Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA

• Published in: Genome research Vol. 31; no. 7; pp. 1280 - 1289
• Main Authors: Vaisvila, Romualdas, Ponnaluri, V.K. Chaithanya, Sun, Zhiyi, Langhorst, Bradley W., Saleh, Lana, Guan, Shengxi, Dai, Nan, Campbell, Matthew A., Sexton, Brittany S., Marks, Katherine, Samaranayake, Mala, Samuelson, James C., Church, Heidi E., Tamanaha, Esta, Corrêa, Ivan R., Pradhan, Sriharsa, Dimalanta, Eileen T., Evans, Thomas C., Williams, Louise, Davis, Theodore B.
• Format: Journal Article
• Language: English
• Published: New York Cold Spring Harbor Laboratory Press 01.07.2021
• Subjects: Bisulfite; Cytosine; Deoxyribonucleic acid; DNA; DNA fragmentation; DNA methylation; DNA sequencing; Genomics; Method
• ISSN: 1088-9051; 1549-5469; 1549-5469
• DOI: 10.1101/gr.266551.120

Bisulfite sequencing detects 5mC and 5hmC at single-base resolution. However, bisulfite treatment damages DNA, which results in fragmentation, DNA loss, and biased sequencing data. To overcome these problems, enzymatic methyl-seq (EM-seq) was developed. This method detects 5mC and 5hmC using two sets of enzymatic reactions. In the first reaction, TET2 and T4-BGT convert 5mC and 5hmC into products that cannot be deaminated by APOBEC3A. In the second reaction, APOBEC3A deaminates unmodified cytosines by converting them to uracils. Therefore, these three enzymes enable the identification of 5mC and 5hmC. EM-seq libraries were compared with bisulfite-converted DNA, and each library type was ligated to Illumina adaptors before conversion. Libraries were made using NA12878 genomic DNA, cell-free DNA, and FFPE DNA over a range of DNA inputs. The 5mC and 5hmC detected in EM-seq libraries were similar to those of bisulfite libraries. However, libraries made using EM-seq outperformed bisulfite-converted libraries in all specific measures examined (coverage, duplication, sensitivity, etc.). EM-seq libraries displayed even GC distribution, better correlations across DNA inputs, increased numbers of CpGs within genomic features, and accuracy of cytosine methylation calls. EM-seq was effective using as little as 100 pg of DNA, and these libraries maintained the described advantages over bisulfite sequencing. EM-seq library construction, using challenging samples and lower DNA inputs, opens new avenues for research and clinical applications.