Single-molecule long-read sequencing reveals the chromatin basis of gene expression
- Yunhao Wang1,2,4,
- Anqi Wang1,2,4,
- Zujun Liu1,2,
- Andrew L. Thurman2,
- Linda S. Powers2,
- Meng Zou2,
- Yue Zhao1,2,
- Adam Hefel2,
- Yunyi Li2,
- Joseph Zabner2 and
- Kin Fai Au1,2,3
- 1Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA;
- 2Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA;
- 3Department of Biostatistics, University of Iowa, Iowa City, Iowa 52242, USA
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↵4 These authors contributed equally to this work.
Abstract
Genome-wide chromatin accessibility and nucleosome occupancy profiles have been widely investigated, while the long-range dynamics remain poorly studied at the single-cell level. Here, we present a new experimental approach, methyltransferase treatment followed by single-molecule long-read sequencing (MeSMLR-seq), for long-range mapping of nucleosomes and chromatin accessibility at single DNA molecules and thus achieve comprehensive-coverage characterization of the corresponding heterogeneity. MeSMLR-seq offers direct measurements of both nucleosome-occupied and nucleosome-evicted regions on a single DNA molecule, which is challenging for many existing methods. 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 the transcription start site for silent and actively transcribed genes, at the single-cell level and in the long-range scale. The heterogeneous patterns of chromatin status 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. In addition, we revealed the coupled changes of chromatin accessibility for two neighboring glucose transporter genes in response to changes in glucose concentration.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.251116.119.
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Freely available online through the Genome Research Open Access option.
- Received April 2, 2019.
- Accepted June 10, 2019.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
