TY - JOUR T1 - Single-molecule long-read sequencing reveals the chromatin basis of gene expression JF - bioRxiv DO - 10.1101/533158 SP - 533158 AU - Yunhao Wang AU - Anqi Wang AU - Zujun Liu AU - Andrew Thurman AU - Linda S. Powers AU - Meng Zou AU - Adam Hefel AU - Yunyi Li AU - Joseph Zabner AU - Kin Fai Au Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/01/29/533158.abstract N2 - 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. ER -