Single-cell genome-wide bisulfite sequencing uncovers extensive heterogeneity in the mouse liver methylome

Silvia Gravina, Xiao Dong, Bo Yu, Jan Vijg

Research output: Contribution to journalArticle

44 Citations (Scopus)

Abstract

Background: Transmission fidelity of CpG DNA methylation patterns is not foolproof, with error rates from less than 1 to well over 10 % per CpG site, dependent on preservation of the methylated or unmethylated state and the type of sequence. This suggests a fairly high chance of errors. However, the consequences of such errors in terms of cell-to-cell variation have never been demonstrated by experimentally measuring intra-tissue heterogeneity in an adult organism. Results: We employ single-cell DNA methylomics to analyze heterogeneity of genome-wide 5-methylcytosine (5mC) patterns within mouse liver. Our results indicate a surprisingly high level of heterogeneity, corresponding to an average epivariation frequency of approximately 3.3 %, with regions containing H3K4me1 being the most variable and promoters and CpG islands the most stable. Our data also indicate that the level of 5mC heterogeneity is dependent on genomic features. We find that non-functional sites such as repeat elements and introns are mostly unstable and potentially functional sites such as gene promoters are mostly stable. Conclusions: By employing a protocol for whole-genome bisulfite sequencing of single cells, we show that the liver epigenome is highly unstable with an epivariation frequency in DNA methylation patterns of at least two orders of magnitude higher than somatic mutation frequencies.

Original languageEnglish (US)
Article number150
JournalGenome Biology
Volume17
Issue number1
DOIs
StatePublished - Jul 5 2016

Fingerprint

bisulfites
genome
Genome
5-Methylcytosine
liver
Liver
mice
methylation
DNA methylation
DNA Methylation
DNA
promoter regions
cells
somatic mutation
CpG Islands
Mutation Rate
Introns
introns
mutation
genomics

Keywords

  • Aging
  • Epigenetic instability
  • Epivariations
  • Single-cell DNA methylomics
  • Single-cell epigenomics

ASJC Scopus subject areas

  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Single-cell genome-wide bisulfite sequencing uncovers extensive heterogeneity in the mouse liver methylome. / Gravina, Silvia; Dong, Xiao; Yu, Bo; Vijg, Jan.

In: Genome Biology, Vol. 17, No. 1, 150, 05.07.2016.

Research output: Contribution to journalArticle

@article{47eea3f205d74a2aaf393a059c46f7a4,
title = "Single-cell genome-wide bisulfite sequencing uncovers extensive heterogeneity in the mouse liver methylome",
abstract = "Background: Transmission fidelity of CpG DNA methylation patterns is not foolproof, with error rates from less than 1 to well over 10 {\%} per CpG site, dependent on preservation of the methylated or unmethylated state and the type of sequence. This suggests a fairly high chance of errors. However, the consequences of such errors in terms of cell-to-cell variation have never been demonstrated by experimentally measuring intra-tissue heterogeneity in an adult organism. Results: We employ single-cell DNA methylomics to analyze heterogeneity of genome-wide 5-methylcytosine (5mC) patterns within mouse liver. Our results indicate a surprisingly high level of heterogeneity, corresponding to an average epivariation frequency of approximately 3.3 {\%}, with regions containing H3K4me1 being the most variable and promoters and CpG islands the most stable. Our data also indicate that the level of 5mC heterogeneity is dependent on genomic features. We find that non-functional sites such as repeat elements and introns are mostly unstable and potentially functional sites such as gene promoters are mostly stable. Conclusions: By employing a protocol for whole-genome bisulfite sequencing of single cells, we show that the liver epigenome is highly unstable with an epivariation frequency in DNA methylation patterns of at least two orders of magnitude higher than somatic mutation frequencies.",
keywords = "Aging, Epigenetic instability, Epivariations, Single-cell DNA methylomics, Single-cell epigenomics",
author = "Silvia Gravina and Xiao Dong and Bo Yu and Jan Vijg",
year = "2016",
month = "7",
day = "5",
doi = "10.1186/s13059-016-1011-3",
language = "English (US)",
volume = "17",
journal = "Genome Biology",
issn = "1474-7596",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Single-cell genome-wide bisulfite sequencing uncovers extensive heterogeneity in the mouse liver methylome

AU - Gravina, Silvia

AU - Dong, Xiao

AU - Yu, Bo

AU - Vijg, Jan

PY - 2016/7/5

Y1 - 2016/7/5

N2 - Background: Transmission fidelity of CpG DNA methylation patterns is not foolproof, with error rates from less than 1 to well over 10 % per CpG site, dependent on preservation of the methylated or unmethylated state and the type of sequence. This suggests a fairly high chance of errors. However, the consequences of such errors in terms of cell-to-cell variation have never been demonstrated by experimentally measuring intra-tissue heterogeneity in an adult organism. Results: We employ single-cell DNA methylomics to analyze heterogeneity of genome-wide 5-methylcytosine (5mC) patterns within mouse liver. Our results indicate a surprisingly high level of heterogeneity, corresponding to an average epivariation frequency of approximately 3.3 %, with regions containing H3K4me1 being the most variable and promoters and CpG islands the most stable. Our data also indicate that the level of 5mC heterogeneity is dependent on genomic features. We find that non-functional sites such as repeat elements and introns are mostly unstable and potentially functional sites such as gene promoters are mostly stable. Conclusions: By employing a protocol for whole-genome bisulfite sequencing of single cells, we show that the liver epigenome is highly unstable with an epivariation frequency in DNA methylation patterns of at least two orders of magnitude higher than somatic mutation frequencies.

AB - Background: Transmission fidelity of CpG DNA methylation patterns is not foolproof, with error rates from less than 1 to well over 10 % per CpG site, dependent on preservation of the methylated or unmethylated state and the type of sequence. This suggests a fairly high chance of errors. However, the consequences of such errors in terms of cell-to-cell variation have never been demonstrated by experimentally measuring intra-tissue heterogeneity in an adult organism. Results: We employ single-cell DNA methylomics to analyze heterogeneity of genome-wide 5-methylcytosine (5mC) patterns within mouse liver. Our results indicate a surprisingly high level of heterogeneity, corresponding to an average epivariation frequency of approximately 3.3 %, with regions containing H3K4me1 being the most variable and promoters and CpG islands the most stable. Our data also indicate that the level of 5mC heterogeneity is dependent on genomic features. We find that non-functional sites such as repeat elements and introns are mostly unstable and potentially functional sites such as gene promoters are mostly stable. Conclusions: By employing a protocol for whole-genome bisulfite sequencing of single cells, we show that the liver epigenome is highly unstable with an epivariation frequency in DNA methylation patterns of at least two orders of magnitude higher than somatic mutation frequencies.

KW - Aging

KW - Epigenetic instability

KW - Epivariations

KW - Single-cell DNA methylomics

KW - Single-cell epigenomics

UR - http://www.scopus.com/inward/record.url?scp=84977525598&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84977525598&partnerID=8YFLogxK

U2 - 10.1186/s13059-016-1011-3

DO - 10.1186/s13059-016-1011-3

M3 - Article

C2 - 27380908

AN - SCOPUS:84977525598

VL - 17

JO - Genome Biology

JF - Genome Biology

SN - 1474-7596

IS - 1

M1 - 150

ER -