Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells

The biological roles of DNA methylation have been elucidated by profiling methods based on whole-genome or reduced-representation bisulfite sequencing, but these approaches do not efficiently survey the vast numbers of non-coding regulatory elements in mammalian genomes. Here we present an extended-...

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Bibliographic Details
Published in:Nature biotechnology 2021-09, Vol.39 (9), p.1086-1094
Main Authors: Shareef, Sarah J., Bevill, Samantha M., Raman, Ayush T., Aryee, Martin J., van Galen, Peter, Hovestadt, Volker, Bernstein, Bradley E.
Format: Article
Language:English
Subjects:
631/1647/2210/2213
631/208/176/1988
631/337/176/1988
631/61/212/177
631/61/514/2254
Agriculture
Analysis
Binding sites
Bioinformatics
Biomedical and Life Sciences
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
Bisulfite
Cell cycle
Copy number
CpG Islands
Deoxyribonucleic acid
DNA
DNA fingerprinting
DNA Methylation
DNA sequencing
Enhancers
Epigenetics
Gene Regulatory Networks
Genetic aspects
Genetic diversity
Genomes
Genomics
High-Throughput Nucleotide Sequencing
Histones - metabolism
Humans
Identification and classification
Leukemia
Life Sciences
Methods
Methylation
Multiplexing
Nucleotide sequence
Regulatory sequences
Representations
Single-Cell Analysis - methods
Sulfites - chemistry
Unicellular organisms
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Description
Summary:The biological roles of DNA methylation have been elucidated by profiling methods based on whole-genome or reduced-representation bisulfite sequencing, but these approaches do not efficiently survey the vast numbers of non-coding regulatory elements in mammalian genomes. Here we present an extended-representation bisulfite sequencing (XRBS) method for targeted profiling of DNA methylation. Our design strikes a balance between expanding coverage of regulatory elements and reproducibly enriching informative CpG dinucleotides in promoters, enhancers and CTCF binding sites. Barcoded DNA fragments are pooled before bisulfite conversion, allowing multiplex processing and technical consistency in low-input samples. Application of XRBS to single leukemia cells enabled us to evaluate genetic copy number variations and methylation variability across individual cells. Our analysis highlights heterochromatic H3K9me3 regions as having the highest cell-to-cell variability in their methylation, likely reflecting inherent epigenetic instability of these late-replicating regions, compounded by differences in cell cycle stages among sampled cells. DNA methylation is efficiently profiled in non-coding regulatory sequences in single cells.
ISSN:1087-0156
1546-1696
DOI:10.1038/s41587-021-00910-x