
Short oligonucleotide probes ......................................... 24
Signal recognition particle (SRP).............................35, 36
Single-molecule FISH (smFISH)..................... 24, 29–32,
36–43, 45–48, 51–67, 122, 124, 125, 127, 128,
132, 133, 135, 138, 196, 197, 207, 208, 211
Single-molecule RNA mobility assay .................. 269–281
Site directed mutagenesis .................................... 434, 437
Size fractionation of total RNA........................... 398–399
Small RNA cDNA libraries.................................. 293–299
Small RNA data analysis ...................................... 396–397
Small RNA extraction ................................................... 424
Spectral unmixing .....................................................24, 26
Spinach (aptamer) .................................82, 84, 86, 89, 92
Split aptamers .................................................................. 91
Spray-induced gene silencing (SIGS) ................. 216, 228
SP6 RNA polymerase..................................................7, 18
Stellaris mRNA probes..............................................41, 47
Streptavidin affinity purification .......................... 286, 295
Suzuki-Miyaura cross-coupling ........................... 473–485
Systematic Evolution of Ligands by EXponential
enrichment (SELEX ) ..................... 76, 80, 81, 83
T
Tagging RNA with agarose beads....................... 246, 248
Tethering assays.................................................... 270, 271
4-Thiouridine (4SU)-labeled RNA.............................. 285
Tissue fixation ................................................................. 11
Tissue permeabilization .................................................. 12
Tobacco mosaic virus (TMV)............................. 105–107,
111, 115, 117
Tobacco rattle virus (TRV)......................... 308, 318, 323
Transcription activator-like effector nucleases
(TALENs) .......................................................... 335
Translating ribosome affinity purification
(TRAP) ........................................... 257, 454–458,
461, 468, 469
Translatomes ........................................................ 451–470
Transport granule ......................................................... 269
TRAP RNA is achieved by direct sequencing
(TRAP-SEQ) ............................................ 451–470
T7 RNA polymerase ..................... 7, 9, 89, 92, 186, 187,
216, 220, 234, 474–476, 479, 480, 482
Tyramide signal amplification (TSA) system ................... 5
U
Urea-PAGE ....................... 288, 294, 296, 298, 302, 304
UV cross-linker ................. 257, 260, 286, 310, 394, 401
V
Verticillium longisporum............................. 228, 230, 236
Virus replication complexes................................. 307, 320
Volocity ............................................................... 26, 30, 31
RNA TAGGING: METHODS AND PROTOCOLS
Index 489
167, 168, 170, 171, 176, 182–188, 191
PP7...............................93, 123, 270, 374–376, 379, 382
Protein-RNA crosslinking ................................... 245, 284
Protoplast transfection.................................................. 423
Proximity biotinylation ....................................... 288, 290,
292, 300, 304
Proximity-CLIP .................................................... 283–305
Pseudomonas aeruginosa ............................................... 158
Q
Quantitative RT-PCR ................................................... 185
R
Radioactive labeling of RNA ............................... 259, 263
Recombination-mediated cassette exchange
(RMCE) .................................................... 374–376
Renilla luciferase......................................... 271, 440–442,
448, 449
Ribosomes .................................................. 35, 36, 38, 46,
47, 454, 455, 457, 461, 467
RNA affinity purifications .................................... 241–252
RNA-binding proteins (RBPs) ........................... 103, 104,
106, 241–252, 255, 269, 278, 284, 285
RNA extractions......................................... 185, 190, 191,
199, 203, 229, 231, 293, 391–395, 397, 406,
455, 461, 462
RNA fractionation by polyacrylamide gel
electrophoresis ................................................... 424
RNA immunoprecipitation.................................. 255–266
RNA interference ........................................ 216, 227, 387
RNA isolation...................................................... 190, 256,
260, 264, 309, 314
RNA labeling.............................................. 7, 9, 117, 150,
216, 220, 233
RNA mobility .............................182, 183, 187, 270, 271
RNA particles ....................................................... 274–277
RNase decontamination ................................................... 9
RNAseq................................................285, 457, 462, 463
RNA silencing .....................................182, 390, 431–449
RNA uptake.......................................................... 215–224
RNA virus ............................................................. 105, 309
RNP footprints..................................................... 294–299
S
Saccharomyces cerevisiae................................................. 107
SDS PAGE.................................................. 264, 266, 311,
312, 321, 436, 444, 445
Seeding cells .................................................................. 273
Seed sterilization .................................................. 415, 420
Short oligonucleotide probes ......................................... 24
Signal recognition particle (SRP).............................35, 36
Single-molecule FISH (smFISH)..................... 24, 29–32,
36–43, 45–48, 51–67, 122, 124, 125, 127, 128,
132, 133, 135, 138, 196, 197, 207, 208, 211
Single-molecule RNA mobility assay .................. 269–281
Site directed mutagenesis .................................... 434, 437
Size fractionation of total RNA........................... 398–399
Small RNA cDNA libraries.................................. 293–299
Small RNA data analysis ...................................... 396–397
Small RNA extraction ................................................... 424
Spectral unmixing .....................................................24, 26
Spinach (aptamer) .................................82, 84, 86, 89, 92
Split aptamers .................................................................. 91
Spray-induced gene silencing (SIGS) ................. 216, 228
SP6 RNA polymerase..................................................7, 18
Stellaris mRNA probes..............................................41, 47
Streptavidin affinity purification .......................... 286, 295
Suzuki-Miyaura cross-coupling ........................... 473–485
Systematic Evolution of Ligands by EXponential
enrichment (SELEX ) ..................... 76, 80, 81, 83
T
Tagging RNA with agarose beads....................... 246, 248
Tethering assays.................................................... 270, 271
4-Thiouridine (4SU)-labeled RNA.............................. 285
Tissue fixation ................................................................. 11
Tissue permeabilization .................................................. 12
Tobacco mosaic virus (TMV)............................. 105–107,
111, 115, 117
Tobacco rattle virus (TRV)......................... 308, 318, 323
Transcription activator-like effector nucleases
(TALENs) .......................................................... 335
Translating ribosome affinity purification
(TRAP) ........................................... 257, 454–458,
461, 468, 469
Translatomes ........................................................ 451–470
Transport granule ......................................................... 269
TRAP RNA is achieved by direct sequencing
(TRAP-SEQ) ............................................ 451–470
T7 RNA polymerase ..................... 7, 9, 89, 92, 186, 187,
216, 220, 234, 474–476, 479, 480, 482
Tyramide signal amplification (TSA) system ................... 5
U
Urea-PAGE ....................... 288, 294, 296, 298, 302, 304
UV cross-linker ................. 257, 260, 286, 310, 394, 401
V
Verticillium longisporum............................. 228, 230, 236
Virus replication complexes................................. 307, 320
Volocity ............................................................... 26, 30, 31
RNA TAGGING: METHODS AND PROTOCOLS
Index 489