1. 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

2. De novo methylation and maintenance methylation of DNA
E. Li and Y. Zhang , Harb Perspect Biol 2014

3. Major phenotypes of loss of function
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
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
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
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

4. 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

5. Proposed models of DNMT targeting
How genomic DNA methylation patterns are regulated remains poorly understood
Proposed models:
Readout of histone modifications
Binding to nucleosomes
recruitment by accessory proteins
RNA-mediated or DNA sequence-specific targeting or repulsion

6. Biotin tagging of DNMT3A2 and DNMT3B1 in mouse embryonic stem cells

7. DNMT3A2 and DNMT3B1 show similar localization to most parts of the genome, but are differently recruited to gene bodies.

8. De novo methylation relative to DNMT binding and chromatin features

9. De novo methylation relative to DNMT binding and chromatin features

10. Methylation analysis at selected sites indicates a role for DNMT3B in methylation fidelity at transcribed genes

11. DNMT3B binding follows co-transcriptional deposition of H3K36me3

12. The H3K36 methyltransferase SETD2 is required for targeting de novo methylation to transcribed
Setd2: mediates H3K36me3 methylation at active genes

13. 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

14. 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