meRanTK: methylated RNA analysis ToolKit

UNLABELLED The significance and function of posttranscriptional cytosine methylation in poly(A)RNA attracts great interest but is still poorly understood. High-throughput sequencing of RNA treated with bisulfite (RNA-BSseq) or subjected to enrichment techniques like Aza-IP or miCLIP enables transcriptome wide studies of this particular modification at single base pair resolution. However, to date, there are no specialized software tools available for the analysis of RNA-BSseq or Aza-IP data. Therefore, we developed meRanTK, the first publicly available tool kit which addresses the special demands of high-throughput RNA cytosine methylation data analysis. It provides fast and easy to use splice-aware bisulfite sequencing read mapping, comprehensive methylation calling and identification of differentially methylated cytosines by statistical analysis of single- and multi-replicate experiments. Application of meRanTK to RNA-BSseq or Aza-IP data produces accurate results in standard compliant formats. AVAILABILITY AND IMPLEMENTATION meRanTK, source code and test data are released under the GNU GPLv3+ license and are available at http://icbi.at/software/meRanTK/ CONTACT: dietmar.rieder@i-med.ac.at.

[1]  J. Oliver,et al.  MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data , 2013, F1000Research.

[2]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[3]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[4]  R. Micura,et al.  Long non-coding RNAs as targets for cytosine methylation , 2013, RNA biology.

[5]  Frank Lyko,et al.  5-methylcytosine in RNA: detection, enzymatic formation and biological functions , 2009, Nucleic acids research.

[6]  Jernej Ule,et al.  NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs , 2013, Cell reports.

[7]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[8]  Bradley R. Cairns,et al.  Identification of direct targets and modified bases of RNA cytosine methyltransferases , 2013, Nature Biotechnology.

[9]  Frank Lyko,et al.  RNA cytosine methylation analysis by bisulfite sequencing , 2008, Nucleic acids research.

[10]  Jef Rozenski,et al.  The RNA modification database, RNAMDB: 2011 update , 2010, Nucleic Acids Res..

[11]  T. Preiss,et al.  Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA , 2012, Nucleic acids research.

[12]  Lee E. Edsall,et al.  Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.

[13]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[14]  A. Milosavljevic,et al.  Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing , 2014, Nucleic acids research.

[15]  M. Schaefer,et al.  RNA 5-Methylcytosine Analysis by Bisulfite Sequencing. , 2015, Methods in enzymology.

[16]  Vahid Khoddami,et al.  Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP , 2014, Nature Protocols.