title: Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity.
abstract: Ribose methylation is one of the two most abundant modifications in human ribosomal RNA and is believed to be important for ribosome biogenesis, mRNA selectivity and translational fidelity. We have applied RiboMeth-seq to rRNA from HeLa cells for ribosome-wide, quantitative mapping of 2'-O-Me sites and obtained a comprehensive set of 106 sites, including two novel sites, and with plausible box C/D guide RNAs assigned to all but three sites. We find approximately two-thirds of the sites to be fully methylated and the remainder to be fractionally modified in support of ribosome heterogeneity at the level of RNA modifications. A comparison to HCT116 cells reveals similar 2'-O-Me profiles with distinct differences at several sites. This study constitutes the first comprehensive mapping of 2'-O-Me sites in human rRNA using a high throughput sequencing approach. It establishes the existence of a core of constitutively methylated positions and a subset of variable, potentially regulatory positions, and paves the way for experimental analyses of the role of variations in rRNA methylation under different physiological or pathological settings.
authors.affiliation: Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200N, Denmark.
authors.forename: Nicolai
authors.initials: N
authors.lastname: Krogh
authors.affiliation: Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark.
authors.forename: Martin D
authors.initials: MD
authors.lastname: Jansson
authors.affiliation: Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark.
authors.forename: Sophia J
authors.initials: SJ
authors.lastname: Häfner
authors.affiliation: Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark.
authors.forename: Disa
authors.initials: D
authors.lastname: Tehler
authors.affiliation: Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200N, Denmark.
authors.forename: Ulf
authors.initials: U
authors.lastname: Birkedal
authors.affiliation: Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200N, Denmark.
authors.forename: Mikkel
authors.initials: M
authors.lastname: Christensen-Dalsgaard
authors.affiliation: Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark anders.lund@bric.ku.dk.
authors.forename: Anders H
authors.initials: AH
authors.lastname: Lund
authors.affiliation: Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200N, Denmark hamra@sund.ku.dk.
authors.forename: Henrik
authors.initials: H
authors.lastname: Nielsen
mesh_terms: D001483:Base Sequence; D045325:HCT116 Cells; D006367:HeLa Cells; D006801:Humans; D008745:Methylation; D012335:RNA, Ribosomal / Q000378:metabolism*; D020537:RNA, Small Nucleolar / Q000378:metabolism; D015203:Reproducibility of Results; D012270:Ribosomes / Q000378:metabolism*; D017423:Sequence Analysis, RNA
chemical_list: D012335:RNA, Ribosomal; D020537:RNA, Small Nucleolar