The poly(A) tail is a homopolymeric stretch of adenosine at the 3'-end of mature RNA transcripts and its length plays an important role in nuclear export, stability, and translational regulation of mRNA. https://www.selleckchem.com/products/EX-527.html Existing techniques for genome-wide estimation of poly(A) tail length are based on short-read sequencing. These methods are limited because they sequence a synthetic DNA copy of mRNA instead of the native transcripts. Furthermore, they can identify only a short segment of the transcript proximal to the poly(A) tail which makes it difficult to assign the measured poly(A) length uniquely to a single transcript isoform. With the introduction of native RNA sequencing by Oxford Nanopore Technologies, it is now possible to sequence full-length native RNA. A single long read contains both the transcript and the associated poly(A) tail, thereby making transcriptome-wide isoform-specific poly(A) tail length assessment feasible. We developed tailfindr-an R-based package for estimating poly(A) tail length from Oxford Nanopore sequencing data. In this chapter, we describe in detail the pipeline for transcript isoform-specific poly(A) tail profiling based on native RNA Nanopore sequencing-from library preparation to downstream data analysis with tailfindr.RNA-seq using long-read sequencing, such as nanopore and SMRT (Single Molecule, Real-Time) sequencing, enabled the identification of the full-length structure of RNA molecules. Several tools for long-read RNA-seq were developed recently. In this section, we introduce an analytical pipeline of long-read RNA-seq for isoform identification and the estimation of expression levels using minimap2, TranscriptClean, and TALON. We applied this pipeline to the public direct RNA-seq data of the HAP1 and HEK293 cell lines to identify transcript isoforms which can be detected only using long-read RNA-seq data.N6-Methyladenosine (m6A) is the most prevalent posttranscriptional modification in eukaryotes and plays a pivotal role in various biological processes, such as splicing, RNA degradation, and RNA-protein interaction. Accurately identification of the location of m6A is essential for related downstream studies. In this chapter, we introduce a prediction framework WHISTLE, which enables us to acquire so far the most accurate map of the transcriptome-wide human m6A RNA-methylation sites (with an average AUC 0.948 and 0.880 under the full transcript or mature messenger RNA models, respectively, when tested on independent datasets). Besides, each individual m6A site was also functionally annotated according to the "guilt-by-association" principle by integrating RNA methylation data, gene expression data and protein-protein interaction data. A web server was constructed for conveniently querying the predicted RNA methylation sites and their putative biological functions. The website supports the query by genes, by GO function, table view, and the download of all the functionally annotated map of predicted map of human m6A epitranscriptome. The WHISTLE web server is freely available at www.xjtlu.edu.cn/biologicalsciences/whistle and http//whistle-epitranscriptome.com .N6-methyladenosine (m6A) is the most prevalent posttranscriptional modification in eukaryotes and plays a pivotal role in various biological processes. A knowledge base with the systematic collection and curation of context specific transcriptome-wide methylations is critical for elucidating their biological functions as well as for developing bioinformatics tools. In this chapter, we present a comprehensive platform MeT-DB V2.0 for elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome. Met-DB V2.0 database contains context specific m6A peaks and single-base sites predicted from 185 samples for 7 species from 26 independent studies. Moreover, it is also integrated with a new database for targets of m6A readers, erasers and writers and expanded with more collections of functional data. The Met-DB V2.0 web interface and genome browser provide more friendly, powerful, and informative ways to query and visualize the data. More importantly, MeT-DB V2.0 offers for the first time a series of tools specifically designed for understanding m6A functions. The MeT-DB V2.0 web server is freely available at http//compgenomics.utsa.edu/MeTDB and www.xjtlu.edu.cn/metdb2 .MODOMICS is an established database of RNA modifications that provides comprehensive information concerning chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. This chapter covers the resources available on MODOMICS web server and the basic steps that can be undertaken by the user to explore them. MODOMICS is available at http//www.genesilico.pl/modomics .A-to-I RNA editing in humans plays a relevant role since it can influence gene expression and increase proteome diversity. In addition, its deregulation has been linked to a variety of human diseases, including neurological disorders and cancer.In the last decade, massive transcriptome sequencing through the RNAseq technology has dramatically improved the investigation of RNA editing at single nucleotide resolution. Nowadays, different bioinformatics resources to discover and/or collect A-to-I events have been released. Hereafter, we initially provide an overview of the state-of-the-art RNA editing databases and, then, we focus on REDIportal, the largest collection of A-to-I events with more than 4.5 million sites from 2660 humans GTEx samples.Circular RNA (or circRNA) is a type of single-stranded covalently closed circular RNA molecule and play important roles in diverse biological pathways. A comprehensive functionally annotated circRNA database will help to understand the circRNAs and their functions. CircFunBase is such a web-accessible database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions. CircFunBase provides visualized circRNA-miRNA interaction networks. In addition, a genome browser is provided to visualize the genome context of circRNA. In this chapter, we illustrate examples of searching for circRNA and getting detailed information of circRNA. Moreover, other circRNA related databases are outlined.