INDEX A Adipocytes...1 81 193 Adipogenesis...1 81 Adipose tissue...1 81 193 AGO (argonaute)...8, 9, 11, 22, 23, 92, 352 Ampli fi cation....8 4 88, 152, 154, 163, 164, 169, 170, 190, 225, 226, 263, 291, 301, 302, 306, 308, 331, 339 Angiogenesis... 4 8, 347, 348 Antisense...2, 7, 9, 37, 119, 121, 130, 131, 150, 199, 200, 212, 215, 219, 221 223, 225, 227, 273, 274, 280, 288, 290, 292, 303 305, 307, 330, 333, 352 Apoptosis... 4 8, 78, 97, 100, 216, 281, 299, 311, 314, 350, 359 363 Arabidopsis... 9, 210, 280 Arti fi cial introns...2 13, 214, 216, 223, 272, 281, 282 Asymmetric assembly...2 73 275 ATP...... 2 4, 26 29, 84, 106, 109, 115, 161, 221 223, 289, 290, 305, 306, 330, 348, 361 Aubergine...8 B Bacteriophage...4 β -actin... 2 18, 273, 283 β -catenin...2 83 286, 292, 349, 364 Biogenesis...6, 10 12, 21, 22, 35, 78, 131, 173, 210 212, 215, 220, 231 233, 281 284, 298, 303, 314, 326, 343 344, 346 348 Bioinformatics... 3 5, 36, 38, 50, 77 81, 92, 98, 100, 118, 212, 236, 271, 300 Biomarkers...3 13 316 BLAST, Blastn, BMI-1... 299, 300, 302 BMP4.....286 C Caenorhabditis elegans...4, 126, 129, 140, 143, 158, 210, 280, 314 Cancer....1 3, 14, 16, 50, 78 79, 92, 93, 99, 118, 157 171, 210, 213, 216, 280, 281, 296, 299, 301, 309, 313 322, 326, 349 350, 353, 357 366 CDK2.....296, 298 300, 360, 363 CDK4/6cell cycle...2 96, 299, 360, 363 CDKN1A...2 95 Cell culture... 8 5, 108, 145, 161, 196 197, 202, 223, 226, 234 239, 249, 258 259, 290, 292, 306, 309 311, 334 336 Central nervous system (CNS)... 38, 44 Chicken...1 4, 17, 96, 132, 135, 210, 283 286, 290 292 Chromosome...3, 11, 71, 72, 94 96, 98 Chromosome X (Hs X-17cl)...8, 11 Cloning......1 2, 13, 22, 83 87, 89, 119, 121 123, 126, 131, 134, 146 148, 150, 152, 155, 157 171, 182, 190, 196, 200 202, 205, 222, 225, 226, 233, 234, 289 291, 305, 308 cmyc......7 9, 247, 254, 296, 362 CNS. See Central nervous system (CNS) Computational prediction... 9 2, 94 98, 100 Cosuppression...4 Cyclin D...2 96, 299, 300, 360 Cytomegalovirus... 2 25, 273, 281 Cytoplasm... 3, 5, 11, 12, 22, 60 63, 78, 92, 158, 173, 181, 182, 197, 198, 210, 211, 213, 216, 257, 272, 282, 286, 288, 303, 327, 328, 344 Cytotoxicity... 2 81, 285, 288 D Database...3 1, 37, 69 75, 80, 81, 94, 95, 98, 99, 101 Depigmentation...3 26 DGCR8. See DiGeorge syndrome critical region gene 8 (DGCR8) DH5 α... 1 47, 159, 164, 202, 222, 225, 226, 289, 291, 305, 308 Diagnostics... 7 9, 196, 222, 259, 289, 306, 314, 331, 359, 362, 365, 366 DIANA LAB microt... 3 8, 42 Dicer......4 6, 9 13, 21 33, 78, 92, 158, 181, 198, 205, 211 213, 218, 220, 232, 233, 257, 272, 273, 275, 285, 298, 327, 328, 344, 345, 347 Shao-Yao Ying (ed.), MicroRNA Protocols, Methods in Molecular Biology, vol. 936, DOI 10.1007/978-1-62703-083-0, Springer Science+Business Media, LLC 2013 371
