MicroRNAs

Cover......Page 1
Half-title......Page 3
Dedication......Page 4
Title......Page 5
Copyright......Page 6
Contents......Page 7
Contributors......Page 10
Foreword......Page 27
Foreword......Page 29
Introduction......Page 31
I Discovery of microRNAs in various organisms......Page 35
Biogenesis and mechanism of action......Page 37
MicroRNA target predictions......Page 40
MicroRNAs control the timing of development......Page 43
MicroRNAs control left/right asymmetry in the nervous system......Page 45
MicroRNAs in ageing......Page 46
References......Page 48
Non-coding RNAs......Page 52
Nucleolar RNA......Page 53
Small interfering RNA (siRNA)......Page 54
MicroRNA (miRNA)......Page 55
Intronic miRNA......Page 57
MiRNAs vs. siRNAs......Page 58
Transposons and intronic miRNA......Page 60
Biogenesis and mechanism of miRNAs......Page 61
Computer search......Page 62
Generation of man-made miRNA......Page 63
Analysis of gene function......Page 65
Design and development of novel gene therapy......Page 67
Development of loss-of-function transgenic animals......Page 68
References......Page 69
Biogenesis of miRNAs......Page 72
miRNA detection by cloning and Northern analysis......Page 74
Microarrays and other high-throughput miRNA expression platforms......Page 76
miRNA sensors......Page 78
miRNA promoter fusions......Page 80
Direct detection of miRNA primary transcripts......Page 81
Detecting mature miRNAs with locked nucleic acid probes......Page 83
References......Page 84
MicroRNA processing......Page 88
Creating Dicer-deficient mouse models......Page 89
Hox genes......Page 90
MicroRNAs in the Hox cluster......Page 91
Hox genes and limb development......Page 92
MicroRNAs in limb development......Page 93
References......Page 97
Introduction......Page 100
Prediction of stem-loop structures......Page 101
Identification of 20 miRNAs from rice......Page 102
Tissue-specific and developmental expression of rice miRNAs......Page 104
Rice microRNA targets prediction......Page 107
Strategies for cloning microRNA......Page 108
MiRNA and siRNA in plants......Page 109
References......Page 110
II MicroRNA functions and RNAi-mediated pathways......Page 113
Introduction......Page 115
Cell culture, mRNA transfections and dual luciferase assays......Page 117
Using mRNA transfection to study miRNA function......Page 118
miCXCR4 targets eIF4E function......Page 122
Similarities of the miRNA mechanism to other translational control paradigms......Page 123
Use of mRNA transfection to assess the generality of the miRNA mechanism......Page 125
The miRNA mechanism and processing bodies......Page 126
Concluding remarks......Page 127
References......Page 128
Introduction......Page 132
Locked Nucleic Acid (LNA) probes......Page 133
In situ hybridization......Page 134
Chick miRNA expression analysis......Page 135
Sensitivity......Page 139
Relevance......Page 140
Concluding remarks......Page 141
References......Page 142
Introduction......Page 145
MicroRNAs in neuronal cell fate determination......Page 146
MicroRNAs in activity-dependent synapse formation and refinement......Page 149
MicroRNAs in neurological disease......Page 154
Concluding remarks and perspectives......Page 156
References......Page 157
Introduction......Page 159
Controls for amount of BCKD activity......Page 161
Potential for MSUD disease with miR expression......Page 164
References......Page 165
Introduction: microRNAs meet plant development......Page 167
The jaw-D mutant......Page 170
The impact of miRNA resistant genes......Page 173
Back to leaf morphogenesis......Page 175
miRNAs are highly specific regulators of plant development......Page 176
Conservation of miRNA pathways in plants......Page 179
References......Page 180
III Computational biology of microRNAs......Page 185
Introduction......Page 187
miRBase Registry......Page 188
Structure of a miRBase Sequence Entry......Page 190
miRBase Targets......Page 194
Browsing and searching miRBase......Page 197
Searching miRBase Targets......Page 198
Summary......Page 199
References......Page 200
Introduction......Page 202
What is known about recognition of microRNA target sites?......Page 203
Overview of different prediction methods......Page 207
Insights from analyzing genome-wide target predictions......Page 211
Conclusions......Page 213
References......Page 214
Introduction......Page 217
