DNA Methylation and Imprinting Notes

Eighth lecture focusing on revelations of biochemistry.
Topics include DNA methylation, Akuri mice, imprinting, and X chromosome inactivation.
DNA methylation is part of epigenetic modification, along with histone tail modification and differential RNA splicing.
Content will be covered in the last exam.

Adding methyl groups to DNA bases, specifically cytosine (C).
Focus on adding methyl groups to CpG islands in promoter or enhancer regions.
This modification silences genes.
Enzymes involved: DNA methyltransferases (DNMTs).
First methylation by de novo methyltransferases, maintained by maintenance methyltransferases.
During cell division, one strand remains methylated, and the other is methylated by maintenance methyltransferasae.
De novo methyltransferases act through a pathway that destroys active histone marks, recruits DNMTs, which leads to DNA methylation.
DNA metal binding proteins bind to these sites and prevent transcription machinery from accessing them.
Defects in these metal binding proteins can cause diseases like Rett syndrome (X-linked mental retardation).

Genetically identical but epigenetically different mice.
Mother's diet influences gene expression in offspring.
Involves metastable epialleles, which are vulnerable to environmental influences.
Akuri gene has a retrovirus insertion (IAP) in the promoter region.
This insertion causes the Akuri gene to be active all the time.
Continuous expression leads to diabetes and changes in coat color in mice.
DNA methylation of the retroviral insertion can turn off the Agouri gene when it should be off.
Methylation depends on the mother's diet.
Akuri mice can be used as a biosensor to detect supplements in the environment; normal coat color indicates sufficient supplements.
This concept might extend to humans, where certain genes can be affected by the mother's nutrition.

Incorrect DNA methylation is prevalent in cancers and aging.
Example: Abnormal DNMT activity in tumor suppressor genes like RP or VHL can cause cancer.
Overactivation of methyltransferases leads to more metal marks and silencing of tumor suppressor genes.

Enzyme recognizes methylated cytosine in one strand.
CpGs are recognized, where cytosine is located next to guanine.
Active site of the enzyme is configured to find the C in the opposite strand in the CPG module.
This mechanism is universal, even in bacteria.

Like other epigenetic modifications, DNA methylation is reversible.
Active reversal uses TET enzymes (demethylases), which create a hydroxylated metal group as a first step.
Passive demethylation occurs during DNA replication, where metal groups dilute away without proper maintenance.

In some genes, only one parental allele is active.
Transcription occurs from only one chromosome (either from mom or dad).
Known imprinted genes: Over 260 in mice, speculated over 300 in humans.
Example: Paternal imprinting
Imprints are erased in germ cells during maturation and then re-established.
De novo methyltransferases add parental-specific imprints during germ cell development.
Mutations in one allele of an imprinted gene can have serious consequences.

Regulated by a cis regulatory enhancer sequence.
Insulator element between enhancer and transcription start site (TSS) that can be recognized by CTCF.
If CTCF binds, it creates a barrier, preventing enhancer regulation.
If insulator region is methylated, CTCF cannot bind, allowing enhancer to regulate TSS.
In paternal chromosomes, DNA methylation allows gene expression.

Can be transcribed in both directions.
In maternal case, an opposing promoter is methylated, preventing transcription in that direction.
In paternal case, this site is not methylated, allowing transcription of a long non-coding RNA.
This RNA brings histone modifying enzymes (G9A, histone three k nine methyltransferase) to modify histones, negatively affecting transcription.

Imprinted genes are found in humans.
Defects can cause disorders like Beckwith-Wiedemann syndrome (BWS), a syndrome of overgrowth.
Imprinted genes are often located in specific regions on chromosomes, affecting overgrowth.

Only one autosomal allele is transcribed for imprinted genes.
Parental origin defines whether the gene is expressed.
Germ cells add imprinting marks specifically in sperm or oocyte.
Marks are established in the germline by de novo methyltransferases and maintained by maintenance methyltransferases.
Defects in imprinting can cause lethality.
Having one normal copy of a gene may not be sufficient if the normal copy is imprinted.