Supplementary Table S2. Sequencing statistics of hMe-Seal, fC-Seal, hmTOP-seq and foTOP-seq from Distribution and regulatory roles of oxidized 5-methylcytosines in DNA and RNA of the Basidiomycete fungi Laccaria bicolor and Coprinopsis cinerea

The formation of three oxidative DNA 5-methylcytosine (5mC) modifications (oxi-mCs), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), by the TET/JBP family of dioxygenases, prompted intensive studies of their functional roles in mammalian cells. However, the functional interplay of these less abundant modified nucleotides in other eukaryotic lineages remains poorly understood. We carried out a systematic study of the content and distribution of oxi-mCs in DNA and RNA of the basidiomycetes Laccaria bicolor and Coprinopsis cinerea which are established models to study DNA methylation, developmental and symbiotic processes. Quantitative liquid chromatography-tandem mass spectrometry revealed persistent but uneven occurrence of 5hmC, 5fC and 5caC in DNA and RNA of the two organisms, which could be upregulated by vitamin C. 5caC in RNA (5carC) was predominantly found in non-ribosomal RNA fractions which potentially include non-coding, messenger and small RNA species. Mapping of 5hmC and 5fC genome-wide using the single CG analysis techniques hmTOP-seq and foTOP-seq pointed at involvement of oxi-mCs in regulation of gene expression and silencing of transposable elements. The implicated diverse roles of 5mC and oxi-mCs in the two fungi highlight the epigenetic importance of the latter modifications which are often neglected in standard whole-genome bisulfite analyses.