Keywords:
Nucleic acids.
;
Electronic books.
Type of Medium:
Online Resource
Pages:
1 online resource (252 pages)
Edition:
1st ed.
ISBN:
9784431555766
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=3567499
DDC:
572.8/8
Language:
English
Note:
Intro -- Preface -- Contents -- Part I: Bioinformatics and Other Methodologies for lncRNAs -- Chapter 1: Complexity of Mammalian Transcriptome Analyzed by RNA Deep Sequencing -- 1.1 Introduction -- 1.2 Definition and Types of Transcripts Encoded by the Genome -- 1.3 Transcriptome Discovery Technology Overview -- 1.3.1 Pre-NGS Era: From Genetic Studies and cDNA Isolation to Microarrays -- 1.3.2 High-Throughput Sequencing Platforms to Study Mammalian Transcriptomes -- 1.3.2.1 RNAseq -- 1.3.2.2 Cap-Analysis Gene Expression (CAGE) -- 1.3.2.3 Paired-End Tag (PET) Sequencing -- 1.3.2.4 Poly(A) Tail-Guided Sequencing (Poly(A)-Seq) -- 1.3.2.5 Further Technology Development -- 1.4 Downstream Applications and Result Overview -- 1.4.1 FANTOM Consortium -- 1.4.2 ENCODE Project -- 1.5 Future Directions in ncRNA-Omics -- 1.6 Conclusion -- References -- Chapter 2: Synthetic Strategies to Identify and Regulate Noncoding RNAs -- 2.1 Introduction -- 2.2 lncRNAs in Disease and Development -- 2.3 Identification and Analysis of Noncoding RNA -- 2.3.1 Synthetic Strategies to Profile RNA Secondary Structure -- 2.3.2 Genome-Wide Techniques to Profile the Structure and Expression of ncRNAs -- 2.4 ncRNA-Induced Triplex Formation and Biological Implications -- 2.5 Synthetic Ligands Targeting RNA Structures: Advances and Challenges -- 2.6 Future Perspectives -- References -- Part II: Atomic and Molecular Structures of lncRNAs -- Chapter 3: Structure and Interaction with Protein of Noncoding RNA: A Case for an RNA Aptamer Against Prion Protein -- 3.1 Introduction -- 3.2 Identification of R12 as an RNA Aptamer Against Bovine Prion Protein (bPrP) -- 3.3 Identification of Two Binding Sites for R12 in the N-Terminal Intrinsically Disordered Region of bPrP -- 3.4 Structure of an R12 Aptamer in a Free Form -- 3.5 Structure of an R12 Aptamer in Complex with a P16 Binding Peptide.
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3.6 Binding Mode of R12 with bPrP -- 3.7 Origin of High Affinity and Specificity of R12 to bPrP -- 3.8 Anti-prion Activity of R12 -- 3.9 Possible Therapeutic Application -- 3.10 Conclusions -- References -- Chapter 4: Characterization of G-Quadruplex DNA- and RNA-Binding Protein -- 4.1 Introduction -- 4.2 Roles of the G-Quadruplex Binding Protein, TLS/FUS, in Telomere -- 4.3 Engineering of the G-Quadruplex RNA-Binding Protein -- 4.4 Conclusions -- References -- Part III: Molecular Functions of lncRNAs -- Chapter 5: Initiation of Transcription Generates Divergence of Long Noncoding RNAs -- 5.1 Introduction -- 5.2 Cell-Type-Specific Expression of Long Noncoding RNAs and Their Possible Functions -- 5.3 Transcriptional Machinery of Eukaryotic Cells -- 5.4 Divergent Transcription from the Mammalian Genome -- 5.5 Molecular Mechanism of Divergent Transcription -- 5.6 "Chance and Necessity" in Origination of Diverse lncRNAs in the Human Genome -- 5.7 Taxonomy of lncRNAs -- 5.8 Conclusions and Future Prospects -- References -- Chapter 6: Beneath the Veil of Biological Complexity There Lies Long Noncoding RNA: Diverse Utilization of lncRNA in Yeast Genomes -- 6.1 Introduction -- 6.2 lncRNAs of Budding and Fission Yeasts -- 6.3 Epigenetic Regulation of Gene Expression via lncRNA Transcription -- 6.3.1 Co-transcriptional Regulation of Histone Modifications -- 6.3.2 Transcriptional Interplay Between mRNAs and lncRNAs -- 6.4 Noncoding Transcripts Required for Chromosome Integrity -- 6.4.1 Centromeric Transcripts -- 6.4.2 Telomeric Transcripts -- 6.5 Coordinated Transcription of mRNA and lncRNA in Response to Environmental Stimuli -- 6.6 Perspectives -- References -- Chapter 7: Long Noncoding RNAs as Structural and Functional Components of Nuclear Bodies -- 7.1 Introduction -- 7.2 LncRNAs as Structural Components of Nuclear Bodies.
