Open AccessLong-range single-molecule mapping of chromatin accessibility in eukaryotes
Author(s) -
Zohar Shipony,
Georgi K. Marinov,
Matthew P. Swaffer,
Nicholas A. SinnottArmstrong,
Jan M. Skotheim,
Anshul Kundaje,
William J. Greenleaf
Publication year - 2020
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/s41592-019-0730-2
Subject(s) - chromatin , nucleosome , chia pet , computational biology , nanopore sequencing , chip sequencing , biology , chromatin remodeling , genetics , dna , histone modifying enzymes , dna methylation , dna sequencing , gene , gene expression
Mapping open chromatin regions has emerged as a widely used tool for identifying active regulatory elements in eukaryotes. However, existing approaches, limited by reliance on DNA fragmentation and short-read sequencing, cannot provide information about large-scale chromatin states or reveal coordination between the states of distal regulatory elements. We have developed a method for profiling the accessibility of individual chromatin fibers, a single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq), enabling the simultaneous, high-resolution, single-molecule assessment of chromatin states at multikilobase length scales. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases with low sequence specificity, in this case EcoGII, an N 6 -methyladenosine (m 6 A) methyltransferase, and the ability of nanopore sequencing to directly read DNA modifications. We demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule nucleosome and transcription factor protection footprints, and quantify the correlation between chromatin states of distal genomic elements.