Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity

Charlton, J. et al. Global delay in nascent strand DNA methylation. Nat. Struct. Mol. Biol. 25, 327–332 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang, Q. et al. Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance. Nat. Genet. 52, 828–839 (2020).

Article  CAS  PubMed  Google Scholar 

Messerschmidt, D. M., Knowles, B. B. & Solter, D. DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev. 28, 812–828 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xu, C. & Corces, V. G. Nascent DNA methylome mapping reveals inheritance of hemimethylation at CTCF/cohesin sites. Science 359, 1166–1170 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ming, X. et al. Kinetics and mechanisms of mitotic inheritance of DNA methylation and their roles in aging-associated methylome deterioration. Cell Res. 30, 980–996 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sen, M. et al. Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development. Nat. Commun. 12, 1286 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Laird, C. D. et al. Hairpin-bisulfite PCR: assessing epigenetic methylation patterns on complementary strands of individual DNA molecules. Proc. Natl Acad. Sci. USA 101, 204–209 (2004).

Article  CAS  PubMed  Google Scholar 

Zhao, L. et al. The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation. Genome Res. 24, 1296–1307 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lepikhov, K. et al. Two are better than one: HPoxBS—hairpin oxidative bisulfite sequencing. Nucleic Acids Res. 46, e88 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Mooijman, D., Dey, S. S., Boisset, J.-C., Crosetto, N. & van Oudenaarden, A. Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction. Nat. Biotechnol. 34, 852–856 (2016).

Article  CAS  PubMed  Google Scholar 

Wangsanuwat, C., Chialastri, A., Aldeguer, J. F., Rivron, N. C. & Dey, S. S. A probabilistic framework for cellular lineage reconstruction using integrated single-cell 5-hydroxymethylcytosine and genomic DNA sequencing. Cell Rep. Methods 1, 100060 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vaisvila, R. et al. Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res. 31, 1280–1289 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Ficz, G. et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473, 398–402 (2011).

Article  CAS  PubMed  Google Scholar 

Cheng, Y., Xie, N., Jin, P. & Wang, T. DNA methylation and hydroxymethylation in stem cells. Cell Biochem. Funct. 33, 161–173 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yu, M. et al. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149, 1368–1380 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sun, Z. et al. Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Genome Res. 31, 291–300 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Schutsky, E. K. et al. Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase. Nat. Biotechnol. 36, 1083–1090 (2018).

Article  CAS  Google Scholar 

Liu, Y. et al. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat. Biotechnol. 37, 424–429 (2019).

Article  CAS  PubMed  Google Scholar 

Liu, Y. et al. Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution. Nat. Commun. 12, 618 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Mulqueen, R. M. et al. Highly scalable generation of DNA methylation profiles in single cells. Nat. Biotechnol. 36, 428–431 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stresemann, C. & Lyko, F. Modes of action of the DNA methyltransferase inhibitors azacytidine and decitabine. Int. J. Cancer 123, 8–13 (2008).

Article  CAS  PubMed  Google Scholar 

Zheng, Y. et al. A unique family of Mrr-like modification-dependent restriction endonucleases. Nucleic Acids Res. 38, 5527–5534 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cohen-Karni, D. et al. The MspJI family of modification-dependent restriction endonucleases for epigenetic studies. Proc. Natl Acad. Sci. USA 108, 11040–11045 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Habibi, E. et al. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell 13, 360–369 (2013).

Article  CAS  PubMed  Google Scholar 

Ramisch, A. et al. CRUP: a comprehensive framework to predict condition-specific regulatory units. Genome Biol. 20, 227 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Smallwood, S. A. et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat. Methods 11, 817–820 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ying, Q. L. et al. The ground state of embryonic stem cell self-renewal. Nature 453, 519–523 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Leitch, H. G. et al. Naive pluripotency is associated with global DNA hypomethylation. Nat. Struct. Mol. Biol. 20, 311–316 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mulholland, C. B. et al. Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals. Nat. Commun. 11, 5972 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

von Meyenn, F. et al. Impairment of DNA methylation maintenance is the main cause of global demethylation in naive embryonic stem cells. Mol. Cell 62, 848–861 (2016).

Article  Google Scholar 

Lu, R. et al. Inhibition of the extracellular signal-regulated kinase/mitogen-activated protein kinase pathway decreases DNA methylation in colon cancer cells. J. Biol. Chem. 282, 12249–12259 (2007).

Article  CAS  PubMed  Google Scholar 

Sarkar, S. et al. Histone deacetylase inhibitors reverse CpG methylation by regulating DNMT1 through ERK signaling. Anticancer Res. 31, 2723–2732 (2011).

CAS  PubMed  Google Scholar 

Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Funaki, S. et al. Inhibition of maintenance DNA methylation by Stella. Biochem. Biophys. Res. Commun. 453, 455–460 (2014).

Article  CAS  PubMed  Google Scholar 

Song, C. X., Diao, J., Brunger, A. T. & Quake, S. R. Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation. Proc. Natl Acad. Sci. USA 113, 4338–4343 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu, L. et al. Crystal structure of TET2–DNA complex: insight into TET-mediated 5mC oxidation. Cell 155, 1545–1555 (2013).

Article  CAS  PubMed  Google Scholar 

Xing, X. et al. Direct observation and analysis of TET-mediated oxidation processes in a DNA origami nano

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