Epigenetics, Methylation, Gene Expression, and Imprinting.

Division of Animal Sciences

• Institution: College of Agriculture, Food and Natural Resources

• Topic: Animal Products and Biotechnology

• Lecture: 5

• Date: 2025/09/09

Epigenetics

Definition of Epigenetics

• Branch of biology focused on causal interactions between genes and their products, leading to phenotype development.

  • Historical Definition: "Conrad Waddington, 1942"

  • Modern Definition: "The study of changes in gene function that are mitotically and/or meiotically heritable without altering DNA sequence."

• Key mechanisms include:

  • DNA methylation

  • Histone methylation

  • Histone acetylation

  • MicroRNA (miRNA)

• Ongoing research continues to identify additional mechanisms.

Phenotypic Differences in Monozygotic Twins

• Reference: Fraga et al., 2005. Proceedings of the National Academy of Sciences (PNAS)

• Example study of twins at various ages:

  • 3-year-old twins

  • 50-year-old twins

• Highlights the impact of environmental factors and lifestyle differences leading to epigenetic differences.

Nature vs. Nurture Debate

Key Concepts

• Information sources:

  • Nuclear (DNA)

  • Environmental effects

• Categories of interactions:

  • Environmental Exposures:

  • Influences during different life stages

  • Impact on phenotypes and biomarkers

  • Genetic Changes:

  • Mutations, DNA adducts

  • Epigenetic Changes:

  • DNA methylation

  • Alterations in proteins and histone marks

• Applications:

  • Disease prevention strategies based on understanding of epigenetics.

Rise of Epigenetics in Research

Publication Trends

• Analysis of publications on epigenetics from 1990-2013

  • Significant increase in publications since 2004

  • Data retrieved from the Web of Science, as of September 30, 2014

X Chromosome Inactivation

Mechanism

• Females have two X chromosomes; however, one is randomly inactivated.

• Historical context:

  • Identified in 1959 by Susumu Ohno

• Characteristics:

  • One of the X chromosomes condenses to form a Barr body.

• Biological Example:

  • Coloration in cats related to X-chromosome inactivation

  • Feline cloning and long non-coding RNA (e.g., XIST vs. TSIX).

Euchromatin vs. Heterochromatin

Distinctions

DNA Methylation and Gene Expression

Overview

• Definition of DNA methylation:

  • Methyl group attached to CpG sites, resulting in 5-methylcytosine (5mc).

  • Recognized since 1948 as a contributor to gene repression.

• Involvement of specific methyltransferases (DNMTs).

• Methylation levels vary across species, with notably low levels in insects.

• Crucial for genomic imprinting.

Overview of DNA Methylation Across Species

• Methylation levels measured using bisulfite conversion and genome-wide sequencing (BS-seq) or amplified fragment length polymorphism (AFLP). The latter is likely to overestimate DNA methylation.

Mechanism of DNA Methylation

• Enzymatic roles of S-adenosyl-L-methionine (SAM) and S-adenosyl-L-homocysteine (SAH) in the methylation process.

• DNA methyltransferases (DNMTs) involved:

  • DNMT1: Maintains methylation; catalytic activity increases with hemi-methylated DNA. Essential for development.

  • DNMT3A/B: Involved in de novo methylation associated with gene repression.

Epigenetic Inheritance and Maintenance of DNA Methylation

• During DNA replication, methylation is inherited:

  • Methylation patterns from the parent strand are maintained in the daughter strands.

• Critical for ensuring genomic stability across cellular generations.

Biological Impact of DNA Methylation

Mechanisms

1. Biochemical Consequences

• Influence of molecular structure and proteins on transcription and chromatin status.

2. Molecular Effects

• Gene transcription

• RNA metabolism

• Transposon silencing

3. Organismal Consequences

• Imprinting, development, and cancer.

Effects on Transcription

• Methylation modifies chromatin structure.

• Unmethylated DNA adopts an open conformation, facilitating transcription.

• Methyl-binding proteins, like Methyl-CpG-binding domain (MBD) proteins, bind to methylated DNA and regulate gene expression.

DNA Methylation on Promoters

• Methylation can either inhibit or promote transcription based on the sensitivity of transcription factors to DNA methylation.

Histone Code

Modification Mechanisms

Histone N-terminal Tails

• Rich in lysine and arginine.

• Modifications include acetylation (activating) and methylation (can be activating or repressing).

Histone Acetylation

• Correlated with transcriptional activation; accomplished by histone acetyltransferases (HATs).

• Acetylation causes chromatin unfolding, permitting transcription.

• Example: H3K9: Acetylation leads to gene activation; di- and tri-methylation lead to gene repression.

Variations in Histone Methylation

• Methylation can occur in three forms: monomethyl, dimethyl, and trimethyl.

• Different methylation patterns have varied functional outcomes regarding transcription repression or readiness.

Genomic Imprinting

Definition

• Monoallelic expression specific to the parent of origin for a small percentage of genes (less than 1%).

• Example: Insulin-like Growth Factor (IGF2), which is paternal-imprinted.

Historical Context

• Imprinting discovered in the 1970s, with critical findings in X chromosome inactivation.

  • Nuclear transfer experiments showed that both parental contributions were necessary for embryonic survival (e.g., Prader-Willi syndrome is maternally silenced).

Fate of Uniparental Embryos

• Normal zygotes compared to parthenogenetic and androgenetic zygotes show the necessity for both maternal and paternal genomes for successful development.

Reasons for Imprinting

• Imprinting disruptions during development can lead to embryonic lethality, highlighting its importance.

• Parental Conflict Hypothesis: Differences in strategies for resource allocation by maternal and paternal genomes impact gene expression.

Nutritional Influence on Epigenetics

Codified Mechanisms

• Dietary sources rich in methionine, serine, folate, biotin, and choline are important for methyl group transfer during DNA and histone methylation processes via SAM.

• Sufficient intake of nutrients influences the global methylation state and histone modifications.

Histone Acetylation

• Acetyl-CoA alters based on metabolic states, affecting histone acetylation levels through HAT activity.

Bioactive Compounds and Epigenetics

Overview

• Compounds can affect epigenetic mechanisms through the donation of methyl and acetyl groups, and by acting as essential cofactors (e.g., Fe, Cu).

Resveratrol

• A dietary polyphenol with potential anticancer properties, affecting cellular growth and inflammation.

• Concentrations have varying effects on cell proliferation, relevant to its proposed mechanisms in cancer therapies.

• Clinical doses cannot be achieved through typical dietary sources like red wine.

Implications for Animal Production

Key Considerations

• Gene expression is a determinant of phenotype variability.

• Anomalies in phenotype may arise from nutritional factors.

• The development of optimal feeding regimens and customized husbandry are crucial for improving animal genetics.

• Understanding whether observed genetic changes are genomic or epigenetic affects is critical for considering interventions like genome editing, which alters either DNA or RNA.