Distinctive chromatin in human sperm packages genes for embryo development (original) (raw)

• Ward, W. S. & Coffey, D. S. DNA packaging and organization in mammalian spermatozoa: comparison with somatic cells. Biol. Reprod. 44, 569–574 (1991)
  Article CAS Google Scholar
• Wykes, S. M. & Krawetz, S. A. The structural organization of sperm chromatin. J. Biol. Chem. 278, 29471–29477 (2003)
  Article CAS Google Scholar
• Balhorn, R., Brewer, L. & Corzett, M. DNA condensation by protamine and arginine-rich peptides: analysis of toroid stability using single DNA molecules. Mol. Reprod. Dev. 56, 230–234 (2000)
  Article CAS Google Scholar
• Gatewood, J. M., Cook, G. R., Balhorn, R., Schmid, C. W. & Bradbury, E. M. Isolation of four core histones from human sperm chromatin representing a minor subset of somatic histones. J. Biol. Chem. 265, 20662–20666 (1990)
  CAS PubMed Google Scholar
• Kimmins, S. & Sassone-Corsi, P. Chromatin remodelling and epigenetic features of germ cells. Nature 434, 583–589 (2005)
  Article ADS CAS Google Scholar
• Nix, D. A., Courdy, S. J. & Boucher, K. M. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 9, 523 (2008)
  Article Google Scholar
• Reik, W., Santos, F. & Dean, W. Mammalian epigenomics: reprogramming the genome for development and therapy. Theriogenology 59, 21–32 (2003)
  Article CAS Google Scholar
• Santos, F., Hendrich, B., Reik, W. & Dean, W. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev. Biol. 241, 172–182 (2002)
  Article CAS Google Scholar
• Rangasamy, D., Berven, L., Ridgway, P. & Tremethick, D. J. Pericentric heterochromatin becomes enriched with H2A.Z during early mammalian development. EMBO J. 22, 1599–1607 (2003)
  Article CAS Google Scholar
• Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006)
  Article CAS Google Scholar
• Bernstein, B. E. et al. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc. Natl Acad. Sci. USA 99, 8695–8700 (2002)
  Article ADS CAS Google Scholar
• Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005)
  Article CAS Google Scholar
• Muller, J. & Kassis, J. A. Polycomb response elements and targeting of Polycomb group proteins in Drosophila . Curr. Opin. Genet. Dev. 16, 476–484 (2006)
  Article Google Scholar
• Schwartz, Y. B. et al. Genome-wide analysis of Polycomb targets in Drosophila melanogaster . Nature Genet. 38, 700–705 (2006)
  Article CAS Google Scholar
• Tanay, A., O’Donnell, A. H., Damelin, M. & Bestor, T. H. Hyperconserved CpG domains underlie Polycomb-binding sites. Proc. Natl Acad. Sci. USA 104, 5521–5526 (2007)
  Article ADS CAS Google Scholar
• Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002)
  Article ADS CAS Google Scholar
• Lee, T. I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313 (2006)
  Article CAS Google Scholar
• Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861–872 (2007)
  Article CAS Google Scholar
• Kopp, J. L., Ormsbee, B. D., Desler, M. & Rizzino, A. Small increases in the level of Sox2 trigger the differentiation of mouse embryonic stem cells. Stem Cells 26, 903–911 (2008)
  Article CAS Google Scholar
• Wernig, M. et al. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature 448, 318–324 (2007)
  Article ADS CAS Google Scholar
• Mohn, F. et al. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol. Cell 30, 755–766 (2008)
  Article CAS Google Scholar
• Illingworth, R. et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 6, e22 (2008)
  Article Google Scholar
• Down, T. A. et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nature Biotechnol. 26, 779–785 (2008)
  Article CAS Google Scholar
• Farthing, C. R. et al. Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genet. 4, e1000116 (2008)
  Article Google Scholar
• Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401–1414 (2007)
  Article CAS Google Scholar
• Glazov, E. A., McWilliam, S., Barris, W. C. & Dalrymple, B. P. Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Mol. Biol. Evol. 25, 939–948 (2008)
  Article CAS Google Scholar
• Takada, S. et al. Delta-like and Gtl2 are reciprocally expressed, differentially methylated linked imprinted genes on mouse chromosome 12. Curr. Biol. 10, 1135–1138 (2000)
  Article CAS Google Scholar
• da Rocha, S. T., Edwards, C. A., Ito, M., Ogata, T. & Ferguson-Smith, A. C. Genomic imprinting at the mammalian Dlk1-Dio3 domain. Trends Genet. 24, 306–316 (2008)
  Article Google Scholar
• Li, S. S., Liu, Y. H., Tseng, C. N. & Singh, S. Analysis of gene expression in single human oocytes and preimplantation embryos. Biochem. Biophys. Res. Commun. 340, 48–53 (2006)
  Article CAS Google Scholar
• Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genet. 39, 457–466 (2007)
  Article CAS Google Scholar
• Fouse, S. D. et al. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell 2, 160–169 (2008)
  Article CAS Google Scholar
• Vire, E. et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439, 871–874 (2006)
  Article ADS CAS Google Scholar
• Schlesinger, Y. et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nature Genet. 39, 232–236 (2007)
  Article CAS Google Scholar
• Ooi, S. K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007)
  Article ADS CAS Google Scholar
• Gordon, M. et al. Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries. Mol. Cell. Biol. 27, 4058–4069 (2007)
  Article CAS Google Scholar
• Zalenskaya, I. A., Bradbury, E. M. & Zalensky, A. O. Chromatin structure of telomere domain in human sperm. Biochem. Biophys. Res. Commun. 279, 213–218 (2000)
  Article CAS Google Scholar
• Bolstad, B. M., Irizarry, R. A., Astrand, M. & Speed, T. P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185–193 (2003)
  Article CAS Google Scholar
• Dudoit, S., Gilbert, H. N. & van der Laan, M. J. Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: focus on the false discovery rate and simulation study. Biom. J. 50, 716–744 (2008)
  Article MathSciNet Google Scholar
• Storey, J. D. & Tibshirani, R. Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA 100, 9440–9445 (2003)
  Article ADS MathSciNet CAS Google Scholar