Promoter Associated RNA

This volume is divided in four sections; covering genome wide approaches, techniques for characterize of paRNA structural features are described, selecting pa-RNA, and paRNA therapeutic potential. Chapters describe how siRNAsdirected against paRNAs can be applied in vivo to modulate transcription of important genes controlled by paRNAs. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Promoter Associated RNA: Methods and Protocols aims to demonstrate paRNAs as new class of regulatory molecules, to further investigate and value as tools for fine transcriptional tuning.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts Includes supplementary material: sn.pub/extras

Inhalt

ChIP-seq for the Identification of Functional Elements in the Human Genome.- Identification of Candidate Functional Elements in the Genome from ChIP-seq Data.- GRO-seq, A Tool for Identification of Transcripts Regulating Gene Expression.-NanoCAGE: A Method for the Analysis of Coding and Non-coding 5'-capped Transcriptomes.- Deep Cap Analysis of Gene Expression (CAGE): Genome-Wide Identification of Promoters, Quantification of their Activity Andtranscriptional Network Inference.- Deep-RACE: Comprehensive Search for Novel ncRNAs Associated to a Specific Locus.- In silico Prediction of RNA Secondary Structure.- Computational Prediction of RNA-Protein Interactions.- Isolation of Nuclear RNA-Associated Protein Complexes.- Identification of Long Non-Coding RNAs Associated to Human Disease Susceptibility.- Targeting Promoter-associated RNAs by siRNAs.- RNA-FISH to Study Regulatory RNA at the Site of Transcription.- Detection and Characterization of R Loop Structures.- Induction of Transcriptional Gene Silencing by Expression of shRNA Directed to c-Myc P2 Promoter in Hepatocellular Carcinoma by Tissue Specific Virosomal Delivery.- Targeting Promoter Associated Non-coding RNA In Vivo.- Manipulation of Promoter-Associated Noncoding RNAs in Mouse Early Embryos for Controlling Sequence-Specific Epigenetic Status.