Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression.
Harris
R Alan
RA
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
Wang
Ting
T
Coarfa
Cristian
C
Nagarajan
Raman P
RP
Hong
Chibo
C
Downey
Sara L
SL
Johnson
Brett E
BE
Fouse
Shaun D
SD
Delaney
Allen
A
Zhao
Yongjun
Y
Olshen
Adam
A
Ballinger
Tracy
T
Zhou
Xin
X
Forsberg
Kevin J
KJ
Gu
Junchen
J
Echipare
Lorigail
L
O'Geen
Henriette
H
Lister
Ryan
R
Pelizzola
Mattia
M
Xi
Yuanxin
Y
Epstein
Charles B
CB
Bernstein
Bradley E
BE
Hawkins
R David
RD
Ren
Bing
B
Chung
Wen-Yu
WY
Gu
Hongcang
H
Bock
Christoph
C
Gnirke
Andreas
A
Zhang
Michael Q
MQ
Haussler
David
D
Ecker
Joseph R
JR
Li
Wei
W
Farnham
Peggy J
PJ
Waterland
Robert A
RA
Meissner
Alexander
A
Marra
Marco A
MA
Hirst
Martin
M
Milosavljevic
Aleksandar
A
Costello
Joseph F
JF
D000483:Alleles; D002460:Cell Line; D018899:CpG Islands / Q000235:genetics; D003596:Cytosine / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics*; D053595:Embryonic Stem Cells / Q000378:metabolism; D044127:Epigenesis, Genetic; D005786:Gene Expression Regulation; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites / Q000378:metabolism
D013447:Sulfites; D003596:Cytosine; C042345:hydrogen sulfite