|
1
|
Stelzer Y, Shivalila CS, Soldner F,
Markoulaki S and Jaenisch R: Tracing dynamic changes of DNA
methylation at single-cell resolution. Cell. 163:218–229. 2015.
View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Smith ZD and Meissner A: DNA methylation:
Roles in mammalian development. Nat Rev Genet. 14:204–220. 2013.
View Article : Google Scholar : PubMed/NCBI
|
|
3
|
He W, Kang X, Du H, Song B, Lu Z, Huang Y,
Wang D, Sun X, Yu Y and Fan Y: Defining differentially methylated
regions specific for the acquisition of pluripotency and
maintenance in human pluripotent stem cells via microarray. PLoS
One. 9:e1083502014. View Article : Google Scholar : PubMed/NCBI
|
|
4
|
Jaenisch R and Bird A: Epigenetic
regulation of gene expression: How the genome integrates intrinsic
and environmental signals. Nat Genet (33 Suppl). S245–S254. 2003.
View Article : Google Scholar
|
|
5
|
Dhiman VK, Attwood K, Campbell MJ and
Smiraglia DJ: Hormone stimulation of androgen receptor mediates
dynamic changes in DNA methylation patterns at regulatory elements.
Oncotarget. 6:42575–42589. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Ping W, Hu J, Hu G, Song Y, Xia Q, Yao M,
Gong S, Jiang C and Yao H: Genome-wide DNA methylation analysis
reveals that mouse chemical iPSCs have closer epigenetic features
to mESCs than OSKM-integrated iPSCs. Cell Death and Disease.
9:1872018. View Article : Google Scholar : PubMed/NCBI
|
|
7
|
Baylin SB: DNA methylation and gene
silencing in cancer. Nat Clin Pract Oncol 1 (2 Suppl). S4–S11.
2005. View Article : Google Scholar
|
|
8
|
Li HJ, Wan RP, Tang LJ, Liu SJ, Zhao QH,
Gao MM, Yi YH, Liao WP, Sun XF and Long YS: Alteration of Scn3a
expression is mediated via CpG methylation and MBD2 in mouse
hippocampus during postnatal development and seizure condition.
Biochim Biophys Acta. 1849:1–9. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Morgan HD, Santos F, Green K, Dean W and
Reik W: Epigenetic reprogramming in mammals. Hum Mol Genet.
14:R47–R58. 2005. View Article : Google Scholar : PubMed/NCBI
|
|
10
|
Gu Y, Zhang Z, Yin J, Ye J, Song Y, Liu H,
Xiong Y, Lu M, Zheng G and He Z: Epigenetic silencing of miR-493
increases the resistance to cisplatin in lung cancer by targeting
tongue cancer resistance-related protein 1 (TCRP1). J Exp Clin
Cancer Res. 36:1142017. View Article : Google Scholar : PubMed/NCBI
|
|
11
|
Dexheimer GM, Alves J, Reckziegel L,
Lazzaretti G and Abujamra AL: DNA methylation events as markers for
diagnosis and management of acute myeloid leukemia and
myelodysplastic syndrome. Dis Markers. 2017:54728932017. View Article : Google Scholar : PubMed/NCBI
|
|
12
|
Seisenberger S, Peat JR, Hore TA, Santos
F, Dean W and Reik W: Reprogramming DNA methylation in the
mammalian life cycle: Building and breaking epigenetic barriers.
Philos Trans R Soc Lond B Biol Sci. 368:201103302013. View Article : Google Scholar : PubMed/NCBI
|
|
13
|
Smallwood SA, Tomizawa S, Krueger F, Ruf
N, Carli N, Segonds-Pichon A, Sato S, Hata K, Andrews SR and Kelsey
G: Dynamic CpG island methylation landscape in oocytes and
preimplantation embryos. Nat Genet. 43:811–814. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Yu B, Russanova VR, Gravina S, Hartley S,
Mullikin JC, Ignezweski A, Graham J, Segars JH, DeCherney AH and
Howard BH: DNA methylome and transcriptome sequencing in human
ovarian granulosa cells links age-related changes in gene
expression to gene body methylation and 3′-end GC density.
Oncotarget. 6:3627–3643. 2015.PubMed/NCBI
|
|
15
|
Guo H, Zhu P, Yan L, Li R, Hu B, Lian Y,
Yan J, Ren X, Lin S, Li J, et al: The DNA methylation landscape of
human early embryos. Nature. 511:606–610. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Jiang Z, Lin J, Dong H, Zheng X, Marjani
SL, Duan J, Ouyang Z, Chen J and Tian XC: DNA methylomes of bovine
gametes and in vivo produced preimplantation embryos. Biol
Reprod. 99:949–959. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
17
|
Guo H, Zhu P, Yan L, Li R, Hu B, Lian Y,
Yan J, Ren X, Lin S, Li J, et al: The DNA methylation landscape of
human early embryos. Nature. 511:606–610. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
18
|
Down TA, Rakyan VK, Turner DJ, Flicek P,
Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, et al: A
Bayesian deconvolution strategy for immunoprecipitation-based DNA
methylome analysis. Nat Biotech. 26:779–785. 2008. View Article : Google Scholar
|
|
19
|
Cao XW, Lin K, Li CY and Yuan CW: A review
of WHO Laboratory Manual for the Examination and Processing of
Human Semen (5th edition). Zhonghua Nan Ke Xue. 17:1059–1063.
