Epigenomics: Allelic Imbalance & Expression

• Lecture given by Associate Professor Zanda Daneberga
• Lecture is part two of lecture five
• Lecture focuses on Epigenomics

Allelic Imbalance in Gene Expression

• Allelic imbalance occurs when the ratio of gene expression levels from two alleles in a diploid genome is not 1 to 1
• This affects 5-20% of autosomal genes
• Variants in gene regulatory sequences or epigenetic marks lead to varied expression levels at two gene copies
• Allelic imbalance typically occurs in early embryogenesis

Monoallelic Expression

• Monoallelic expression refers to when only one of two gene copies is active while the other is silent
• About 0.5% to 15% of autosomal genes show random monoallelic gene expression
• Different cells express only one allele independently of the genomic sequence, in a cell-type-specific manner

Types of Monoallelic Expression:

• Somatic rearrangement
• Random allelic silencing or activation
• Genomic imprinting
• X chromosome inactivation

Somatic Rearrangement

• Somatic rearrangement involves changes in DNA organization to make a functional gene at one gene copy, but not the other
• Choice of one gene copy is random

Somatic Rearrangement - Example

• Immunoglobulin and T-cell receptor genes undergo somatic rearrangement
• Somatic rearrangement occurs in B- and T-cell lineages
• Bacteria and viruses are recognized by B and T cells of the immune system via antigen receptors, resulting in antibodies
• The mechanism involves cutting and pasting DNA sequences to rearrange genes in somatic cells, creating antibody diversity

Random Allelic Silencing or Activation

• Expression comes from only one gene copy due to different epigenetic changes
• Impacts olfactory receptor genes in sensory neurons, other chemosensory or immune system genes, and up to 10% of genes in other cell types
• Involves a random choice of one gene copy in a specific cell type

Genomic Imprinting

• Epigenetic silencing of gene copy in imprinted regions
• There are over 100 known genes with developmental functions
• The imprinted region is marked epigenetically based on parental origin
• Parental gametogenesis

Sex Chromosome Inactivation

• Epigenetic gene dosage compensation mechanisms for genes on sex chromosomes vary across species
• Humans equalize X-chromosome gene dosage between sexes by inactivating one X chromosome in females
• The X chromosome is randomly inactivated in humans (paternal or maternal)

X Chromosome Inactivation Specifics

• Epigenetic silencing of X chromosome linked genes on one female chromosome
• Impacts most X-linked genes in females
• Involves random choice of one X chromosome in early embryogenesis
• XX female pluripotent progenitor cells have two active X chromosomes, products of escape genes are expressed equally
• Upon differentiation, a 2x dose of the escape gene product induces the XIST gene (X-inactive specific transcript, which encodes ncRNA molecule), from future inactive X
• The XIST gene encodes ncRNA (epigenetic initiator)
• The XIST gene ensures epigenetic changes silence the X chromosome
• Inactivation occurs around days 3-7 of embryonic development
• After XIST is induced, silencing of genes on the inactive X chromosome occurs
• Inactivation involves methylation of cytosine and H4 histone hypo-acetylation

Environmental Influence on the Epigenome: Dutch Hunger Winter (1944–1945)

• The famine impacts the birth weights of children
• Those exposed the last few months of pregnancy had small birth weights
• Those exposed in the first three months of pregnancy gave birth to abnormal-size babies
• Body mass in adulthood: babies who were born small stayed small
• Those exposed early in pregnancy had higher obesity rates

Epigenetics

• Insulin-like growth factor II (IGF2) is a key factor in human growth and development, maternally imprinted
• Methylation of five CpG dinucleotides within the IGF2 differentially methylated region (DMR) was measured six decades later
• Higher obesity rates relate to less methylation on the CpG island of the imprinted allele
• Small body mass in adulthood shows no epigenetic changes

Cancer Epigenomics

• In cancer tissues, DNA methylation is classically reduced globally
• Hypomethylating oncogene promoters reduces defence against repetitive sequences, leading to genome instability and chromosome structural changes
• Decreased gene methylation has subsequent effects on transcription

Chromatine Structure of Cancer Cells

• Somatic Stem cell state:
  • ↑ H3K9me2/3
  • ↑ DNA methylation?
  • ↓ Gene activity
• Cancer stem cell-like state:
  • ↓H3K9me2/3
  • ↓DNA methylation
  • ↑ Gene activity
• Differentiated cell:
  • ↑H3K9me2/3
  • ↑ DNA methylation
  • ↓ Gene activity

Aberration of the Epigenome Due to the Aging Process

• Intra-individual changes in global DNA hypomethylation are observed over time
• DNA methylation changes may predispose to cancer by inducing a more stem-cell-like state

Pathological Epigenetic Regulation in Genetic Neurodevelopmental Disorders

• Rett Syndrome:
  • Involves DNA methylation, histone methylation, and histone acetylation epigenetic modifications
  • Changes in the MeCP2 gene (methyl-CpG-binding protein-2) sequence lead to a reduced function
  • Normally recognizes methylated CpG islands and acts as a transcriptional repressor leading to aberrant changes in epigenetic regulation

Psychiatric Disorders

• Addiction to Cocaine:
  • Increased histone acetylation and DNA methylation, and reduced histone methylation
  • Acute and chronic cocaine exposure induces differential H3 and H4 acetylation
  • Chronic cocaine exposure reduces H3K9 di-methylation, mediated by the HMT G9a
  • Chronic cocaine exposure increases MeCP2 and MBD1 expression
• Depression:
  • Repressed histone acetylation, and increased histone and DNA methylation
  • HDAC2 and HDAC5 are downregulated upon chronic social defeat stress
  • Repressive methyl marks on H3 are upregulated in the promoter region of BDNF after chronic social defeat stress
  • Increased DNA methylation levels at GABA receptorcoding gene

Summary

• The epigenome = key interface between environment and genome.