This volume details state-of-the-art computational methods designed to manage, analyze, and generally leverage epigenomic and epitranscriptomic data. Chapters guide readers through fine-mapping and quantification of modifications, visual analytics, imputation methods, supervised analysis, and integrative approaches for single-cell data. 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. Cutting-edge and thorough, Computational Epigenomics and Epitranscriptomics aims to provide an overview of epiomic protocols, making it easier for researchers to extract impactful biological insight from their data.

This detailed book describes some of the most recent advances and up-to-date methodologies to detect, quantify, analyze, and elucidate the biological function of different types of RNA modifications. Importantly, the methodologies and tools described herein can be applied to a wide variety of organisms and can be used to address biological and clinical questions. Beginning with a section on bioinformatics tools, the collection continues with sections on detecting RNA modifications using Nanopore direct RNA sequencing, next-generation sequencing approaches, qPCR- and molecular biology-based methods, mass spectrometry- and NMR-based methods, as well as approaches to assess kinetics, determinants, and functions of RNA modifications. Written for the highly successful Methods in Molecular Biology series style, chapters include introduction 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 practical, RNA Modifications: Methods and Protocols serves as an ideal guide for those working directly in the fields of epitranscriptomics and post-transcriptional gene regulation, as well as for scientists and clinicians interested in bioinformatic tools to study RNA modifications and techniques to dissect their roles in physiology and disease. Chapter 20 is available open access under a CC BY 4.0 license.

Following the formulation of the central dogma of molecular biology and the later discovery of classes of non-coding RNAs, the primary focus of Genetics was essentially on variation of DNA aiming at elucidating biological pathways perturbed in diseases. Recently, extensive attention has shifted towards the study of posttranscriptional RNA modifications occurring in both protein-coding as well as non-coding RNAs, revealing a novel and finer layer of complexity in gene regulation. This, in turn, has led to the birth of the novel field of ‘Epitranscriptomics’. The recent increase of applications of high-throughput sequencing technology (HTS) has allowed the unprecedented opportunity to identify on a transcriptome-wide scale, millions of RNA modifications in human genes, counting today more than 140 distinct types such as: methylation (e.g. m6A, m1A, m5C, hm5C, 2’OMe) methylation (e.g. m6A, m1A, m5C, hm5C, 2’OMe), pseudourylation (?), deamination (e.g. A-to-I RNA editing). The scope of this Research Topic was to collect both reviews and research articles addressing the wet lab approaches and bioinformatics methodologies necessary to aid in the identification of novel RNA modifications and characterization of their biological functions. Among the articles embracing the aim of the Research Topic, we have collected four original research and methods articles, five reviews, and a technology article.

This book reviews a novel and exciting field of cellular and molecular biology called epitranscriptomics, which focuses on changes in an organism’s cells resulting from the posttranscriptional modification of cellular RNA. RNA-binding proteins (RBPs) play a crucial role in these posttranscriptional modifications and also support several cellular processes necessary for maintaining RNA homeostasis. Exploring the mechanisms underlying RNA modifications and RBP function is an emerging area of biomedical research, taking the study of gene regulation a step beyond epigenetics. This book reveals that the RNA molecule is not just an information-carrying molecule with some secondary structures. Accordingly, how RNA is modified, regulated, packaged, and controlled is an important aspect. Leading experts address questions such as where the over 170 distinct posttranscriptional RNA modifications are located on the genome, what percentage of mRNAs and noncoding RNAs these modifications include, and how an RNA modification impacts a person’s biology. In closing, the book reviews the role of RNA modifications and RBPs in a variety of diseases and their pathogenesis. Addressing some of the most exciting challenges in epitranscriptomics, this book provides a valuable and engaging resource for researchers in academia and industry studying the phenomena of RNA modification.

The State of the Art in Transcriptome AnalysisRNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript le

This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls. Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA.