CUT&Tag-BS: an efficient and low-cost method for simultaneous profiling of histone modification and DNA methylation

It remains a challenge to decipher the complex relationship between DNA methylation, histone modification, and the underlying DNA sequence with limited input material. Here, we developed an efficient, low-input, and low-cost method for simultaneous profiling of genomic binding sites of histone modification and methylation status of the underlying DNA at single-base resolution from the same cells in a single experiment by integrating CUT&Tag with tagmentation-based bisulfite sequencing (CUT&Tag-BS). We demonstrated the validity of our method for both active and repressive histone modifications using 250,000 mouse ESCs. CUT&Tag-BS showed similar enrichment patterns of histone modification to those observed in non-bisulfite-treated control; it further revealed that H3K4me1-marked regions are mostly CpG-poor, lack of methylation concordance, and exhibit prevalent DNA methylation heterogeneity among the cells. We anticipate that CUT&Tag-BS will be widely applied to directly address the genomic relationship between DNA methylation and histone modification, especially in low-input scenario with precious biological samples. Overall design: CUT&Tag-BS was performed for H3K4me1, H3K9me3, and H3K27me3 using 250,000 (or fewer) mouse E14 embryonic stem cells. The resulting libraries were sequenced with either paired-end 35-bp (run1) or 75-bp reads (run2). To benchmark our method, we also prepared corresponding non-bisulfite-treated CUT&Tag libraries as controls.