Open AccessDiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide
Author(s) -
Nicolas Altemose,
Annie Maslan,
Owen K. Smith,
Kousik Sundararajan,
Rachel Brown,
Reet Mishra,
Angela M. Detweiler,
Norma Neff,
Karen H. Miga,
Aaron F. Straight,
Aaron Streets
Publication year - 2022
Publication title -
nature methods
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 19.469
H-Index - 318
eISSN - 1548-7105
pISSN - 1548-7091
DOI - 10.1038/s41592-022-01475-6
Subject(s) - biology , methylated dna immunoprecipitation , chromatin , dna methylation , dna sequencing , computational biology , centromere , dna , genome , single molecule real time sequencing , genetics , dna nanoball sequencing , epigenomics , histone , cpg site , chip sequencing , nucleosome , genomic library , gene , dna sequencer , gene expression , chromosome , base sequence
Studies of genome regulation routinely use high-throughput DNA sequencing approaches to determine where specific proteins interact with DNA, and they rely on DNA amplification and short-read sequencing, limiting their quantitative application in complex genomic regions. To address these limitations, we developed directed methylation with long-read sequencing (DiMeLo-seq), which uses antibody-tethered enzymes to methylate DNA near a target protein's binding sites in situ. These exogenous methylation marks are then detected simultaneously with endogenous CpG methylation on unamplified DNA using long-read, single-molecule sequencing technologies. We optimized and benchmarked DiMeLo-seq by mapping chromatin-binding proteins and histone modifications across the human genome. Furthermore, we identified where centromere protein A localizes within highly repetitive regions that were unmappable with short sequencing reads, and we estimated the density of centromere protein A molecules along single chromatin fibers. DiMeLo-seq is a versatile method that provides multimodal, genome-wide information for investigating protein-DNA interactions.