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Methods. 2014 Oct 1;69(3):274-81. doi: 10.1016/j.ymeth.2014.06.008. Epub 2014 Jun 27.

A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.

Author information

1
Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China. Electronic address: jia.meng@xjtlu.edu.cn.
2
Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China.
3
School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou 221116, China.
4
School of Automation, Northwestern Polytechnical University, Xi'an 710072, China.
5
Department of Cellular Structural Biology, University of Texas Health Science Center at San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, TX 78229, USA.
6
Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, TX 78229, USA; Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, TX 78229, USA.
7
Department of Electrical and Computer Engineering, University of Texas at San Antonio, TX 78249, USA; Department of Cellular Structural Biology, University of Texas Health Science Center at San Antonio, TX 78229, USA. Electronic address: yufei.huang@utsa.edu.

Abstract

Despite the prevalent studies of DNA/Chromatin related epigenetics, such as, histone modifications and DNA methylation, RNA epigenetics has not drawn deserved attention until a new affinity-based sequencing approach MeRIP-Seq was developed and applied to survey the global mRNA N6-methyladenosine (m(6)A) in mammalian cells. As a marriage of ChIP-Seq and RNA-Seq, MeRIP-Seq has the potential to study the transcriptome-wide distribution of various post-transcriptional RNA modifications. We have previously developed an R/Bioconductor package 'exomePeak' for detecting RNA methylation sites under a specific experimental condition or the identifying the differential RNA methylation sites in a case control study from MeRIP-Seq data. Compared with other relatively well studied data types such as ChIP-Seq and RNA-Seq, the study of MeRIP-Seq data is still at very early stage, and existing protocols are not optimized for dealing with the intrinsic characteristic of MeRIP-Seq data. We therein provide here a detailed and easy-to-use protocol of using exomePeak R/Bioconductor package along with other software programs for analysis of MeRIP-Seq data, which covers raw reads alignment, RNA methylation site detection, motif discovery, differential RNA methylation analysis, and functional analysis. Particularly, the rationales behind each processing step as well as the specific method used, the best practice, and possible alternative strategies are briefly discussed. The exomePeak R/Bioconductor package is freely available from Bioconductor: http://www.bioconductor.org/packages/release/bioc/html/exomePeak.html.

KEYWORDS:

Differential RNA methylation; MeRIP-Seq; N6-methyladenosine (m6A); RNA methylation; exomePeak

PMID:
24979058
PMCID:
PMC4194139
DOI:
10.1016/j.ymeth.2014.06.008
[Indexed for MEDLINE]
Free PMC Article

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