A One-Step Chemoselective Strategy for Hydroxymethylcytosine Sequencing in DNA and RNA.

5-Hydroxymethylcytosine (5hmC) is a relatively stable chemical mark formed by oxidation of 5-methylcytosine in DNA, while its RNA counterparts, 5-hydroxymethylcytidine (hm5C) and 2'-O-methyl-5-hydroxymethylcytidine (hm5Cm), have recently emerged as potential regulators of post-transcriptional processes. Existing 5hmC enrichment methods rely on antibodies or enzymatic β-glucosyltransferase labeling, are largely DNA-specific, and are not readily applicable to RNA. Here we report bisulfite-assisted labeling by thiol sequencing (BALT-seq), a one-step chemoselective strategy that installs a biotin-thioether handle directly onto hydroxymethylcytosine in DNA or RNA under mild acidic bisulfite conditions, without using enzymes. Mechanistic studies show that thiol capture of the bisulfite-activated 5hmC intermediate competes with canonical cytosine-5-methylenesulfonate formation, yielding a stable adduct that DNA polymerases bypass efficiently and that resists APOBEC-mediated deamination. In mouse embryonic stem cells, BALT-seq produces genome-wide 5hmC profiles highly concordant with 5hmC-Seal, TAB-seq, and oxBS-seq, recovers expected gene-body and chromatin-state enrichment, and extends to low-input cell-free DNA. On RNA, BALT-seq enriches hm5C/hm5Cm-containing transcripts more effectively than antibody-based hMeRIP and reveals structured modification landscapes across tRNA species and LINE/LTR repeat families. BALT-seq thus establishes a unified, enzyme-free chemical platform for hydroxymethylcytosine profiling across DNA, cell-free DNA, and RNA.