2011.(In Chinese). PubMed/NCBI
|
|
20
|
Yoshida K, Sekiguchi K, Mizuno N, Kasai K,
Sakai I, Sato H and Seta S: The modified method of two-step
differential extraction of sperm and vaginal epithelial cell DNA
from vaginal fluid mixed with semen. Forensic Sci Int. 72:25–33.
1995. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Scacheri PC, Crawford GE and Davis S:
Statistics for ChIP-chip and DNase hypersensitivity experiments on
NimbleGen arrays. Methods Enzymol. 411:270–282. 2006. View Article : Google Scholar : PubMed/NCBI
|
|
22
|
Holliday R and Pugh JE: DNA modification
mechanisms and gene activity during development. Science.
187:226–232. 1975. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
Jones PA: Functions of DNA methylation:
Islands, start sites, gene bodies and beyond. Nat Rev Genet.
13:484–492. 2012. View
Article : Google Scholar : PubMed/NCBI
|
|
24
|
Xiao Y, Yu F, Pang L, Zhao H, Liu L, Zhang
G, Liu T, Zhang H, Fan H, Zhang Y, et al: MeSiC: a model-based
method for estimating 5 mC levels at single-CpG resolution from
MeDIP-seq. Sci Rep. 5:146992015. View Article : Google Scholar : PubMed/NCBI
|
|
25
|
He S, Sun H, Lin L, Zhang Y, Chen J, Liang
L, Li Y, Zhang M, Yang X, Wang X, et al: Passive DNA demethylation
preferentially up-regulates pluripotency-related genes and
facilitates the generation of induced pluripotent stem cells. J
Biol Chem. 292:18542–18555. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
26
|
Vinci G, Buffat C, Simoncini S, Boubred F,
Ligi I, Dumont F, Le Bonniec B, Fournier T, Vaiman D, Dignat-George
F and Simeoni U: Gestational age-related patterns of AMOT
methylation are revealed in preterm infant endothelial progenitors.
PLoS One. 12:e01863212017. View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Beck S and Rakyan VK: The methylome:
Approaches for global DNA methylation profiling. Trends Genet.
24:231–237. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
28
|
Zhu P, Guo H, Ren Y, Hou Y, Dong J, Li R,
Lian Y, Fan X, Hu B, Gao Y, et al: Single-cell DNA methylome
sequencing of human preimplantation embryos. Nat Genet. 50:12–19.
2018. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Miura F, Enomoto Y, Dairiki R and Ito T:
Amplification-free whole-genome bisulfite sequencing by
post-bisulfite adaptor tagging. Nucleic Acids Res. 40:e1362012.
View Article : Google Scholar : PubMed/NCBI
|
|
30
|
Taiwo O, Wilson GA, Morris T, Seisenberger
S, Reik W, Pearce D, Beck S and Butcher LM: Methylome analysis
using MeDIP-seq with low DNA concentrations. Nat Protoc. 7:617–636.
2012. View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Harrison A and Parle-McDermott A: DNA
methylation: A timeline of methods and applications. Front Genet.
2:742011. View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Wardenaar R, Liu H, Colot V, Colomé-Tatché
M and Johannes F: Evaluation of MeDIP-chip in the context of
whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis.
Methods Mol Biol. 1067:203–224. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
33
|
Cortijo S, Wardenaar R, Colomé-Tatché M,
Johannes F and Colot V: Genome-wide analysis of DNA methylation in
Arabidopsis using MeDIP-chip. Methods Mol Biol. 1112:125–149. 2014.
View Article : Google Scholar : PubMed/NCBI
|
|
34
|
Seifert M, Cortijo S, Colomé-Tatché M,
Johannes F, Roudier F and Colot V: MeDIP-HMM: Genome-wide
identification of distinct DNA methylation states from high-density
tiling arrays. Bioinformatics. 28:2930–2939. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
35
|
Smith ZD, Chan MM, Mikkelsen TS, Gu H,
Gnirke A, Regev A and Meissner A: A unique regulatory phase of DNA
methylation in the early mammalian embryo. Nature. 484:339–344.
2012. View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Smith ZD, Chan MM, Humm KC, Karnik R,
Mekhoubad S, Regev A, Eggan K and Meissner A: DNA methylation
dynamics of the human preimplantation embryo. Nature. 511:611–615.
2014. View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Klose RJ and Bird AP: Genomic DNA
methylation: The mark and its mediators. Trends Biochem Sci.
31:89–97. 2006. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Guo F, Li X, Liang D, Li T, Zhu P, Guo H,
Wu X, Wen L, Gu TP, Hu B, et al: Active and passive demethylation
of male and female pronuclear DNA in the mammalian zygote. Cell
Stem Cell. 15:447–459. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
39
|
Hajkova P, Jeffries SJ, Lee C, Miller N,
Jackson SP and Surani MA: Genome-wide eprogramming in the mouse
germ line entails the base excision repair pathway. Science.
329:78–82. 2010. View Article : Google Scholar : PubMed/NCBI
|