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7.2.1 NEAT1 lncRNA Functions as a Platform for Paraspeckle Formation -- 7.2.2 The Biological Functions of NEAT1 lncRNA -- 7.2.3 Intergenic Spacer (IGS) lncRNAs Are Required for the Formation of Nucleolar Detention Centers (DCs) -- 7.2.4 The Roles of Satellite III (satIII) lncRNAs in Nuclear Stress Body Formation -- 7.2.5 Histone mRNA Precursors in Histone Locus Bodies (HLBs) -- 7.3 LncRNAs as Functional Components of Nuclear Bodies -- 7.3.1 Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) lncRNA in Nuclear Speckles and Taurine Upregulated Gene 1 (TUG1) lncRNA in Polycomb Bodies -- 7.3.2 Gomafu lncRNA Plays a Role in Splicing Factor 1 Retention -- 7.3.3 Prader-Willi Syndrome (PWS) Region Small Nucleolar lncRNAs (sno-lncRNAs) Function as a Molecular Sink for Splicing Factor -- 7.3.4 Colon Cancer Associated Transcript 1 (CCAT1) lncRNA -- 7.3.5 The meiRNA lncRNA Controls Meiosis Initiation in Schizosaccharomyces pombe -- 7.4 Conclusions and Perspectives -- References -- Part IV: Biological Actions of lncRNAs -- Chapter 8: Long Noncoding RNA in Epigenetic Gene Regulation -- 8.1 Introduction -- 8.2 Genomic Imprinting Cluster -- 8.2.1 Igf2 Imprinting Cluster -- 8.2.2 Igf2r Imprinting Cluster -- 8.2.3 Kcnq1 Imprinting Cluster -- 8.2.4 Gnas Imprinting Cluster -- 8.2.5 Dlk1-Dio3 Imprinting Cluster -- 8.2.6 PWS/AS Imprinting Cluster -- 8.3 Conclusions and Future Directions -- References -- Chapter 9: Mechanisms of Long Noncoding Xist RNA-Mediated Chromosome-Wide Gene Silencing in X-Chromosome Inactivation -- 9.1 Introduction -- 9.2 X-Inactivation: Paradigm of lncRNA-Regulated Gene Regulation -- 9.3 Epigenetic Modifications on the Inactive X-Chromosome -- 9.4 Functional Domains of Xist RNA Required for Localization of Xist RNA on the Xi -- 9.5 hnRNP U as Anchor Points for Xist RNA on the Xi.
