title: Genome-wide detection of high abundance N6-methyladenosine sites by microarray.
abstract: N(6)-methyladenosine (m(6)A), the most abundant internal RNA modification, functions in diverse biological processes, including regulation of embryonic stem cell self-renewal and differentiation. As yet, methods to detect m(6)A in the transcriptome rely on the availability and quality of an m(6)A antibody and are often associated with a high rate of false positives. Here, based on our observation that m(6)A interferes with A-T/U pairing, we report a microarray-based technology to map m(6)A sites in mouse embryonic stem cells. We identified 72 unbiased sites exhibiting high m(6)A levels from 66 PolyA RNAs. Bioinformatics analyses suggest identified sites are enriched on developmental regulators and may in some contexts modulate microRNA/mRNA interactions. Overall, we have developed microarray-based technology to capture highly enriched m(6)A sites in the mammalian transcriptome. This method provides an alternative means to identify m(6)A sites for certain applications.
authors.affiliation: Department of Computer Science, University of Toronto, Toronto M5S 3G4, Canada.
authors.forename: Yue
authors.initials: Y
authors.lastname: Li
authors.affiliation: Tumor Initiation and Maintenance Program, Sanford Burnham Medical Research Institute, San Diego, California 92037, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Computer Science, University of Toronto, Toronto M5S 3G4, Canada Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto M5S 3E1, Canada.
authors.forename: Zhaolei
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Department of Biology, San Diego State University, San Diego, California, 92115, USA.
authors.forename: Alicia Viridiana
authors.initials: AV
authors.lastname: Zamudio
authors.affiliation: Tumor Initiation and Maintenance Program, Sanford Burnham Medical Research Institute, San Diego, California 92037, USA.
authors.forename: Jing Crystal
authors.initials: JC
authors.lastname: Zhao
mesh_terms: D000241:Adenosine / Q000031:analogs & derivatives* / Q000378:metabolism; D000818:Animals; D020029:Base Pairing; D002460:Cell Line; D019295:Computational Biology / Q000379:methods; D053595:Embryonic Stem Cells / Q000166:cytology*; D020869:Gene Expression Profiling / Q000379:methods*; D055106:Genome-Wide Association Study; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000032:analysis* / Q000737:chemistry
chemical_list: D012333:RNA, Messenger; C010223:N-methyladenosine; D000241:Adenosine
keywords: METTL14; METTL3; N6-methyladenosine; RNA methylation; mouse embryonic stem cells; two-color microarray