Targeted gene activation using RNA-guided nucleases / Alexander Brown, Wendy S. Woods, and Pablo Perez-Pinera. Knockdown of nuclear-located enhancer RNAs and long ncRNAs using locked nucleic acid GapmeRs / Benoit T. Roux, Mark A. Lindsay, and James A. Heward -- Visualization of enhancer-derived noncoding RNA / Youtaro Shibayama, Stephanie Fanucchi, and Musa M. Mhlanga -- UV-RNA immunoprecipitation (UV-RIP) protocol in neurons / Katie Schaukowitch, Jae-Yeol Joo, and Tae-Kyung Kim -- Mapping long noncoding RNA chromatin occupancy using capture hybridization analysis of RNA targets (CHART) / Keith W. Vance -- Detecting long-range enhancer-promoter interactions by quantitative chromosome conformation capture / Wulan Deng and Gerd A. Blobel -- Deciphering noncoding RNA and chromatin interactions : multiplex chromatin interaction analysis by paired-end tag sequencing (mChIA-PET) / Jocelyn Choy and Melissa J. Fullwood -- Identification of transcribed enhancers by genome-wide chromatin imunoprecipitation sequencing / Steven Blinka [and others] -- Global run-on sequencing (GRO-Seq) / Alessandro Gardini -- Computational approaches for mining GRO-Seq data to identify and characterize active enhancers / Anusha Nagari [and others] -- Evaluating the stability of mRNAs and noncoding RNAs / Ana Carolina Ayupe and Eduardo M. Reis -- Novel method to quantify RNA-protein interactions in situ using FMTRIP and proximity ligation / C. Zurla [and others] -- In silico promoter recognition from deepCAGE data / Xinyi Yang and Annalisa Marsico -- Bioinformatics pipeline for transcriptome sequencing analysis / Sarah Djebali [and others] -- CRISPR/Cas9 genome editing in embryonic stem cells / Guillaume Andrey and Malte Spielmann -- Targeted gene activation using RNA-guided nucleases / Alexander Brown, Wendy S. Woods, and Pablo Perez-Pinera.
Summary:
This volume provides a comprehensive overview of the experimental and computational methodologies used to study the function of long non-coding RNA (ncRNAs) expressed from enhancers. Chapter detail both wet-lab and dry-lab techniques and annotating long ncRNAs and exploring transcription by assessing where transcription starts and generally how it occurs.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, Enhancer RNAs: Methods and Protocols aims to ensure successful results in this rapidly developing field.
Series:
Methods in molecular biology, 1064-3745 ; 1468 Springer protocols, 1949-2448
This resource is supported by the Institute of Museum and Library Services under the provisions of the Library Services and Technology Act as administered by State Library of Iowa.