372 MICRORNA PROTOCOLS Dicer-like...9, 11, 212, 303 Differentiation...1 5, 21, 48, 78, 79, 92, 105 115, 130, 234, 249, 254, 257 268, 300, 311, 314, 345, 347, 358 360 DiGeorge syndrome critical region gene 8 (DGCR8)...15, 21, 22, 343, 345 DMEM. See Dulbecco s modi fi ed eagle medium (DMEM) DNA chip...2 59, 263 265, 267 DNA constructs...8 4 DNA mirna...1 6 DNA RNA hybrid...2 16 DNA/RNA methylation...3, 11, 63, 296 DNAse... 1 53, 175, 178, 259, 263, 264, 316, 318, 322 Donor introns...7 Drosha....5, 10, 12, 21 23, 78, 91, 157, 181, 197, 198, 204, 205, 211, 232, 233, 257, 303, 327, 328, 343 Drosophila... 1 31, 151 Drosophila melanogaster...1 5, 210, 280 Drug development...9 8 dsdna... 8 7, 334 Dulbecco s modi fi ed eagle medium (DMEM)... 85, 106, 148, 150, 161, 165, 166, 196, 202, 235, 236, 239, 243, 249, 258, 260, 306 E EBV. See Epstein-Barr virus (EBV) E-cadherin...2 84, 349, 350, 364 EGFP..... 1 48, 198, 204, 214, 215, 217 219, 225, 227, 273 275, 278, 282, 283, 290, 305 Embryonic development...1 7, 79, 105, 118, 210 Embryonic stem cells (ESC)...4, 50, 58, 79, 234, 235, 237, 240, 244, 247 255, 296, 297, 363 Enrichment analysis...9 1 101 Epstein-Barr virus (EBV)... 143, 146, 153 ES cells (ESC). See Embryonic stem cells (ESC) Evolution... 3, 7, 9, 11, 46, 48, 50, 64, 96, 210, 212, 213, 220, 272, 303, 359 Exons...... 3, 6, 10 12, 69, 71, 72, 75, 78, 100, 138, 198, 210, 211, 214 217, 223, 224, 226, 227, 282, 283, 303, 326, 327 Exosomes... 3, 315 Exportin-5...5, 10, 22, 78, 91, 158, 211, 303, 344 F FASTA... 3 6, 44, 70, 71, 74, 80, 81 Feather... 2 84, 286 Fine tuning... 6, 7, 11, 50, 64, 117, 210, 242, 298, 302 Fish...... 2 10, 218, 219, 274, 280, 282 Fragile X mental retardation protein...2 13 Functional annotation...7 3, 94, 95, 97 98 G Galaxy.....3 6, 38 40, 42, 43 GAPDH. See Glyceraldehydes phosphate dehydrogenase (GAPDH) Gene cloning...2 91 endogenous...4 function... 2, 4, 6, 14 17, 78, 97, 216, 281 homogenous... 6 9, 296, 297 host...3, 69 73, 75, 131 splicing...2 13 therapy... 1 4 16, 287, 351 transfer...4 tumor...1 4, 50, 63, 78, 79, 296, 297, 300, 302 Gene gene interactions...3 8 Gene ontology (GO)...73 75, 95, 97, 98, 100 Gene silencing... 2, 4 6, 10, 11, 14, 15, 78, 92, 118, 119, 209 227, 257, 272 275, 278, 280 284, 286 288, 297, 298, 327 in vivo...2 09 227 Genome... 2, 7, 8, 10 16, 36, 37, 39, 40, 43, 47 49, 71, 74, 75, 77, 80, 81, 91, 96, 99, 129, 133, 157, 162, 209, 210, 220, 234, 249, 300, 314, 343, 359 Glyceraldehydes phosphate dehydrogenase (GAPDH)... 153, 154, 263, 264, 285, 287 GO. See Gene ontology (GO) H Heat-shock proteins...8 4, 86, 123, 147, 165, 191, 193, 339 HEK 293 cells... 8 5, 87, 309 HeLa cells... 1 20, 123, 202 Herpes....1 6 High throughput sequencing... 3 8, 182 Human immunode fi ciency virus (HIV)... 