title: Experimental Approaches for Target Profiling of RNA Cytosine Methyltransferases.
abstract: RNA cytosine methyltransferases (m(5)C-RMTs) constitute an important class of RNA-modifying enzymes, methylating specific cytosines within particular RNA targets in both coding and noncoding RNAs. Almost all organisms express at least one m(5)C-RMT, and vertebrates often express different types or variants of m(5)C-RMTs in different cell types. Deletion or mutation of particular m(5)C-RMTs is connected to severe pathological manifestations ranging from developmental defects to infertility and mental retardation. Some m(5)C-RMTs show spatiotemporal patterns of expression and activity requiring careful experimental design for their analysis in order to capture their context-dependent targets. An essential step for understanding the functions of both the enzymes and the modified cytosines is defining the one-to-one connection between particular m(5)C-RMTs and their target cytosines. Recent technological and methodological advances have provided researchers with new tools to comprehensively explore RNA cytosine methylation and methyltransferases. Here, we describe three complementary approaches applicable for both discovery and validation of candidate target sites of specific m(5)C-RMTs.
authors.affiliation: HHMI, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA; Current address: Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Vahid
authors.initials: V
authors.lastname: Khoddami
authors.affiliation: HHMI, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA.
authors.forename: Archana
authors.initials: A
authors.lastname: Yerra
authors.affiliation: HHMI, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA. Electronic address: brad.cairns@hci.utah.edu.
authors.forename: Bradley R
authors.initials: BR
authors.lastname: Cairns
mesh_terms: D044503:5-Methylcytosine / Q000302:isolation & purification / Q000378:metabolism*; D000818:Animals; D003596:Cytosine / Q000737:chemistry / Q000378:metabolism*; D019175:DNA Methylation / Q000235:genetics; D006801:Humans; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D012359:tRNA Methyltransferases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D044503:5-Methylcytosine; D003596:Cytosine; D012359:tRNA Methyltransferases
keywords: 5-Azacytidine; Aza-IP; Bisulfite sequencing; DNMT2; NSUN family; RNA cytosine methylation