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Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation Tuncay Baubec, Daniele F. Colombo, Christiane Wirbelauer, Juliane Schmidt1, Lukas Burger, Arnaud R. Krebs, Altuna Akalin & Dirk Schubeler De novo methylation and maintenance methylation of DNA E. Li and Y. Zhang , Harb Perspect Biol 2014 Function of mammalian DNA methyltransferases DNA methyltransferase Species Major activity Major phenotypes of loss of function Dnmt1 Mouse Maintenance methylation of CpG Genome-wide loss of DNA methylation, embryonic lethality at embryonic day 9.5 (E9.5), abnormal expression of imprinted genes, ectopic X-chromosome inactivation, activation of silent retrotransposon. In cancer cell lines, it leads to cell cycle arrest and mitotic defects. Dnmt3a Mouse De novo methylation of CpG Postnatal lethality at 4–8 wk, male sterility, and failure to establish methylation imprints in both male and female germ cells Dnmt3b Mouse De novo methylation of CpG Demethylation of minor satellite DNA, embryonic lethality around E14.5 days with vascular and liver defects. (Embryos lacking both Dnmt3a and Dnmt3b fail to initiate de novo methylation after implantation and die at E9.5.) DNMT3B Human De novo methylation of CpG ICF syndrome: immunodeficiency, centromeric instability, and facial anomalies. Loss of methylation in repetitive elements and pericentromeric heterochromatin. E. Li and Y. Zhang , Harb Perspect Biol 2014 Mammalian DNA methyltransferases. PWWP: a highly conserved “proline-tryptophan-tryptophan-proline” motif involved in heterochromatin association ATRX: a cysteine-rich region containing a zinc finger and PHD domain implicated in protein–protein interactions E. Li and Y. Zhang , Harb Perspect Biol 2014 Proposed models of DNMT targeting • How genomic DNA methylation patterns are regulated remains poorly understood Proposed models: 1. Readout of histone modifications 2. Binding to nucleosomes 3. recruitment by accessory proteins 4. RNA-mediated or DNA sequence-specific targeting or repulsion Biotin tagging of DNMT3A2 and DNMT3B1 in mouse embryonic stem cells DNMT3A2 and DNMT3B1 show similar localization to most parts of the genome, but are differently recruited to gene bodies. De novo methylation relative to DNMT binding and chromatin features De novo methylation relative to DNMT binding and chromatin features Methylation analysis at selected sites indicates a role for DNMT3B in methylation fidelity at transcribed genes DNMT3B binding follows co-transcriptional deposition of H3K36me3 The H3K36 methyltransferase SETD2 is required for targeting de novo methylation to transcribed Setd2: mediates H3K36me3 methylation at active genes The PWWP domain of DNMT3B is required for targeting de novo methylation to transcribed Mutations in the PWWP domain of DNMT3B1 S277P: ICF syndrome-related mutation in the PWWP domain leads to loss of binding at active gene bodies Conclusion • Deferential binding and methylation patterns - DNMT3B1 and DMT3A2 • DNMT3B1 recruitment to active genes via H3K36me3 levels - de novo methylation of active genes - suggesting a direct requirement for H3K36me3