16, 58, 59, 215, 282 Hybridization...3, 13, 27, 30 32, 106, 107, 111, 115, 130, 221, 223, 225, 227, 249 251, 254 255, 264, 265, 267, 275, 276, 278, 289, 290, 292, 304, 307, 315, 330, 333 Hyperpigmentation...3 39 Hypoxia... 3 47, 348 I Induced pluripotent stem cells (ips/ipsc)...79, 247 255, 295 311 Ingenuity Pathway Analysis (IPA)... 38, 41 42, 44 In situ hybridization... 1 3, 130 Intronic mirna-expression construct... 8 9, 106, 108 Introns.... 3, 69 75, 77 81, 91, 130, 171, 197, 209 227, 271, 279 292, 295 311, 325 341 IPA. See Ingenuity Pathway Analysis (IPA) ips/ipsc. See Induced pluripotent stem cells (ips/ipsc)
K KEGG...7 3 75, 97, 98, 100 Klf4...... 79, 247, 254, 296, 299, 302 L Lentiviral vector... 1 48, 150 let-7... 5, 6, 12 14, 130, 193, 211, 253, 267 lin-4... 5, 6, 12 14, 130, 211 Loss-of-function...8, 14, 16 17, 280, 283 Luciferase assay... 8 5, 88, 89, 120, 145, 151 153 Luciferase reporter gene assay...1 17 126 M Melanin...2 86, 287, 326, 329, 332, 334 338, 345, 349 Metastasis... 9, 350, 360 366 Microarray... 1 3, 79, 93, 94, 98, 99, 105 107, 110 112, 114, 115, 182, 187, 248 251, 253, 296, 303, 315, 322 Microprocessor...5, 21, 198, 343 MicroRNA (mirna) biogenesis...1 0, 22, 35, 232, 233, 282 284, 298, 303, 343 344, 346, 347 expression patterns... 1 30, 258 functional analysis...2, 130, 144, 157 171 inhibitors...2 32, 233, 238 241, 352 intergenic mirnas...6, 7, 12, 69, 72, 210 212, 326 328 intronic mirna...6 8, 11, 12, 14, 15, 17, 69 75, 77 81, 91, 130, 131, 138, 209 227, 271 273, 275, 279 292, 295 311, 325 341 mimics...2 32, 234, 236 244 miranalyzer...3 7, 38, 40 41, 43, 44 pre-mirnas... 5, 10, 15, 23, 24, 80, 81, 89, 91, 92, 197, 215, 233, 241, 272 275, 278, 281, 303, 315, 327, 328, 343 pri-mrnas... 5, 10 12, 15, 21, 23, 78, 91, 96, 131, 157, 158, 197, 198, 204, 211 220, 222 223, 225 227, 232, 303, 315, 327, 328, 343, 344 pro fi le... 4 8, 50, 75, 94, 99, 100, 106, 130, 248 249, 254, 258, 263 265, 267, 314 regulatory element...1 18 targeting sequence... 9 1, 92, 118, 119, 125, 126 target protectors... 2 32, 240 targets... 3 8, 41 42, 44, 73, 91 101, 170, 204, 236, 352, 357 366 mir-124a... 2 65, 266 mir-125...265 mir-138... 118 121, 123 125 mir-302... 79, 249, 265, 295 311, 363 364 mir-302 cluster...2 52, 298, 303, 305 308 mir Tyr...2 38 341 mir Tyro... 3 29, 331 340 MICRORNA PROTOCOLS 373 Mouse embryonic carcinoma (EC) P19 cell... 1 05 115, 257 268 mrna target...6, 8, 11, 39, 41, 44, 50, 59, 91, 92, 129, 144, 153 154, 181, 199, 204, 231, 232, 236, 237, 242 244, 248, 280, 285, 326 328, 344, 358 Mutagenesis... 1 4, 84 87, 89 N Nanog.....5 0, 79, 247, 248, 296, 297, 299, 302 NCBI Ref Seq data base...7 1 Neural differentiation...1 50 115 Neuronal differentiation...2 57 268 Noncoding RNA (ncrna)...2 9, 11, 21, 36, 37, 48, 50, 63, 77, 91, 117, 257, 276, 314, 326, 328, 358, 359 Northern blotting...2 4 31, 96, 130, 182 O Oct3/4... 