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9.6 Mechanism of Xist RNA-Induced Gene Silencing in Cis -- 9.7 Mechanism of Chromosome-Wide Spreading of Gene Silencing Across the Inactive X-Chromosome -- 9.8 Conclusions -- References -- Part V: Potential Outcomes for Clinical Medicine -- Chapter 10: Regulation of pRB and p53 Pathways by the Long Noncoding RNAs ANRIL, lincRNA-p21, lincRNA-RoR, and PANDA -- 10.1 Introduction -- 10.2 ANRIL, a Long Noncoding RNA in the INK4 Locus -- 10.2.1 ANRIL and INK4 Locus -- 10.2.2 Transcriptional Regulation of the INK4 Locus by ANRIL -- 10.2.3 Trans-acting Gene Regulation by ANRIL -- 10.2.4 Regulation of ANRIL -- 10.2.5 Association of ANRIL with Disease -- 10.3 lncRNAs Induced by p53 -- 10.3.1 lincRNA-p21 -- 10.3.2 PANDA -- 10.3.3 lincRNA-RoR -- 10.4 Conclusion -- References -- Chapter 11: The Role of Androgen-Regulated Long Noncoding RNAs in Prostate Cancer -- 11.1 Introduction -- 11.1.1 The Emergence of Long Noncoding RNAs in Prostate Cancer Biology -- 11.1.2 Prostate Cancer-Associated Noncoding RNAs -- 11.1.3 Significance of Androgen Signaling in Prostate Cancer -- 11.1.3.1 The Structure and Mechanisms of Action of the Androgen Receptor (AR) -- 11.1.3.2 The Roles of AR in Prostate Cancer Progression -- 11.1.3.3 Model Cells for Investigating AR Signaling in CRPC -- 11.1.4 Diverse Functions of Antisense ncRNAs -- 11.1.5 Global Analysis of the AR-Mediated Transcriptional Program -- 11.1.6 Integrative Analysis to Discover the Androgen-Regulated Transcriptional Program -- 11.2 Identification and Androgen-Regulation of Long Noncoding RNA, CTBP1-AS -- 11.2.1 An Overview of Our Study -- 11.2.2 Cloning and Detection of CTBP1-AS -- 11.2.3 Clinical Significance of CTBP1-AS in Prostate Cancer -- 11.2.3.1 CTBP1-AS Is Upregulated in Prostate Cancer -- 11.2.3.2 Loss of CTBP1 Is Associated with Poor Prognosis of Prostate Cancer Patients.
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11.2.4 CTBP1 Interacts with AR as a Co-repressor -- 11.3 Potential Therapeutic Target of Androgen-Regulated Long Noncoding RNA in Prostate Cancer -- 11.3.1 CTBP1-AS Activates AR Signaling -- 11.3.2 Xenograft Model of Prostate Cancer -- 11.4 Investigation of Nuclear Function of Androgen-Regulated lncRNA -- 11.4.1 CTBP1-AS Induces Histone Deacetylation at CTBP1 Promoter for Transcriptional Repression -- 11.4.2 lncRNA Associated Protein -- 11.4.2.1 Identification of PSF as an Interacting Partner of CTBP1-AS -- 11.4.2.2 Identification of RNA-Associated Proteins by Mass Spectrometry -- 11.5 Functional Analysis of lncRNA -- 11.5.1 Cell Cycle Analysis -- 11.5.1.1 PSF Downstream Signals Regulate Prostate Cancer Cell Cycle Progression -- 11.5.2 Genome-Wide Transcriptional Program -- 11.5.2.1 CTBP1-AS and PSF Function Cooperatively to Modulate Global Androgen Signaling -- 11.5.2.2 ChIP-Sequence Analysis to Determine PSF-Binding Regions -- 11.6 Summary and Future Plan -- 11.6.1 Summary of CTBP1-AS Function -- 11.6.2 Usage of Androgen-Regulated lncRNAs for Therapeutic Targets and Biomarkers of CRPC -- References -- Chapter 12: Macrophage Activation as a Model System for Understanding Enhancer Transcription and eRNA Function -- 12.1 Macrophage Activation as a Model System -- 12.2 Studying Enhancers with High-Throughput Sequencing -- 12.3 Transcription at Enhancers -- 12.4 An Order of Events for Enhancer Transcription -- 12.5 Enhancer Transcription as a Marker of Activity -- 12.6 The Functionality of eRNAs -- 12.7 Concluding Remarks -- References -- Chapter 13: Long Noncoding RNA Functions as a Regulator for Steroid Hormone Receptor-Related Breast and Prostate Cancers -- 13.1 Introduction -- 13.2 Steroid Hormone Receptor Associated lncRNAs -- 13.2.1 SRA -- 13.2.2 Gas5 -- 13.2.3 PCGEM1 and PRNCR1 -- 13.3 eRNA.
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13.4 Other Functional Breast/Prostate Cancer Related lncRNAs.
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