RT Journal
A1 Sun, Zhiyi
A1 Vaisvila, Romualdas
A1 Hussong, Laura-Madison
A1 Yan, Bo
A1 Baum, Chloé
A1 Saleh, Lana
A1 Samaranayake, Mala
A1 Guan, Shengxi
A1 Dai, Nan
A1 Corrêa, Ivan R.
A1 Pradhan, Sriharsa
A1 Davis, Theodore B.
A1 Evans, Thomas C.
A1 Ettwiller, Laurence M.
T1 Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
JF Genome Research 
JO Genome Research 
YR 2021 
FD February 01 
VO 31 
IS 2 
SP 291 
OP 300 
DO 10.1101/gr.265306.120 
UL http://genome.cshlp.org/content/31/2/291.abstract 
AB The predominant methodology for DNA methylation analysis relies on the chemical deamination by sodium bisulfite of unmodified cytosine to uracil to permit the differential readout of methylated cytosines. Bisulfite treatment damages the DNA, leading to fragmentation and loss of long-range methylation information. To overcome this limitation of bisulfite-treated DNA, we applied a new enzymatic deamination approach, termed enzymatic methyl-seq (EM-seq), to long-range sequencing technologies. Our methodology, named long-read enzymatic modification sequencing (LR-EM-seq), preserves the integrity of DNA, allowing long-range methylation profiling of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) over multikilobase length of genomic DNA. When applied to known differentially methylated regions (DMRs), LR-EM-seq achieves phasing of >5 kb, resulting in broader and better defined DMRs compared with that previously reported. This result showed the importance of phasing methylation for biologically relevant questions and the applicability of LR-EM-seq for long-range epigenetic analysis at single-molecule and single-nucleotide resolution.