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  • 1
    Publication Date: 2011-04-05
    Description: Methylation at the 5' position of cytosine in DNA has important roles in genome function and is dynamically reprogrammed during early embryonic and germ cell development. The mammalian genome also contains 5-hydroxymethylcytosine (5hmC), which seems to be generated by oxidation of 5-methylcytosine (5mC) by the TET family of enzymes that are highly expressed in embryonic stem (ES) cells. Here we use antibodies against 5hmC and 5mC together with high throughput sequencing to determine genome-wide patterns of methylation and hydroxymethylation in mouse wild-type and mutant ES cells and differentiating embryoid bodies. We find that 5hmC is mostly associated with euchromatin and that whereas 5mC is under-represented at gene promoters and CpG islands, 5hmC is enriched and is associated with increased transcriptional levels. Most, if not all, 5hmC in the genome depends on pre-existing 5mC and the balance between these two modifications is different between genomic regions. Knockdown of Tet1 and Tet2 causes downregulation of a group of genes that includes pluripotency-related genes (including Esrrb, Prdm14, Dppa3, Klf2, Tcl1 and Zfp42) and a concomitant increase in methylation of their promoters, together with an increased propensity of ES cells for extraembryonic lineage differentiation. Declining levels of TETs during differentiation are associated with decreased hydroxymethylation levels at the promoters of ES cell-specific genes together with increased methylation and gene silencing. We propose that the balance between hydroxymethylation and methylation in the genome is inextricably linked with the balance between pluripotency and lineage commitment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ficz, Gabriella -- Branco, Miguel R -- Seisenberger, Stefanie -- Santos, Fatima -- Krueger, Felix -- Hore, Timothy A -- Marques, C Joana -- Andrews, Simon -- Reik, Wolf -- G0801156/Medical Research Council/United Kingdom -- G0801727/Medical Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2011 May 19;473(7347):398-402. doi: 10.1038/nature10008. Epub 2011 Apr 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB22 3AT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21460836" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies/immunology ; Cell Differentiation/*genetics ; Cell Line ; Cell Lineage/genetics ; CpG Islands/genetics ; Cytosine/*analogs & derivatives/analysis/immunology/metabolism ; *DNA Methylation ; DNA-Binding Proteins/deficiency ; Down-Regulation ; Embryoid Bodies/cytology/metabolism ; Embryonic Stem Cells/*cytology/*metabolism ; Euchromatin/genetics/metabolism ; Exons/genetics ; *Gene Expression Regulation, Developmental ; Gene Silencing ; Genome/genetics ; Mice ; Pluripotent Stem Cells/cytology/metabolism ; Promoter Regions, Genetic/genetics ; Proto-Oncogene Proteins/deficiency ; Reproducibility of Results ; Sequence Analysis, DNA ; Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-07-12
    Description: Adverse prenatal environments can promote metabolic disease in offspring and subsequent generations. Animal models and epidemiological data implicate epigenetic inheritance, but the mechanisms remain unknown. In an intergenerational developmental programming model affecting F2 mouse metabolism, we demonstrate that the in utero nutritional environment of F1 embryos alters the germline DNA methylome of F1 adult males in a locus-specific manner. Differentially methylated regions are hypomethylated and enriched in nucleosome-retaining regions. A substantial fraction is resistant to early embryo methylation reprogramming, which may have an impact on F2 development. Differential methylation is not maintained in F2 tissues, yet locus-specific expression is perturbed. Thus, in utero nutritional exposures during critical windows of germ cell development can impact the male germline methylome, associated with metabolic disease in offspring.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404520/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404520/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Radford, Elizabeth J -- Ito, Mitsuteru -- Shi, Hui -- Corish, Jennifer A -- Yamazawa, Kazuki -- Isganaitis, Elvira -- Seisenberger, Stefanie -- Hore, Timothy A -- Reik, Wolf -- Erkek, Serap -- Peters, Antoine H F M -- Patti, Mary-Elizabeth -- Ferguson-Smith, Anne C -- 095606/Wellcome Trust/United Kingdom -- 095645/Wellcome Trust/United Kingdom -- P30 DK036836/DK/NIDDK NIH HHS/ -- P30DK036836/DK/NIDDK NIH HHS/ -- R00 HD064793/HD/NICHD NIH HHS/ -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2014 Aug 15;345(6198):1255903. doi: 10.1126/science.1255903. Epub 2014 Jul 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK. ; Research Division, Joslin Diabetes Center and Harvard Medical School, 1 Joslin Place, Boston, MA 02215, USA. ; The Babraham Institute, Babraham, Cambridge, and Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK. ; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. Faculty of Sciences, University of Basel, Basel, Switzerland. Swiss Institute of Bioinformatics, Basel, Switzerland. ; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. Faculty of Sciences, University of Basel, Basel, Switzerland. ; Research Division, Joslin Diabetes Center and Harvard Medical School, 1 Joslin Place, Boston, MA 02215, USA. afsmith@mole.bio.cam.ac.uk mary.elizabeth.patti@joslin.harvard.edu. ; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK. afsmith@mole.bio.cam.ac.uk mary.elizabeth.patti@joslin.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25011554" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caloric Restriction ; *DNA Methylation ; Epigenesis, Genetic ; Female ; Fetal Nutrition Disorders/genetics/*metabolism ; Insulin/secretion ; Male ; Metabolic Diseases/metabolism ; Mice ; Mice, Inbred ICR ; Nucleosomes/metabolism ; Pregnancy ; *Prenatal Exposure Delayed Effects ; Spermatozoa/*metabolism/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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