Lecture 17 and 18: Epigenetics and Imprinting

Epigenetic Phenomena

Genomic imprinting, X chromosome inactivation, and position effects

All change phenotype without altering genotype.

Genomic Imprinting

A process where genes are expressed in a parent-of-origin specific manner, often associated with differential DNA methylation.

X Chromosome Inactivation

A mechanism in individuals with multiple Xs where one X chromosome is randomly inactivated to equalize gene dosage between sexes.

Position Effects

Phenomenon where the expression of a gene is influenced by its location within the genome.

How can DNAme affect transcription

1. Direct methylation of CG-rich promoters

2. Inhibition of transcription factor binding to enhancers

3. Recruitment of repressive methyl-binding proteins.

De novo DNA methylation proteins

DNMT3A and its cofactor DNMT3L are essential for establishing new DNA methylation patterns in oocytes and sperm.

ICF Syndrome

A disorder linked to mutations in DNMT3B, characterized by immunodeficiency, centromeric instability, and facial anomalies, affecting centromeric DNA methylation.

Oocyte DNAme regions

During growth, oocytes are methylated at the gene bodies of transcribed active genes.

Steps of DNAme in oocyte genome

Transcribed regions are defined by RNA pol II → catalyzes transcription

Histone methyltransferase SETD2 acts as writer → deposits H3K36me3

DNMT3A/B is recruited to marker via PWWP domain

DNMT3A/B methylates regions

CpG Islands

GC-rich sequences at promoter regions of 70% of genes that are usually unmethylated to facilitate transcription.

H3K4me3 and CGIs relationship

H3K4me3 prevents DNMT3A and 3B from methylating CpG islands, keeping them unmethylated.

Demethylation differences in PGCs

DNA methylation marks at imprinted genes are erased in the germline, while preimplantation PGCs maintain marks.

H3K9me3 and imprinted DNA maintenance

Zinc-finger proteins mark imprinted DMRs

SETDB1 is recruited and deposits H3K9me4 on DNA methylated allele

H3K9me3 marker regions are preferentially maintained by DNMT1 cofactor UHRF1

parthenogenetic embryos

embryo develops from an unfertilized egg cell - no male contribution

lethality of parthenogenetic embryos hypotheses

extra-genetic sperm contribution or activation by fertilization is required

• gynogenetic embryos are fertilized by sperm then removed → sperm extra-genetic components do not rescue phenotype

homozygosity of parthenogenetic embryos for most markers

• gynogenetic embryos can be made from two non-identical maternal pronuclei

non-equivalence of maternal and paternal genetic contributions

Characteristics of imprinted genes

1. Monoallelic expression

2. Clustered in chromosomal domains

3. Linked to epigenetic marks on parental alleles.

DNAme regulation of imprinted genes

Paternally expressed genes can silence the maternal copy through methylation at CG-rich promoters.

Silence maternal allele by cis-acting long non coding RNA expressed from maternal allele - own promoter is silenced by DNAme mark inherited from sperm

When do germ cells acquire DNAme

Male germ cells acquire de novo DNA methylation post-implantation

Female germ cells acquire it during oocyte growth.

Critical enzyme in DNAme

DNMT3A is the enzyme absolutely required for establishing DNA methylation.

Mammalian species without genomic imprinting

Genomic imprinting is not observed in egg-laying monotremes like the platypus and echidna.