79, 297 oligo (dt)...152, 259, 263, 276, 277 Oral cancer... 1 18, 313 323 P p21cip1/waf1...295 p16ink4a, p14/p19arf...2 99 302 PIWI... 8 9, 258 Poliomyelitis...1 6 Post-transcriptional gene regulation...5 Post-transcriptional gene silencing (PTGS)...5, 11 Program... 1 3, 14, 16, 36 40, 44, 51, 57, 63, 80, 81, 97 101, 110, 124, 151, 152, 154, 163, 168, 170, 196, 249, 288, 300 Promoters... 6, 7, 9, 12, 17, 50, 69, 72, 78, 118, 130 134, 138 140, 144, 146, 171, 196, 204, 211, 212, 214, 215, 218, 225, 232, 233, 244, 273, 281, 282, 291, 315, 328 Prostate cancer... 1 60, 213, 281, 309, 353, 357 366 psm30... 196, 198 204 psm155... 196, 198 204 PTGS. See Post-transcriptional gene silencing (PTGS) R RA. See Retinoic acid (RA) Real time polymerase chain reaction (RT-PCR)...37, 81, 96, 107, 110, 143 145, 151 154, 160, 162, 182, 184 185, 190 191, 193, 248, 263, 264, 319 321 Real time quantitative polymerase chain reaction (RT-qPCR)...146, 155, 182, 185, 190, 191, 193, 259, 264 266 Red fl uorescent membrane protein (rgfp)...213 219, 221 227, 274, 281 283, 285, 289 292, 298, 303, 305 310
374 MICRORNA PROTOCOLS Reprogram... 7 9, 247, 248, 296, 297, 299 302, 309, 363, 364 Restriction enzymes...8 4 88, 119, 125, 126, 132, 134, 135, 138, 139, 144, 147, 158, 159, 162, 164, 196, 201, 202, 205, 216, 221 225, 289, 305, 307, 308, 330, 331, 333 Retinoic acid (RA)...105, 258, 260 262, 264 266 Retrotransposon...7, 50, 257, 258 Retroviral vector...1 48, 158, 160, 204, 291 Retroviruses...7, 64 rgfp. See Red fl uorescent membrane protein (rgfp) RhoC......1 18, 119, 121, 123, 125 Ribonuclear protein (RNP)...3, 10, 212, 213, 216, 272 Ribonuclease RNAse III... 3 6, 10, 12, 22, 78, 91, 92, 157, 181, 198, 211, 303, 343, 344 Ribosomes... 3, 92, 344 RNA activation (RNAa)...9 RNA hybride... 9 8, 250 RNAi. See RNA interference (RNAi) RNAi-mediated methylation... 2 13, 272 RNA-induced silencing complex (RISC)... 6, 8, 10, 11, 15, 22, 78, 92, 212, 217, 219, 220, 231 233, 244, 257, 273 275, 327, 328, 344, 351 RNA interference (RNAi)...2, 4 6, 9, 11 15, 77, 81, 181, 195, 199, 204, 205, 210, 211, 215, 216, 218, 220, 257, 272, 280, 282, 283, 327, 328 RNA polymerase II (pol II)...2, 3, 6, 9, 12, 78, 91, 144, 181, 196, 198, 204, 210, 211, 215, 216, 232, 258, 280 284, 303, 320, 327, 328, 343 RNA polymerase III (pol III)...12, 196, 204, 281, 320, 327, 328 RNAs ds RNA... 4 6, 9 11, 13, 22, 78, 198, 216, 281, 288, 344 hairpin-like RNAs... 1 4, 195, 213, 217, 272, 278 non-coding RNAs (nc RNAs)... 2 9, 11, 21, 36, 37, 48, 50, 63, 77, 91, 117, 257, 276, 314, 326, 328, 358, 359 nuclear RNA...3 4, 6, 178, 303 pirnas... 8 9, 258 rasirna...9 si RNAs... 4 6, 8 12, 17, 50, 63, 78, 195, 197 200, 204, 210 212, 216 220, 233, 244, 258, 273 276, 278, 280, 281, 284, 286 288, 303 small modulatory ds RNAs...5 small nuclear RNAs (snrnas)... 