TY - JOUR
T1 - A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package
AU - Meng, Jia
AU - Lu, Zhiliang
AU - Liu, Hui
AU - Zhang, Lin
AU - Zhang, Shaowu
AU - Chen, Yidong
AU - Rao, Manjeet K.
AU - Huang, Yufei
N1 - Funding Information:
National Natural Science Foundation of China (No. 61170134 ) to S.Z.; National Natural Science Foundation of China (No. 81373469 ) to Z.L.; National Institutes of Health ( NIH-NCIP30CA54174 ) to Y.C.; National Science Foundation ( CCF-0546345 ) to Y.H.; Qatar National Research Fund ( 09-874-3-235 ) to Y.C. and Y.H.; National Natural Science Foundation of China ( 61201408 ) and the Fundamental Research Funds for the Central Universities ( 2014QNA84 ) to H.L.; Jiangsu Natural Science Foundation ( SBK2014041258 ) to J.M.; China Postdoctoral Science Foundation ( 2012M511816 ) and the Fundamental Research Funds for the Central Universities ( 2014QNB47 ) to L.Z.; We thank computational support from the UTSA Computational System Biology Core, funded by the National Institute on Minority Health and Health Disparities ( G12MD007591 ) from the National Institutes of Health.
Publisher Copyright:
© 2014 Elsevier Inc.
Copyright:
Copyright 2015 Elsevier B.V., All rights reserved.
PY - 2014/10/1
Y1 - 2014/10/1
N2 - 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 (m6A) 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.
AB - 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 (m6A) 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.
KW - Differential RNA methylation
KW - ExomePeak
KW - MeRIP-Seq
KW - N6-methyladenosine (m6A)
KW - RNA methylation
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U2 - 10.1016/j.ymeth.2014.06.008
DO - 10.1016/j.ymeth.2014.06.008
M3 - Article
C2 - 24979058
AN - SCOPUS:84927136712
VL - 69
SP - 274
EP - 281
JO - Methods
JF - Methods
SN - 1046-2023
IS - 3
ER -