Journal: bioRxiv

Article Title: LEMONmethyl-seq: Targeted long-read DNA methylation profiling reveals dynamics of CRISPR epigenome editing and endogenous DNA methylation patterns

doi: 10.64898/2026.02.24.707761

Figure Lengend Snippet: (a) Comparison of Q5U and KeyPo SE polymerases for LEMONmethyl-seq. Agarose gel of LEMONmethyl PCR products generated from three different primer sets amplifying EM-converted unmethylated lambda DNA. (b) Comparison of Q5U and KeyPo SE across three different primer sets amplifying human genomic loci. Agarose gel of PCR products from LEMONmethyl PCR using ACTB , CLTA , and CD55 primer sets on EM-converted human genomic DNA. (c) EpiMark Taq polymerase and KeyPo SE comparison. Agarose gel of PCR products from amplification across lambda DNA primer set and two human genomic loci, CD55 and CD81 . (d) CD55 PCR amplification efficiency comparison between undigested and restriction enzyme digested gDNA to enrich the target region before EM conversion. For the digested sample, gDNA was digested with EcoNI and BstXI in buffer r3.1 and purified prior to EM conversion. (e) False positive comparison between LEMONmethyl-seq performed with Q5U and KeyPo SE polymerases. LEMONmethyl-seq workflow was performed on control, unmethylated lambda DNA using lambda primer set #3. Any methylation calling corresponds to a false positive.

Article Snippet: PCR amplification of EM-converted DNA was performed with 2 × KeyPo SE Master Mix (Vazyme, PK510-01) according to the manufacturer’s instructions.

Techniques: Comparison, Agarose Gel Electrophoresis, Generated, Lambda DNA Preparation, Amplification, Purification, Control, Methylation