The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
Dynamic CpG island methylation landscape in oocytes and preimplantation embryos
Open accessAbstract
Elucidating how and to what extent CpG islands (CGIs) are methylated in germ cells is essential to understand genomic imprinting and epigenetic reprogramming. Here we present, to our knowledge, the first integrated epigenomic analysis of mammalian oocytes, identifying over a thousand CGIs methylated in mature oocytes. We show that these CGIs depend on DNMT3A and DNMT3L but are not distinct at the sequence level, including in CpG periodicity. They are preferentially located within active transcription units and are relatively depleted in H3K4me3, supporting a general transcription-dependent mechanism of methylation. Very few methylated CGIs are fully protected from post-fertilization reprogramming but, notably, the majority show incomplete demethylation in embryonic day (E) 3.5 blastocysts. Our study shows that CGI methylation in gametes is not entirely related to genomic imprinting but is a strong factor in determining methylation status in preimplantation embryos, suggesting a need to reassess mechanisms of post-fertilization demethylation.
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Cites
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
Krueger, F., & Andrews, S. R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr167 · Cited by 5,297
Self-citationHistone H3K27ac separates active from poised enhancers and predicts developmental state
Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302
Genome-scale DNA methylation maps of pluripotent and differentiated cells
Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature · doi:10.1038/nature07107 · Cited by 2,536
Conserved role of intragenic DNA methylation in regulating alternative promoters
Maunakea, A. K., Nagarajan, R. P., Bilenky, M., Ballinger, T. J., D’Souza, C., Fouse, S. D., Johnson, B. E., Hong, C., Nielsen, C., Zhao, Y., et al. (2010) · Nature · doi:10.1038/nature09165 · Cited by 1,743
DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA
Ooi, S. K. T., Qiu, C., Bernstein, E., Li, K., Jia, D., Yang, Z., Erdjument-Bromage, H., Tempst, P., Lin, S.-P., Allis, C. D., et al. (2007) · Nature · doi:10.1038/nature05987 · Cited by 1,567
Dnmt3L and the Establishment of Maternal Genomic Imprints
Bourc'his, D., Xu, G.-L., Lin, C.-S., Bollman, B., & Bestor, T. H. (2001) · Science · doi:10.1126/science.1065848 · Cited by 1,439
Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting
Kaneda, M., Okano, M., Hata, K., Sado, T., Tsujimoto, N., Li, E., & Sasaki, H. (2004) · Nature · doi:10.1038/nature02633 · Cited by 1,387
Self-citationEpigenetic reprogramming in mammals
Morgan, H. D., Santos, F., Green, K., Dean, W., & Reik, W. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi114 · Cited by 1,342
Hata, K., Okano, M., Lei, H., & Li, E. (2002) · Development · doi:10.1242/dev.129.8.1983 · Cited by 1,039
Self-citationEpigenetic events in mammalian germ-cell development: reprogramming and beyond
Sasaki, H., & Matsui, Y. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2295 · Cited by 871
Cited by
Functions of DNA methylation: islands, start sites, gene bodies and beyond
Jones, P. A. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3230 · Cited by 6,061
DNA methylation: roles in mammalian development
Smith, Z. D., & Meissner, A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3354 · Cited by 3,045
Function and information content of DNA methylation
Schübeler, D. (2015) · Nature · doi:10.1038/nature14192 · Cited by 2,060
Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
Smallwood, S. A., Lee, H. J., Angermueller, C., Krueger, F., Saadeh, H., Peat, J., Andrews, S. R., Stegle, O., Reik, W., & Kelsey, G. (2014) · Nature Methods · doi:10.1038/nmeth.3035 · Cited by 1,125
Self-citationReversing DNA Methylation: Mechanisms, Genomics, and Biological Functions
Wu, H., & Zhang, Y. (2014) · Cell · doi:10.1016/j.cell.2013.12.019 · Cited by 1,065
“…DNA demethylation, a subset of maternally derived methylated CpG-rich sequences, including many maternal ICRs and some retroviral repeats such as the intracisternal A particle (IAP) type, remain fully or partially methylated (Lane et al., Cell 15 2003; Smallwood et al., 2011; Smith et al., 2012).”
Metadata
- Authors
- Smallwood, S. A., Tomizawa, S.-I., Krueger, F., Ruf, N., Carli, N., Segonds-Pichon, A., Sato, S., Hata, K., Andrews, S. R., & Kelsey, G.
- Venue
- Nature Genetics
- Published
- 2011-06-26
- Volume
- 43
- Issue
- 8
- Pages
- 811-814
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2044282102
- Cited by
- 699
- References
- 31
- FWCI
- 22.57
- Type
- journal article
- Language
- en
- Open access
- green
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