Understanding Epigenetics

Epigenetics

• Genetics is the study of inheritance
• "Gen(e)" means "to produce," within the context of reproduction
• "Epi" signifies "above," "upon," or "in addition to"
• Epigenetics literally refers to the study of traits above inheritance

Epigenetics as an Odd Phenomenon

• This raises the question of whether Lamarckism is making a return
• A modified "agouti" gene in mice leads to yellow coat color and extreme obesity
• Female mice fed a specific diet during gestation produce wild-type offspring, despite inheriting the modified "agouti" gene
• Long-term studies on Dutch citizens who survived the World War II famine indicate an increased risk of heart disease, diabetes, and obesity compared to individuals who did not experience a famine

Five Features of Epigenetic Modifications

• Epigenetic modification patterns change chromatin structure
• They are transmissible during cell division
• They are reversible
• They are directly linked to gene transcription
• They do not alter DNA sequence

Position Effects in Epigenetics

• Euchromatin consists of loosely compacted genomic regions (chromatin) with higher transcriptional activity
• Heterochromatin is densely compacted chromatin, with lower transcriptional activity
• Some genomic regions are constitutively heterochromatin
• Facultative heterochromatin regions switch between euchromatin and heterochromatin states
• Genomic regions can be "transcriptional hotspots" or "transcriptional coldspots"
• These characteristics are termed "position effects"
• This is an important consideration for generating transgenic model organisms

Nucleosome Structure

• It consists of DNA wound around 8 histone proteins
• Composed of a H2A-H2B dimer and a H3-H4 tetramer
• Histone proteins enable DNA to coil around it
• The structure offers the context behind heterochromatin (more compact) vs. euchromatin (less compact)

Chromatin Modifiers

• Acetylation relaxes histone/DNA interaction by neutralizing positively charged histones
• Histone acetyltransferases (HATs) add acetyl groups to histones, leading to euchromatin
• Histone deacetylases (HDACs) remove acetyl groups from histones, leading to heterochromatin
• Methylation is associated with heterochromatin, but can also lead to euchromatin
• Histone methyltransferases (HMTs) add methyl groups to histones
• Histone demethylases (HDMTs) remove methyl groups from histones

Position Effect Variegation (PEV)

• Position effect variegation (PEV) occurs when heterochromatic areas spread into euchromatin, silencing gene transcription
• PEV was first discovered in a Drosophila mutant line, where an inversion on the X chromosome placed the white gene near the centromere in a heterochromatic region
• The wild-type allele for the white gene produces red eyes, and the gene was named after a mutant phenotype
• PEV created a mosaic where some cells in the fly compound eye were wild-type and other cells were mutated, even though the flies are genotypically wild-type

PEV and Chromatin Structure

• When the white gene is outside of heterochromatin in some cells, this leads to wild-type eye colour
• When the white gene is inside of heterochromatin in some cells, this leads to mutant eye colour

Mutations That Affect Chromatin

• E(var) mutations are enhancers of position effect variegation and enhance mutant phenotypes by encouraging the spread of heterochromatin
• Su(var) mutations are suppressors of position effect variegation and restrict heterochromatin spread, encouraging wild-type phenotype

X-Inactivation in Female Placental Mammals

• It occurs early in embryonic development
• A given cell inactivates either the maternally or paternally inherited X chromosome on a random basis
• All cells in a female's body are mosaics of two cell types: one expresses the maternal X chromosome, and the other expresses the paternal X chromosome
• This is also considered an epigenetic phenomenon

Colour-Blind Mosaicism

• This is X-inactivation and and colour vision for a female carrier for colorblindness

Long noncoding RNA & X-inactivation

• Long noncoding RNAs (lncRNA): These RNAs lack open reading frames
• lncRNAs play a role in gene regulation in eukaryotic cells
• lncRNAs were studied in stem cells of mice embryos
• They act as scaffolds that link to regulatory proteins, affecting chromatin structure
• X-inactivation-specific transcript (Xist) is an example of a lncRNA

Xist & X-Inactivation Process

• The Xist gene is in the X-inactivation center (XIC) on the X chromosome
• It is active in heterochromatic X chromosomes
• It is inactive in euchromatic X chromosome
• Xist RNA is produced on the X chromosome to be inactivated
• It spreads along the length of the chromosome and inactivates almost all the genes, silencing the chromosome

Genomic Imprinting

• This is an example of a heritable epigenetic phenomenon
• It involves genes whose expression in offspring depends on the parent that passed it on
• Maternal imprinting: the allele passed on by the mother is inactivated, so offspring express the allele from the father
• Paternal imprinting: the allele passed on by the father is inactivated, so offspring express the allele from the mother
• This can be X-linked or autosomal

Maternal Imprinting

• It means only females switch alleles off when passing them on; their children are not affected
• In a pedigree analysis, Joan is affected (black), but has no affected children
• Some children are carriers (grey), meaning their mother "imprinted" the disease allele
• Joan's carrier son, Jim, has affected children
• It means only females switch the allele off when passing it on, and males do not
• Therefore, only affected males or carrier males can have affected children

Paternal Imprinting

• The opposite of maternal imprinting
• It means only males switch the allele off when passing it on
• Michael is affected (black) but has no affected children, but all children are carriers
• Only Michael's daughter, Anne, has affected children
• Therefore, only affected females or carrier females can have affected children
• Anne's children had a 50% chance of being affected, while Tom's children had a 0% chance

IGF2 and H19

• Both genes are close to each other on chromosome 11 and play a role in embryonic growth
• IGF2 (insulin growth factor 2) is only expressed on the paternally inherited chromosome
• H19 is only expressed on the maternally inherited chromosome
• Russell-Silver syndrome results when both chromosomes display maternal expression patterns; infants with this condition tend to be born underweight
• Beckwith-Wiedemann syndrome results when both chromosomes display paternal expression patterns and condition involves overgrowth of tissue
• In maternal chromosomes, an enhancer drives H19 expression, and an insulator protein blocks IGF2 expression. In paternal chromosomes, methylation blocks H19 expression, so the enhancer drives IGF2 expression

Epigenetics as an Odd Phenomenon Explained

• In mice that have the modified agouti gene will lead to yellow coat color and extreme obesity
• The modified diet was rich in methyl factors, which led to increased methylation and silencing of the modified agouti gene
• Long-term studies of Dutch citizens that survived a famine during world war 2 indicates increased risk of heart disease, diabetes, and obesity compared to people that did not experience a famine
• IGF2 gene is less methylated in citizens born during the famine
• Siblings in the same families born after the famine have higher methylation of IGF2