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Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania.

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Kawasaki, Fumiko 
Beraldi, Dario 
Hardisty, Robyn E 
McInroy, Gordon R 


BACKGROUND: 5-Hydroxymethyluracil (5hmU) is a thymine base modification found in the genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we develop a method for the genome-wide mapping of 5hmU-modified loci based on a chemical tagging strategy for the hydroxymethyl group. RESULTS: We apply the method to generate genome-wide maps of 5hmU in the parasitic protozoan Leishmania sp. In this genus, another thymine modification, 5-(β-glucopyranosyl) hydroxymethyluracil (base J), plays a key role during transcription. To elucidate the relationship between 5hmU and base J, we also map base J loci by introducing a chemical tagging strategy for the glucopyranoside residue. Observed 5hmU peaks are highly consistent among technical replicates, confirming the robustness of the method. 5hmU is enriched in strand switch regions, telomeric regions, and intergenic regions. Over 90% of 5hmU-enriched loci overlapped with base J-enriched loci, which occurs mostly within strand switch regions. We also identify loci comprising 5hmU but not base J, which are enriched with motifs consisting of a stretch of thymine bases. CONCLUSIONS: By chemically detecting 5hmU we present a method to provide a genome-wide map of this modification, which will help address the emerging interest in the role of 5hmU. This method will also be applicable to other organisms bearing 5hmU.



5-Formyluracil (5fU), 5-Hydroxymethyluracil (5hmU), Base J, Genome-wide mapping, Leishmania donovani, Leishmania major, Chromosome Mapping, DNA, Protozoan, Glucosides, Leishmania, Pentoxyl, Uracil

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Genome Biology

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Wellcome Trust (099232/Z/12/Z)
FK is supported by the Wellcome Trust, DB is supported by the Herchel Smith Fund, REH is supported by the University of Cambridge and the Herchel Smith Fund, GRM was supported by Trinity College and the Herchel Smith fund, PVD is supported by Marie Curie fellowship and the Wellcome Trust. The Balasubramanian group is core-funded by a Wellcome Trust Senior Investigator Award (099232/Z/12/Z) and Cancer Research UK(C14303/A17197).