RT Journal Article
SR Electronic
T1 Single-molecule long-read sequencing reveals the chromatin basis of gene expression
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 533158
DO 10.1101/533158
A1 Yunhao Wang
A1 Anqi Wang
A1 Zujun Liu
A1 Andrew Thurman
A1 Linda S. Powers
A1 Meng Zou
A1 Adam Hefel
A1 Yunyi Li
A1 Joseph Zabner
A1 Kin Fai Au
YR 2019
UL http://biorxiv.org/content/early/2019/01/29/533158.abstract
AB Genome-wide chromatin accessibility and nucleosome occupancy profiles have been widely investigated, while the long-range dynamics remains poorly studied at the single-cell level. Here we present a new experimental approach MeSMLR-seq (methyltransferase treatment followed by single-molecule long-read sequencing) for long-range mapping of nucleosomes and chromatin accessibility at single DNA molecules, and thus achieve comprehensive-coverage characterization of the corresponding heterogeneity. We applied MeSMLR-seq to haploid yeast, where single DNA molecules represent single cells, and thus we could investigate the combinatorics of many (up to 356) nucleosomes at long range in single cells. We illustrated the differential organization principles of nucleosomes surrounding transcription start site for silently- and actively-transcribed genes, at the single-cell level and in the long-range scale. The heterogeneous patterns of chromatin statuses spanning multiple genes were phased. Together with single-cell RNA-seq data, we quantitatively revealed how chromatin accessibility correlated with gene transcription positively in a highly-heterogeneous scenario. Moreover, we quantified the openness of promoters and investigated the coupled chromatin changes of adjacent genes at single DNA molecules during transcription reprogramming.