DNA Methylation Patterns
Speaker: Bhupendra Singh Rawat
Ph.D scholar 1st
• Demethylation during early development
• De novo methylation at the time of implantaton
• Post-implantation methylation changes
• Tissue-specific methylation patterns
• Future prospects
• DNA methylation is
a biochemical process
involving the addition of
a methyl group to
the cytosine or adenine
• DNA methylation alters
the expression of genes
in cells as cells divide and
differentiate from ESCs
into specific tissues.
The methylation reaction
(Leonhardt and Cremer, 1995)
• DNA methylation causes transcriptional repression
• H3K9 and H3K27 methylation causes transcriptional
• H3K4 methylation causes transcriptional activation
• Acetylation of histones generally leads to transcriptional
In DNA where methylations are happening?
• CpG islands
How to know which region of DNA undergoing
• HpaII (CCGG) and HhaI (GCGC)
Mammalian DNA methylation machinery
Gopalakrishnan et al., 2008
DNA methylation and transcriptional repression
Singal and Ginder, 1999
Demethylation during early development
• Methylation pattern of parental gametes are largely
erased in the preimplantation stage(morula and
A. Active demethylation: begins in the zygote.
B. Passive demethylation: occurs during first few early
replication cycles. Dnmt1 relocate from nucleus to
De novo methylation at the time of implantaton
• Mediated by Dnmt3a and Dnmt3b.
• Generate bimodal pattern of methylation.
• CpG islands remain protected.
Mechanism of CpG island protection
Cedar and Bergman, 2009
H3K4me3 may be involved in CpG island protection
Post-implantation methylation changes
• Post-implantation methylation changes are of tissue
specific or gene specific nature.
• Example: silencing of pluripotency genes like Oct-3/4
Inactivation of pluripotency genes.
Cedar and Bergman, 2012
• Another major event occurring after implantation
throughout all cells of the embryo is the inactivation of
one X-chromosome in female animals.
• This is also achieved by changes in chromatin structure
followed by de novo methylation of CpG island
• Probably it also mediated by histone methylases capable
of generating heterochromatin and then recruiting Dnmts
that carry out targeted local methylation many days after
the initial inactivation event (Cedar and Bergman, 2009).
Tissue-specific methylation patterns
• Tissue specific genes: non CpG island promoter
(methylated at implantation).
• These promoters are demethylated during tissue
development for which cell-type-specific factors
recognize them and then recruit demethylases.
• This demethylation occurs in an active manner(not
require DNA replication) and is mediated by cis acting
sequences and trans acting factors (Kirillov et al., 1996).
• CpG island methylation sometimes leads to up
regulation of gene.
• How cell target de novo methylations to specific sites on
• A complex of protein bound at specific gene.
• Almost all the sites that undergo targetted de novo
methylation are known polycomb targets (Straussman et
• Mammals have 2 main polycomb complexes: PRC1 and
• Polycomb complex has an ability to recruit Dnmt3a and
Targeted de novo methylation by polycomb
Cedar and Bergman, 2012
DNA methylation and polycomb complexes:
linking development to cancer
Gopalakrishnan et al., 2008
PRC 1 PRC 2
• DNA methylation patterns are erased during pre-
implantation and then re-established throughout
development via sequence information in the DNA.
• Once established, DNA methylation patterns can be
maintained autonomously through many cell divisions.
• DNA methylation inhibits gene expression by affecting
• Changes in methylation during post-implantation
development are usually secondary to factor-mediated gene
activation or repression, but this subsequent methylation
pattern provides long-term stability.
• What is the mechanism involved in setting up methylation
patterns? How is local sequence information translated in
• How does methylation play a role in lineage determination
• What are the roles of environment and aging on DNA
methylation? What are methylation’s effects on disease
• How histone and DNA methylation are coordinated at
1. Cedar, H. and Bergman, Y. 2009. Linking DNA methylation and histone
modification: patterns and paradigms. Nature Reviews Genetics. 10: 295-
2. Cedar, H. and Bergman, Y. 2012. Programming of DNA methylation
patterns. Annu. Rev. Biochem. 81: 97–117.
3. Gopalakrishnan, S., Van Emburgh, B.O., Robertson,K.D. 2008. DNA
methylation in development and human disease. Mutation Research. 647:
4. Kirillov, A., Kistler, B., Mostoslavsky, R., Cedar, H., Wirth, T. and Bergman,
Y. 1996. A role for nuclear NF-κB in B-cell-specific demethylation of the
Igκlocus. Nat. Genet. 13: 435–41.
5. Leonhardt, H. and Cremer, T. 1995. Functional Analysis of DNA
Methylation in Development and Disease. an der Fakultät für Biologie. 1-
6. Singal, R. and Ginder G.D. 1999. DNA Methylation. Blood. 93: 4059-4070.
7. Straussman, R., Nejman, D., Roberts, D., Steinfeld ,I. and Blum, B. 2009.
Developmental programming of CpG island methylation profiles in the
human genome. Nat. Struct. Mol. Biol. 16: 564–71.
- inhibition of DNMT1, -
- replication dependent
- replication independent
- clearly demonstrated in some cases
- unknown mechanism, unknown demethylase. DNA repair/glycosylase?
- DNA methylation is stable but reversible