Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing

5-Methylcytosine (m5C) is one of the major post-transcriptional modifications in mRNA and is highly involved in the pathogenesis of various diseases. However, the capacity of existing assays for accurately and comprehensively transcriptome-wide m5C mapping still needs improvement. Here, we developed a deaminase and reader protein assisted RNA methylation analysis, termed DRAM, in which deaminases (APOBEC1 and TadA-8e) are fused with m5C reader proteins (ALYREF and YBX1) to identify the m5C sites through deamination events neighboring the methylation sites. This antibody-free and bisulfite-free approach provided transcriptome-wide editing regions which were highly overlapped with the publicly available BS-seq datasets. Notably, DRAM-seq even discovered a new m5C methylation locus in KAT7, a previously demonstrated key aging regulator. In addition, DRAM system even supports ultra-low input RNA (10ng) and monitor the dynamic accumulation of cellular m5C. We anticipated that the DRAM system could pave the way for uncovering further biological functions of m5C modifications.