1;Preface;62;Contents;103;Contributors;124;Chapter 1: Transcriptional and Posttranscriptional Programming by Long Noncoding RNAs;144.1;1.1 Introduction;144.2;1.2 Pervasive ncRNA Transcription at Gene Regulatory Regions and the Link to Transcription;174.3;1.3 Transcriptional Silencing by Noncoding Transcription via Transcriptional Interference;204.4;1.4 Heritable Epigenetic Gene Inactivation via Noncoding Transcription;234.5;1.5 LncRNAs Mediate Long-Range Gene Silencing Through the Recruitment of Polycomb Repressor Complexes;244.6;1.6 LncRNA-Mediated Targeting of Activator Complexes in Epigenetic Gene Activation;284.7;1.7 Transcriptional Regulation of Heat Shock Response by lncRNAs;304.8;1.8 LncRNAs Regulate Transcription by Modulating Protein Activity;314.9;1.9 LncRNAs Regulates mRNA Splicing, Stability, and Translation;324.10;1.10 Conclusions and Future Perspectives;334.11;References;345;Chapter 2: Long Noncoding RNA as a Regulator for Transcription;415.1;2.1 Introduction;415.2;2.2 Long ncRNAs;425.2.1;2.2.1 Length of Long ncRNAs;425.2.2;2.2.2 Single- or Double-Stranded Long ncRNAs;435.2.3;2.2.3 Subcellular Localization;435.2.4;2.2.4 Transcription of Long ncRNAs;435.3;2.3 Long ncRNAs Regulate Transcription;445.3.1;2.3.1 Transcriptional Regulation Through Targeting Basic Transcription Factors and RNA Polymerase II by Long ncRNAs;445.3.1.1;2.3.1.1 Alu RNA;445.3.1.2;2.3.1.2 Dehydrofolate Reductase ncRNA;445.3.2;2.3.2 Transcriptional Regulation Through Histone Modification by the Long ncRNAs;455.3.2.1;2.3.2.1 Steroid Receptor RNA Activator;455.3.2.2;2.3.2.2 Embryonic Ventral Forebrain-2;465.3.2.3;2.3.2.3 HOX Antisense Intergenic RNA;475.3.2.4;2.3.2.4 Cyclin D1;475.3.3;2.3.3 DNA Methylation;475.3.3.1;2.3.3.1 P15AS;485.3.3.2;2.3.3.2 Khps1;485.4;2.4 ncRNAs as a Sensor for Cellular Signals;485.5;2.5 Mechanisms of Transcriptions of Long ncRNAs;495.6;2.6 Perspectives;505.7;References;516;Chapter 3: Long Noncoding RNAs and X Chromosome Inactivation;546.1;3.1 Introduction;546.2;3.2 Cis-Regulatory Factors in XCI;566.3;3.3 Xist Versus Tsix;586.4;3.4 Trans-Regulatory Factors and Initiation of XCI;606.5;3.5 Establishment of the Inactive X;616.6;3.6 Xist Spreading, Xi Organization, and Nuclear Organization;646.7;3.7 Other Functional ncRNAs;666.8;3.8 Conclusion;676.9;References;687;Chapter 4: TERRA: Long Noncoding RNA at Eukaryotic Telomeres;767.1;4.1 Eukaryotic Telomeres;767.1.1;4.1.1 Saccharomyces cerevisiae Telomeres;777.1.2;4.1.2 Schizosaccharomyces pombe Telomeres;817.1.3;4.1.3 Plant Telomeres;827.1.4;4.1.4 Drosophila melanogaster Telomeres;837.1.5;4.1.5 Mammalian Telomeres;847.2;4.2 TERRA: TElomeric Repeat-Containing RNA;877.2.1;4.2.1 TERRA Discovery and Biogenesis;877.2.2;4.2.2 TERRA Localization;897.2.3;4.2.3 TERRA and Interaction with Proteins;917.2.4;4.2.4 Regulation of TERRA Levels;927.2.5;4.2.5 TERRA-Associated Functions;967.3;4.3 Conclusions and Future Directions;977.4;References;988;Chapter 5: Transcription of Satellite DNAs in Mammals;1068.1;5.1 Introduction;1068.2;5.2 General Organization of Centromeric and Pericentric Regions in Mouse and Human Chromosomes;1078.2.1;5.2.1 Mouse Chromosomes;1088.2.2;5.2.2 Human Chromosomes;1098.3;5.3 Expression of Centromeric and Pericentric Sequences in Cell Lines and Tissues;1098.3.1;5.3.1 Development and Cell Differentiation;1128.3.2;5.3.2 Response to Environmental Stimuli;1128.3.3;5.3.3 Regulation During the Cell Cycle;1138.4;5.4 Molecular Mechanisms Underlying Expression of CT and PCT Sequences;1158.4.1;5.4.1 Transcription Factors;1158.4.2;5.4.2 Epigenetic Regulation;1168.4.2.1;5.4.2.1 DNA Methylation;1168.4.2.2;5.4.2.2 Histone Modifications;1178.5;5.5 Role of Pericentric and Centromeric Functions;1208.5.1;5.5.1 Structural Components of Pericentric and Centromeric Structure and Function;1208.5.2;5.5.2 Position Effect;1238.5.3;5.5.3 Sequestration of Transcription and Splicing Factors;1238.5.4;5.5.4 Stabilization