RNA-RNA and RNA-DNA Interactions

by Chao Zeng, Michiaki Hamada (Editor), Tsukasa Fukunaga (Editor)

Overview

This comprehensive book covers RNA-RNA and RNA-DNA interactions from experimental techniques to information technology. Chapter detail experimental approaches to study RNA-RNA and RNA-DNA Interactions and computational approaches to STUDY RNA-RNA and RNA-DNA Interactions. Written in the highly successful Methods in Molecular Biology series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory prools, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, RNA-RNA and RNA-DNA Interactions provides knowledge and tools necessary for researchers to explore the fascinating study of RNA-RNA and RNA-DNA interactions.

Product Details

ISBN-13:	9781071646694
Publisher:	Springer US
Publication date:	09/14/2025
Series:	Methods in Molecular Biology , #2949
Pages:	220
Product dimensions:	7.01(w) x 10.00(h) x (d)

Table of Contents

Protein-centric mapping of RNA-DNA interactions with RedChIP.- Mapping of RBP-mediated RNA-RNA interactome with RIC-seq.- Integrated analysis of crosslink-ligation data for the detection of RNA 2D/3D structures and interactions in vivo.- ChRD-PET: A method for mapping RNA-DNA interactions.- ADAR1 RNA editing enzyme regulates telomeric R-loop formation.- Tethered function assay for analyzing PIWI-piRNA-mediated co-transcriptional silencing.- LncRNA:DNA binding prediction using LongTarget and its revised version.- Prediction of RNA joint secondary structures based on integer programming.- Thorough RNA interactome data analysis based on Direct Duplex Detection data.- HybridMPI/OpenMP implementation of RIblast for transcriptome-scale lncRNA–RNA interaction prediction.- Target RNA recognition of microRNA-mediated RNA silencing.- Unveiling functional long-range RNA structures via RIC-seq analysis.- In silico design of interacting RNA sequences using the MODENA web server.- Machine learning approaches for predicting RNA-RNA/DNA interactions.- Identification and sequence characterization of semi-extractable RNAs.