The miRNA target prediction program DIANA-microT......Page 218
Status of target prediction......Page 220
Feature extraction......Page 221
Support vector machines for miRNA prediction......Page 222
TarBase......Page 224
MicroRNA Genomics Resource and Cluster Server......Page 225
References......Page 226
Introduction......Page 229
Energy minimization......Page 230
Length normalization......Page 231
Comparative analysis of orthologous targets......Page 232
Target prediction on a per-gene basis......Page 233
Target prediction on a per-miRNA basis......Page 235
Genome-wide multi-species target prediction......Page 236
Selection of candidates......Page 237
Acknowledgements......Page 238
References......Page 239
Introduction......Page 240
Motifs describe microRNA target sites......Page 241
Genetic programming creates target site motifs......Page 242
ROC describes the overall performance of target site predictors......Page 243
Near-perfect binding in the miRNA 5’ end is the most important target site motif......Page 244
Weighted sequence motifs give good target site predictions......Page 245
Weighted sequence motifs give more specific predictions than predictions based on sequence and thermodynamics alone......Page 246
Target site conservation improves specificity......Page 247
References......Page 248
A random model......Page 251
Cases in which microRNAs hit genomic repeats or regulatory elements within 3’-UTRs......Page 252
References......Page 254
IV Detection and quantitation of microRNAs......Page 257
Introduction......Page 259
LNA (locked nucleic acid) – a synthetic RNA mimic for high-affinity miRNA targeting......Page 260
Use of LNA probes in miRNA Northern blot analysis......Page 261
In situ detection of miRNAs in animals and plants using LNA-modified oligonucleotide probes......Page 264
Functional microRNA analysis using LNA-antimiRs......Page 267
References......Page 268
Introduction......Page 272
The Invader assay......Page 273
Oligonucleotide designs for the miRNA Invader assay......Page 275
Invader microRNA assay......Page 276
Specificity of the microRNA Invader assay......Page 277
MicroRNA Invader assay using cell-lysate and total RNA......Page 279
Biplex Invader assay......Page 280
Concluding remarks......Page 281
References......Page 282
Introduction......Page 285
Single molecule detection platform......Page 287
Dual-color coincident event counting......Page 289
Absolute miRNA quantitation......Page 291
Sensitivity and dynamic range of the assay......Page 292
Assay specificity......Page 293
Quantitation of miRNA expression in cancer tissues......Page 294
References......Page 296
Introduction......Page 299
Chemistry of TaqMan® microRNA assays......Page 300
Performance of TaqMan® microRNA assays......Page 301
Development of endogenous controls for TaqMan® microRNA assays......Page 302
Expression profiling of miRNAs......Page 304
Detection of microRNA length polymorphisms......Page 308
Conclusions......Page 309
References......Page 310
Introduction......Page 313
Methodology......Page 314
Reverse transcription......Page 315
MicroRNA and mRNA primer design......Page 316
Cloning and sequencing of miRNA amplification products......Page 317
Amplification of endogenous miRNAs......Page 319
Discussion......Page 320
References......Page 321
V MicroRNAs in disease biology......Page 342
Introduction......Page 344
Abnormal microRNA expression and function in cancer......Page 345
c-Myc regulated microRNAs......Page 350
Concluding remarks......Page 353
References......Page 354
Introduction......Page 358
MicroRNAs are expressed in tissue-specific pattern......Page 359
MicroRNAs are frequently located in cancer-associated genomic regions (CAGRs)......Page 360
MicroRNA expression signature in hematological malignancies......Page 361
MicroRNA expression signature in solid tumors......Page 364
Conclusions......Page 367
References......Page 368
Cloning and profiling miRNAs......Page 371
MicroRNAs in mouse development......Page 373
Oncogenic and anti-oncogenic miRNAs......Page 376
The miR-15~16 cluster and the leukemia connection......Page 377
miR-17~92......Page 378
let-7 and the Ras connection......Page 380
Further examples......Page 381
References......Page 382
Introduction......Page 387
Biogenesis of miR-122......Page 388
miR-122 and liver tumor......Page 391
