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

ABSTRACT: 5-hydroxymethyluracil (5hmU) is a thymine base modification found in genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we developed a method for the genome-wide mapping of 5hmU-modified loci based on a chemical tagging strategy for the hydroxymethyl group. We applied the method to generate genome-wide maps of 5hmU in parasitic protozoan Leishmania, where 5hmU forms enzymatically via hydroxylation of thymine. In the genus, another thymine modification 5-(β-glucopyranosyl) hydroxymethyluracil (base J) plays key roles during transcription. To elucidate relationships between 5hmU and base J, we also mapped base J loci by introducing a chemical tagging strategy for the glucopyranoside residue. Results: Observed 5hmU peaks were highly consistent among technical replicates, confirming the robustness of the method. 5hmU were particularly enriched in strand switch regions, telomeric regions and intergenic regions. Over 90% of 5hmU-enriched loci overlapped with base J-enriched loci, which occurred mostly within strand switch regions. We also identified loci comprising 5hmU but not base J. These 5hmU-specific loci were enriched with motifs consisting of a stretch of thymine bases and associated with higher RNA levels. Conclusions: By chemically detecting 5hmU we provide the first genome-wide map of 5hmU, which will help addressing the emerging interest in the role of 5hmU. The presence of 5hmU-specific loci may suggest that 5hmU has unique roles.

ORGANISM(S): Leishmania major Leishmania donovani

PROVIDER: GSE83384 | GEO | 2016/12/15

SECONDARY ACCESSION(S): PRJNA325744

REPOSITORIES: GEO

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