Identifying mRNA editing deaminase targets by RNA-Seq.

  title={Identifying mRNA editing deaminase targets by RNA-Seq.},
  author={Brad R. Rosenberg and Scott B. Dewell and F. Nina Papavasiliou},
  journal={Methods in molecular biology},
RNA editing deaminases act on a variety of targets in different organisms. A number of such enzymes have been shown to act on mRNA, with the resultant nucleotide changes modifying a transcript's information content. Though the deaminase activity of mRNA editing enzymes is readily demonstrated in vitro, identifying their physiological targets has proved challenging. Recent advances in ultra high-throughput sequencing technologies have allowed for whole transcriptome sequencing and expression… 

Parallel Evolution and Lineage-Specific Expansion of RNA Editing in Ctenophores.

Despite their compact genomes, a wide variety of epigenomic mechanisms employed by ctenophores and other non-bilaterian basal metazoans can provide novel insights into the evolutionary origins of biological novelties.

When MicroRNAs Meet RNA Editing in Cancer: A Nucleotide Change Can Make a Difference

  • Yumeng WangHan Liang
  • Biology
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 2018
The current knowledge of miRNA editing in cancer is summarized, the mechanisms on how miRNA‐related editing events modulate the initiation and progression of human cancer are discussed, and the challenges and future directions of studying miRNAs are discussed.

Transposase mediated construction of RNA-seq libraries.

Two transposon-based methods that efficiently construct high-quality RNA-seq libraries from double-stranded cDNA with only two enzymatic reactions are presented.

Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver

These studies define selective, tissue-specific targets of Apobec-1-dependent RNA editing and show the functional consequences of editing are both transcript- and tissue- specific.

Epitranscriptomics of cardiovascular diseases (Review)

This review aimed to provide an overview of the most recent findings of key epitranscriptomic modifications in both coding and non-coding RNAs, and the methods used for their detection and important associations with genetic variations in the context of CVD.

Transposase mediated construction of RNA-seq libraries Material Supplemental

This paper is distributed exclusively by Cold Spring Harbor Laboratory Press for the first time and is distributed at a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described.

Towards a Systems Immunology Approach to Understanding Correlates of Protective Immunity against HCV

This review focuses on recent progress in understanding immunity to HCV using systems biology, specifically transcriptomic and epigenetic studies and proposed strategies moving forward towards an integrated systems immunology approach for predicting and evaluating the efficacy of the next generation of HCV vaccines.



Editor meets silencer: crosstalk between RNA editing and RNA interference

  • K. Nishikura
  • Biology
    Nature Reviews Molecular Cell Biology
  • 2006
A→I RNA editing seems to have additional functions, including the regulation of retrotransposons and gene silencing, which adds a new urgency to the challenges of fully understanding ADAR functions.

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

An unbiased genome-wide approach was used to identify 239 sites (in 207 target genes), with stringent criteria for editing, which included 10 of the 13 known edited genes and suggested that many more human genes may be edited at lower frequencies.

TopHat: discovering splice junctions with RNA-Seq

The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer.

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3′ untranscribed regions, as well as new candidate microRNA precursors.

Targeted Disruption of the Mouse apobec-1 Gene Abolishes Apolipoprotein B mRNA Editing and Eliminates Apolipoprotein B48 (*)

A site-specific C to U editing reaction modifies nuclear apolipoprotein B100 (apoB100) mRNA, producing apolipoprotein B48 in the mammalian small intestine. This reaction is mediated by a

Detection of Undegraded Oligonucleotides in Vivo by Fluorescence Resonance Energy Transfer

The results indicated that unfertilized sea urchin eggs had nucleolytic activity and analysis in vitro on supernatant of the egg homogenate indeed demonstrated the existence of nucleases.

The Sequence Alignment/Map format and SAMtools

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

A quantitative sequencing-based method is developed for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome, and it is demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.