EM-seq: Detection of DNA Methylation at Single Base Resolution from Picograms of DNA

Vaisvila, R.; Ponnaluri, V. K. C.; Sun, Z.; Langhorst, B. W.; Saleh, L.; Guan, S.; Dai, N.; Campbell, M. A.; Sexton, B. S.; Marks, K.; Samaranayake, M.; Samuelson, J. C.; Church, H. E.; Tamanaha, E.; Correa, I. R.; Pradhan, S.; Dimalanta, E. T.; Evans, T. C.; Williams, L.; Davis, T. B.

doi:10.1101/2019.12.20.884692

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bioRxiv · 10.1101/2019.12.20.884692

EM-seq: Detection of DNA Methylation at Single Base Resolution from Picograms of DNA

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Abstract

Bisulfite sequencing is widely used to detect 5mC and 5hmC at single base resolution. However, bisulfite treatment damages DNA resulting in fragmentation, loss of DNA and biased sequencing data. To overcome this, we developed Enzymatic Methyl-seq (EM-seq), an enzymatic based approach that uses as little as 100 pg of DNA. EM-seq outperformed bisulfite converted libraries in all metrics examined including coverage, duplication, sensitivity and nucleotide composition. EM-seq libraries displayed even GC distribution, improved correlation across input amounts as well as increased representation of genomic features. These data indicate that EM-seq is more accurate and reliable than whole genome bisulfite sequencing (WGBS).

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Vaisvila, R., Ponnaluri, V. K. C., Sun, Z., Langhorst, B. W., Saleh, L., Guan, S., Dai, N., Campbell, M. A., Sexton, B. S., Marks, K., Samaranayake, M., Samuelson, J. C., Church, H. E., Tamanaha, E., Correa, I. R., Pradhan, S., Dimalanta, E. T., Evans, T. C., Williams, L., Davis, T. B.. 2019-12-23. EM-seq: Detection of DNA Methylation at Single Base Resolution from Picograms of DNA. https://doi.org/10.1101/2019.12.20.884692

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