Validation of a potential mRNA target for miR-122......Page 393
Other potential targets of miR-122......Page 395
References......Page 396
Glioblastoma multiforme: a lethal brain tumor still missing a thorough comprehension of molecular oncogenesis......Page 399
MicroRNAs and cancer......Page 400
MicroRNAs in brain......Page 401
Microarray analysis of the microRNA signature of glioblastoma tissue samples......Page 402
MicroRNA expression analysis in human glioblastoma cell lines......Page 404
Expression profiling-based grouping of glioblastoma patients’ and cell line samples......Page 405
Concluding remarks......Page 407
References......Page 409
Clinical phenotypes of Fragile X syndrome......Page 412
Biological functions of FMRP......Page 413
Role of microRNA pathway in FMRP-mediated translational control......Page 416
Small RNAs in FMR1 gene silencing?......Page 417
Summary......Page 418
References......Page 419
Introduction......Page 421
Case report and results......Page 424
Discussion......Page 425
References......Page 428
Introduction......Page 429
Differentiation of HL-60 cells......Page 430
Alteration in expression profiles of mRNAs and miRNAs......Page 431
Expression profile of miRNA during TPA-induced differentiation......Page 432
Co-existence of miRNAs and their target mRNA during the differentiation of HL-60 cells......Page 436
References......Page 438
Introduction......Page 441
MiRNA expression during muscle differentiation......Page 442
miRNAs are differentially expressed in muscle regeneration......Page 445
MiR-181 is required for muscle cell terminal differentiation......Page 447
The homeobox protein Hox-A11 is a direct target of miR-181a......Page 449
Conclusions......Page 451
References......Page 452
Identification of viral miRNAs......Page 454
Herpesviruses......Page 455
Epstein–Barr virus......Page 456
Kaposi’s sarcoma-associated herpesvirus......Page 457
Murine herpesvirus-68......Page 458
Human cytomegalovirus......Page 459
Adenovirus......Page 465
Human immunodeficiency virus (HIV)......Page 467
Primate foamy virus-1......Page 468
Conclusion......Page 469
References......Page 473
Introduction......Page 476
Preparation of size-selected RNA from total RNA......Page 477
Reagents......Page 479
Detection and functional analysis of miRNAs in HIV-1-infected cells......Page 481
Reverse transcriptase exhibits in vitro RNA polymerase activity......Page 483
References......Page 488
VI MicroRNAs in stem cell development......Page 492
Introduction......Page 494
Obstacles that preclude the identification of siRNAs involved in transcriptional silencing in ES cells......Page 495
miRNAs in ES cells......Page 500
miRNA clusters pre-miR-290-295/pre-miR-371-373 and pre-miR-367-pre-miR-302a-d......Page 502
Potential early embryo specific function of pre-miR-290-295/pre-miR-371-373......Page 509
Concluding remarks......Page 510
References......Page 512
MiRNA biogenesis......Page 516
miRNAs and differentiation of hematopoietic cells......Page 518
MiRNAs in B-cell lymphoma and leukemia......Page 521
References......Page 522
Introduction......Page 525
MiRNAs expressed in human ESCs (hESCs)......Page 528
MiR-124a and miR-9 affect neural differentiation in mESCs......Page 529
Transcriptional regulation of microRNAs in ESCs......Page 530
Predicting microRNAs from the genome......Page 531
Predicting mRNA cis-elements to which microRNAs bind......Page 532
Other microRNA target regions in mRNAs......Page 533
Conclusions and future work......Page 534
References......Page 535
Introduction......Page 538
Cell lysis and reverse transcription......Page 539
Pre-PCR......Page 540
Results and discussion......Page 541
References......Page 543
Ago/Piwi protein family comprises two sub-families......Page 546
Functions of Piwi proteins in Drosophila......Page 547
Functions of Piwi proteins in other organisms......Page 548
Discovery of piRNAs......Page 549
Biogenesis of piRNAs......Page 550
Biological function of piRNAs......Page 553
Function of piRNAs in transposon silencing......Page 554
Function of piRNAs in transcriptional repression......Page 555
Function of piRNAs in translational regulation and mRNA stability......Page 556
References......Page 557
MicroRNAs in immunology......Page 561
MicroRNAs in cardiology......Page 563
MicroRNAs in unicellular organisms......Page 567
References......Page 568
Index......Page 571