Massively multiplex single-molecule oligonucleosome footprinting
- University of California San Francisco, United States
- Stanford University, United States
- Vector Institute, Canada
- Pacific Biosciences of California, Inc, United States
- University of California, San Francisco, United States
Abstract
Our understanding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge the divide between these approaches, we present the single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA). SAMOSA is a high-throughput single-molecule sequencing method that combines adenine methyltransferase footprinting and single-molecule real-time DNA sequencing to natively and nondestructively measure nucleosome positions on individual chromatin fibres. SAMOSA data allows unbiased classification of single-molecular 'states' of nucleosome occupancy on individual chromatin fibres. We leverage this to estimate nucleosome regularity and spacing on single chromatin fibres genome-wide, at predicted transcription factor binding motifs, and across both active and silent human epigenomic domains. Our analyses suggest that chromatin is comprised of a diverse array of both regular and irregular single-molecular oligonucleosome patterns that differ subtly in their relative abundance across epigenomic domains. This irregularity is particularly striking in constitutive heterochromatin, which has typically been viewed as a conformationally static entity. Our proof-of-concept study provides a powerful new methodology for studying nucleosome organization at a previously intractable resolution, and offers up new avenues for modeling and visualizing higher-order chromatin structure.
Data availability
All raw data will be made available at GEO Accession GSE162410; processed data is available at Zenodo (https://doi.org/10.5281/zenodo.3834705). All scripts and notebooks for reproducing analyses in the paper are available at https://github.com/RamaniLab/SAMOSA.
-
Massively multiplex single-molecule oligonucleosome footprintingZenodo , zenodo.3834706.
-
Massively multiplex single-molecule oligonucleosome footprintingNCBI Gene Expression Omnibus, GSE162410.
Article and author information
Author details
Funding
Sandler Foundation
- Vijay Ramani
American Cancer Society
- Laura J Hsieh
National Institutes of Health (R01GM123977)
- Hani Goodarzi
National Institutes of Health (R35GM127020)
- Geeta J Narlikar
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2020, Abdulhay et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 6,867
- views
-
- 648
- downloads
-
- 90
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Citations by DOI
-
- 90
- citations for umbrella DOI https://doi.org/10.7554/eLife.59404
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Massively multiplex single-molecule oligonucleosome footprinting
eLife 9:e59404.
https://doi.org/10.7554/eLife.59404
