DNA methylation where does it occur?

! CpG islands usually unmethylated ! Intergenic regions usually methylated ! Repetitive elements usually methylated

DNA methylation is mutagenic

! CpGs under-represented in the genome
! as methylated C is prone to deamination to T

H 3C

Cytosine

5-methyl Cytosine

Thymine

What is the function of DNA methylation at intergenic regions?

! Maintain genomic integrity?
! Dnmt1 null cells display genomic instability ! Silence cryptic transcription start sites or cryptic splice sites

What is the function of DNA methylation at repetitive elements?

! Maintain genomic integrity
! silencing of repeats to prevent transposition ! mutation of the repeats (meC to T) to prevent transposition ! silencing of repeats, so avoid transcriptional interference from strong promoters ! methylation of repeats may prevent illegitimate recombination

What is the function of DNA methylation at repetitive elements?

! Genome defense model (Prof. Timothy Bestor)
! DNA methylation is mutagenic, so must also be a benefit i.e. protect the genome from transposable elements

DNA methylation and cancer

! In cancer, historically the earliest epigenetic aberration found was a genomewide lack of methylation, -! hypomethylation at intergenic regions/ repeats, and genomic instability (covered in Cancer Epigenetics lectures later) Feature found in all cancers ever studied, more consistently than genetic mutations!

DNA demethylation
! DNA methylation is mitotically heritable, and originally thought to be irremovable, except by failure to maintain methylation by DNMT1 DNA demethylation shown to occur in early development, in primordial germ cell development and at later specific stages of differentiation (covered in
Epigenetic Reprogramming lectures later)

Around year 2000, shown this could happen without DNA replication, so could also be an active process

DNA demethylation how does it occur?

! Passive DNA demethylation
-! Dilution of DNA methylation with every cell division, when DNMT1 is not expressed or not in the nucleus

! Active DNA demethylation,

-! Not simple removal of methyl group, as C-C bond is very difficult to remove -! Enzymatic removal via intermediates, using multiple different systems -! TET proteins main players, plus AID

Summary of DNA methylation

! ! ! ! ! ! ! Occurs at CpG dinucleotides Associated with gene silencing when found at promoters Helps to maintain genomic stability Laid down by DNA methyltransferases Mitotically heritable, due to features of DNMT1 Can be removed passively, or actively which involves TET proteins Essential for viability, as DNMT knockouts die in utero