Long Non-Coding RNAs (eBook)

Preface 6
Contents 10
Contributors 12
Chapter 1: Transcriptional and Posttranscriptional Programming by Long Noncoding RNAs 14
1.1 Introduction 14
1.2 Pervasive ncRNA Transcription at Gene Regulatory Regions and the Link to Transcription 17
1.3 Transcriptional Silencing by Noncoding Transcription via Transcriptional Interference 20
1.4 Heritable Epigenetic Gene Inactivation via Noncoding Transcription 23
1.5 LncRNAs Mediate Long-Range Gene Silencing Through the Recruitment of Polycomb Repressor Complexes 24
1.6 LncRNA-Mediated Targeting of Activator Complexes in Epigenetic Gene Activation 28
1.7 Transcriptional Regulation of Heat Shock Response by lncRNAs 30
1.8 LncRNAs Regulate Transcription by Modulating Protein Activity 31
1.9 LncRNAs Regulates mRNA Splicing, Stability, and Translation 32
1.10 Conclusions and Future Perspectives 33
References 34
Chapter 2: Long Noncoding RNA as a Regulator for Transcription 41
2.1 Introduction 41
2.2 Long ncRNAs 42
2.2.1 Length of Long ncRNAs 42
2.2.2 Single- or Double-Stranded Long ncRNAs 43
2.2.3 Subcellular Localization 43
2.2.4 Transcription of Long ncRNAs 43
2.3 Long ncRNAs Regulate Transcription 44
2.3.1 Transcriptional Regulation Through Targeting Basic Transcription Factors and RNA Polymerase II by Long ncRNAs 44
2.3.1.1 Alu RNA 44
2.3.1.2 Dehydrofolate Reductase ncRNA 44
2.3.2 Transcriptional Regulation Through Histone Modification by the Long ncRNAs 45
2.3.2.1 Steroid Receptor RNA Activator 45
2.3.2.2 Embryonic Ventral Forebrain-2 46
2.3.2.3 HOX Antisense Intergenic RNA 47
2.3.2.4 Cyclin D1 47
2.3.3 DNA Methylation 47
2.3.3.1 P15AS 48
2.3.3.2 Khps1 48
2.4 ncRNAs as a Sensor for Cellular Signals 48
2.5 Mechanisms of Transcriptions of Long ncRNAs 49
2.6 Perspectives 50
References 51
Chapter 3: Long Noncoding RNAs and X Chromosome Inactivation 54
3.1 Introduction 54
3.2 Cis-Regulatory Factors in XCI 56
3.3 Xist Versus Tsix 58
3.4 Trans-Regulatory Factors and Initiation of XCI 60
3.5 Establishment of the Inactive X 61
3.6 Xist Spreading, Xi Organization, and Nuclear Organization 64
3.7 Other Functional ncRNAs 66
3.8 Conclusion 67
References 68
Chapter 4: TERRA: Long Noncoding RNA at Eukaryotic Telomeres 76
4.1 Eukaryotic Telomeres 76
4.1.1 Saccharomyces cerevisiae Telomeres 77
4.1.2 Schizosaccharomyces pombe Telomeres 81
4.1.3 Plant Telomeres 82
4.1.4 Drosophila melanogaster Telomeres 83
4.1.5 Mammalian Telomeres 84
4.2 TERRA: TElomeric Repeat-Containing RNA 87
4.2.1 TERRA Discovery and Biogenesis 87
4.2.2 TERRA Localization 89
4.2.3 TERRA and Interaction with Proteins 91
4.2.4 Regulation of TERRA Levels 92
4.2.5 TERRA-Associated Functions 96
4.3 Conclusions and Future Directions 97
References 98
Chapter 5: Transcription of Satellite DNAs in Mammals 106
5.1 Introduction 106
5.2 General Organization of Centromeric and Pericentric Regions in Mouse and Human Chromosomes 107
5.2.1 Mouse Chromosomes 108
5.2.2 Human Chromosomes 109
5.3 Expression of Centromeric and Pericentric Sequences in Cell Lines and Tissues 109
5.3.1 Development and Cell Differentiation 112
5.3.2 Response to Environmental Stimuli 112
5.3.3 Regulation During the Cell Cycle 113
5.4 Molecular Mechanisms Underlying Expression of CT and PCT Sequences 115
5.4.1 Transcription Factors 115
5.4.2 Epigenetic Regulation 116
5.4.2.1 DNA Methylation 116
5.4.2.2 Histone Modifications 117
5.5 Role of Pericentric and Centromeric Functions 120
5.5.1 Structural Components of Pericentric and Centromeric Structure and Function 120
5.5.2 Position Effect 123
5.5.3 Sequestration of Transcription and Splicing Factors 123
5.5.4 Stabilization of Specific Protein Encoding Transcripts 124
5.6 Conclusion 124
References 125
Chapter 6: Multiple Roles of Alu-Related Noncoding RNAs 130
6.1 Introduction 130
6.2 Alu: Birth and Evolution 131
6.3 Cellular Levels, Maturation, and Localization of Alu RNAs 134
6.4 Transcriptional Regulation of Alu RNA Expression 135
6.5 Alu RNA in Transcription Regulation 137
6.6 Alu RNA and Alu RNP in Translation Regulation 138
6.7 Alu Elements as Source and Target of miRNAs 141
6.8 Alu RNA Editing and Nuclear Retention 143
6.9 Unique Alu-Derived Transcription Units 145
6.10 Conclusion 148
References 149
Chapter 7: roX RNAs and Genome Regulation in Drosophila Melanogaster 158
7.1 Introduction 158
7.1.1 Genome Regulation and Large, Noncoding RNAs 158
7.2 Noncoding RNAs in Drosophila: A Wealth of Transcripts with Few Known Functions 159
7.3 roX RNAs and Dosage Compensation 159
7.4 Proteins of the MSL Complex 161
7.5 Separate Domains of roX1 Regulate X-Localization and Histone Modification 163
7.6 Ancestral Origins of Complexes that Dosage Compensate Sex Chromosomes 164
7.7 Regulation of Heterochromatic Genes by roX and a Subset of MSL Proteins 165
7.8 Conclusions 167
References 167
Chapter 8: Transcription of Satellite DNAs in Insects 172
8.1 Satellite DNAs in Insects 172
8.2 Functional Elements Within satDNAs 174
8.3 Preserved satDNA Repeats in Insects 175
8.4 Transcription of Insects satDNAs 176
8.4.1 Hymenoptera 179
8.4.2 Diptera 179
8.4.3 Orthoptera 180
8.4.4 Coleoptera 181
8.5 Heterochromatin Formation in Drosophila: Role of Heterochromatic Transcripts 182
8.6 Possible Regulatory Role of satDNAs and Their Transcripts 184
8.7 Conclusion 185
References 186
Chapter 9: Long Nonprotein-Coding RNAs in Plants 190
9.1 Introduction 191
9.2 Natural Antisense Transcripts Include a Major Class of Long ncpRNA in Plants 193
9.3 Long and Short npcRNAs Are Involved in the RNA Silencing Mechanism 196
9.3.1 The miRNA Pathway 196
9.3.2 The siRNA Pathway 198
9.3.3 The ta-siRNA Pathway 199
9.3.4 The nat-siRNA Pathway 200
9.4 Biological Roles of npcRNAs in Plants 201
9.4.1 Implication of npcRNAs in Circadian Cycle 201
9.4.2 Epigenetic Regulation and npcRNA 202
9.5 npcRNAs Interacting with Specific RNA-Binding Proteins May Create Cellular Networks 203
9.6 Concluding Remarks 205
References 205
Index 212