Module 4: DNA Methylation — Quick Notes

Alterations to DNA and chromatin structure that affect traits, not caused by changes in the DNA sequence itself.
Epigenetics can be passed to other cells or generations, but is not as stably inherited as genetic changes.
Epigenetics = “Over”-genetics; regulates how the genome is read without changing the sequence.

Genetic variation: changes in the DNA base sequence; inheritance is typically permanent barring mutation.
Epigenetic variation: modifications in DNA and histone proteins that do not change the DNA base sequence; inheritance is possible but not guaranteed; marks can be reset.
Genetic variation is usually conserved across cell types; epigenetic variation can differ between cell types and respond to the environment.

Addition of a methyl group to cytosine; most common at the CpG dinucleotide, denoted $mCpG$ .
Other contexts occur: $CHG$ or $CHH$ (H = A, C, or T).
Catalyzed by DNA methyltransferases (DNMTs), e.g., $DNMT1$ , $DNMT3$ .
Promoter methylation tends to repress transcription; methylated promoters are less transcribed than unmethylated ones.

CpG dinucleotides occur less often than expected in mammalian genomes; uneven distribution due to evolutionary mutation.
CpG islands: CpG-rich segments (~1–2 kb) near promoters; often unmethylated when genes are active.
CpG islands are useful for identifying genes and serve as markers in genome annotation pipelines.

The mCpG site sits in the major groove and can block transcription factor binding.
mCpG recruits regulatory proteins that repress transcription and attracts histone deacetylases (HDACs), further repressing transcription.

In mammals, the inactive X chromosome is extensively methylated.
Repetitive sequence regions tend to be methylated.
DNA methylation is involved in imprinting, where gene expression depends on parental origin.
Overall, methylation is associated with transcriptional repression.

Queen and worker bees share the same genome but differ in phenotype due to diet.
Royal jelly suppresses Dnmt3, leading to queen traits (larger size, ovaries).
Demonstrates epigenetic control of development via DNA methylation changes.

RNA interference (RNAi) pathway used to inhibit Dnmt3 expression, impacting queen development.
Mechanism: dsRNA is processed by Dicer → siRNA + RISC → mRNA cleavage and gene silencing.

Techniques evolved from restriction enzymes to bisulfite-based methods.
Major categories: methylation-sensitive restriction enzyme methods and bisulfite sequencing (plus sequencing-based approaches).
Timeline of methods includes MS-HRM, MeDIP-Seq, MethylC-Seq, BS-Seq, etc.

Unmethylated cytosines are converted to uracil (read as thymine after sequencing); methylated cytosines remain as cytosine.
Compare treated (bisulfite) vs untreated sequences to identify methylated sites.
This enables base-resolution maps of cytosine methylation across the genome.

Epigenetic marks can persist across generations, but may be reset depending on context (reproduction mode, environmental cues).
Mechanisms include ncRNAs, histone modifications, and DNA methylation dynamics.

During DNA replication, hemimethylated sites form; maintenance DNMTs are attracted to methyl groups and copy methylation to the newly synthesized strand.
Methylation can be reversed (demethylation) in germline or in response to environmental stimuli.

Environment can influence epigenetic variation; genetic variation is more stable.
Epigenetic marks and genetic variation interact to shape phenotypes and adaptation.

Epigenetics: heritable changes in gene expression not due to DNA sequence changes.
$mCpG$ : methylated cytosine at CpG; primary methylation context in mammals.
CpG islands: promoter-proximal, CpG-rich regions often unmethylated when genes are active.
DNMTs: enzymes that catalyze DNA methylation (e.g., $DNMT1$ , $DNMT3$ ).
Bisulfite sequencing: gold-standard method for base-resolution DNA methylation mapping.
Epigenetic inheritance is possible but not guaranteed; marks can be reset or persist across generations depending on context.