3, 4, 169, 276, 320 small RNAs...2 9, 36, 37, 106 110, 112, 114, 130, 131, 157, 158, 162, 168, 169, 178, 185, 186, 218, 234, 244, 248, 250, 254, 258, 273, 275 277, 280, 283, 284, 314, 321, 322 sno RNAs...2, 3, 6, 7, 145, 151, 171, 276 splicing...3, 4, 6, 7, 12, 211, 212, 216, 217, 282, 298, 303, 327 ss RNA...1, 4, 5, 12, 77, 117, 129, 210, 211, 216, 280, 281, 286, 326, 328 tasirnas...9 trna... 2, 3, 186 wave... 4 9, 51, 63 RNP. See Ribonuclear protein (RNP) RT-PCR. See Real time polymerase chain reaction (RT-PCR) RT-qPCR. See Real time quantitative polymerase chain reaction (RT-qPCR) S Saliva... 3 13 322 Skin... 1 4, 283 288, 309, 325, 326, 332, 335 339, 343 354 Skin whitening...3 25, 326, 332, 335 340, 349 Small-hairpin RNA (shrna)...195 206, 217, 303 Small RNA library... 1 06 110, 130 snornp...3 Somatic cell... 7 9, 247, 249, 296 298, 300, 309 Sox2......50, 79, 247, 248, 296, 297, 302, 363 Sponge...1 43, 144, 146 155, 232, 233, 352, 353 Stem cell... 4, 50, 60, 79, 105, 106, 112 114, 215, 234, 235, 237, 240, 244, 247 255, 281, 296 299, 302, 345, 358, 363 Subcellular fractionation... 1 73, 179 Synaptoneurosomes...1 73 179 Synaptosomes... 1 73, 174 T TaqMan microrna assays...1 45, 151, 162, 167 169, 171, 259, 266, 315 320 Target prediction...3 8, 41 42, 73, 75, 92, 94, 96 98, 100, 300 Targetrons...7 Target validation...8 3 90 TAR-RNA-binding protein (TRBP)...22 Telomerase... 3, 301, 302 Therapeutics...2 03, 216, 281, 351 Transfection... 1 5, 23, 79, 84, 85, 87 89, 119, 120, 123 124, 152, 158 160, 166, 170, 202, 205, 213 215, 217 219, 223, 226, 233, 234, 236 244, 273 275, 278, 286 288, 290, 292, 298, 306, 309 311, 327, 331 332, 334 336, 340, 364 Transgenes... 3, 5, 11
Transgenic animal...1 4, 16 17, 196, 279 292 Transposons... 7 9, 11 TRBP. See TAR-RNA-binding protein (TRBP) Tumor suppressor...7 8, 92, 297, 314, 359, 362, 363, 366 Tyrosinase (Tyr)...287, 326 329, 332, 334 336, 349 U Untranslated regions (UTR)...5, 6, 10, 11, 50, 73, 78, 83, 85, 86, 89, 91, 92, 96, 118, 119, 121, 125, 126, 132, 134, 138, 143, 144, 149, 152, 153, 155, 210, 213, 237, 242, 243, 272, 288, 305, 307, 308, 314, 343, 358 V Vaccine (antiviral)... 14, 16 Vertebrates...3, 10, 11, 14, 96, 101, 210, 212, 283 Virus...... 5, 7, 11, 143, 148 150, 154, 166, 170, 215, 289 292 W MICRORNA PROTOCOLS 375 WALDI. See Weighted average length of diced RNA (WALDI) Web resources... 9 8, 100 Weighted average length of diced RNA (WALDI)... 24, 30, 33 Western blotting...1 43 146, 153, 169, 171, 178, 197, 202, 205, 215, 296, 332, 334, 335 Work fl ow... 3 5 44, 235, 236 Wound healing...3 43 354 X Xenopus, oocytes...4, 23 Xist... 1 1 Z Zebra fi sh... 1 0, 13, 14, 16, 17, 50, 210, 212, 217, 218, 220, 272 273, 281, 283, 286 Zinc fi nger protein-9 gene... 8, 212, 272 Zygote... 7, 296, 299