RT Journal
A1 Yan, Bo
A1 Wang, Duan
A1 Vaisvila, Romualdas
A1 Sun, Zhiyi
A1 Ettwiller, Laurence
T1 Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
JF Genome Research 
JO Genome Research 
YR 2022 
FD November 01 
VO 32 
IS 11-12 
SP 2079 
OP 2091 
DO 10.1101/gr.277080.122 
UL http://genome.cshlp.org/content/32/11-12/2079.abstract 
AB Covalent modifications of genomic DNA are crucial for most organisms to survive. Amplicon-based high-throughput sequencing technologies erase all DNA modifications to retain only sequence information for the four canonical nucleobases, necessitating specialized technologies for ascertaining epigenetic information. To also capture base modification information, we developed Methyl-SNP-seq, a technology that takes advantage of the complementarity of the double helix to extract the methylation and original sequence information from a single DNA molecule. More specifically, Methyl-SNP-seq uses bisulfite conversion of one of the strands to identify cytosine methylation while retaining the original four-bases sequence information on the other strand. As both strands are locked together to link the dual readouts on a single paired-end read, Methyl-SNP-seq allows detecting the methylation status of any DNA even without a reference genome. Because one of the strands retains the original four nucleotide composition, Methyl-SNP-seq can also be used in conjunction with standard sequence-specific probes for targeted enrichment and amplification. We show the usefulness of this technology in a broad spectrum of applications ranging from allele-specific methylation analysis in humans to identification of methyltransferase specificity in complex bacterial communities.