RT Journal
A1 Spektor, Roman
A1 Tippens, Nathaniel D.
A1 Mimoso, Claudia A.
A1 Soloway, Paul D.
T1 methyl-ATAC-seq measures DNA methylation at accessible chromatin
JF Genome Research 
JO Genome Research 
YR 2019 
FD June 01 
VO 29 
IS 6 
SP 969 
OP 977 
DO 10.1101/gr.245399.118 
UL http://genome.cshlp.org/content/29/6/969.abstract 
AB Chromatin features are characterized by genome-wide assays for nucleosome location, protein binding sites, three-dimensional interactions, and modifications to histones and DNA. For example, assay for transposase accessible chromatin sequencing (ATAC-seq) identifies nucleosome-depleted (open) chromatin, which harbors potentially active gene regulatory sequences; and bisulfite sequencing (BS-seq) quantifies DNA methylation. When two distinct chromatin features like these are assayed separately in populations of cells, it is impossible to determine, with certainty, where the features are coincident in the genome by simply overlaying data sets. Here, we describe methyl-ATAC-seq (mATAC-seq), which implements modifications to ATAC-seq, including subjecting the output to BS-seq. Merging these assays into a single protocol identifies the locations of open chromatin and reveals, unambiguously, the DNA methylation state of the underlying DNA. Such combinatorial methods eliminate the need to perform assays independently and infer where features are coincident.