HUGE lecture 10 09/29/2026

What demonstrates that all cells within an organism harbor the same genome

nuclear transplant demonstrates that all cells within an organism harbor the same genome

What did John Gurdon win a Nobel prize for

Paper published in 1966 where he enucleated frog egg with UV radiation, took nuclei from somatic cell, implanted into the enucleated egg, and grew an adult nuclear transplant frog

Who is Dolly the sheep

first mammal to be cloned from an adult somatic cell

What did cloning experiments demonstrate

Cloning experiments demonstrated that somatic cells contain all the DNA required to form a new individual

How do cells adopt different fates during development

Cells undergo changes in gene expression that are stable (heritable) through cell division but that do not alter DNA sequence

Epigenetics

heritable changes in gene expression that are not due to changes in DNA sequence

What are the three epigenetic mechanisms

1. DNA methylation

2. Histone modification

3. Non-coding RNA

What does DNA methylation do

Regulates gene expression

What does histone modification do

Controls chromatin remodeling and assembly changing transcription facotr accessibility to promoters

What does non-coding RNA do

Regulates gene expression and protein synthesis

Where does DNA methylation occur on the pyrimidine ring

DNA methylation occurs at the 5 position of the pyrimidine ring

Where does DNA methylation occur in the genome

pDyrNimAidminetrhinygla. tTiohnisomcectuhryslaatitoCn pisGasdsoincuiacteledowtidthesreipnretshseiognenome

What is CpG methylation associated with

CpG methylation is associated with repression of gene transcription

DNA methyltransferases

Enzymes that add methyl groups to cytosine (CpG dinucleotides)

What are the three types of DNA methyltransferases we should know

DNMT1, DNMT3A, DNMT3B

What is DNMT1 also known as

maintenance methyltransferase

What does DNMT1 do

acts upon hemi-methylated DNA and methylates the other strand during cellular division

Where is DNA demethylation considered important

in the brain

What enzyme is responsibel for DNA demethylation in the brain

TET enzymes

What does DNA demethylation do in the brain

Regulates gene expression involved in key brain functions like learning, memory, and demethylation neuronal plasticity

What does DNA demethylation allow for

Allows for dynamic changes in neural activity based on experience and environment

Why is the mechanism of demethylation specifically important in neurons

neurons are not dividing- normally you can demethylate passively through cell division but neurons don’t divide

What are DNMT3A/B known as

de novo methyltransferases

What do DNMT3A and DNMT3B do

methylate CpGs regardless of mitosis/cell division

What does unmethylated CpG mean for transcription

transcription on

What does methylated CpG mean for transcription

transcription off

What state are most CpG dinucleotides in the genome

methylated

Where are islands of unmethylated CpG dinucleotides located

near gene promoters

What do CpG islands do

destabilize nucleosomes allowing binding of proteins that promote a transcriptionally active chromatin state

What are the two ways CpG methylation represses gene transcription

1. Block transcription factors

2. Recruit transcriptional repressors

Transcriptional repressor example

methyl-CpG binding protein 2 (MECP2)- variants in females cause developmental delay syndrome, Rett syndrome

What chromosome is MECP2 on and what does variation do to males

MECP2 is on chrX- variation is lethal in males

Gene-environment interaction

environment changes how your genes affect your health

What is MeDIP

methylated dna immunoprecipitation followed by sequencing (antibody binds methylated DNA, isolate it, then sequence)

Bisulfite sequencing

unmethylated cytosines converted to uracil (C>T) via deamination, followed by sequencing

How can you detect DNA methylation through NGS

PacBio or Oxford Nanopore sequencing

How can you associate DNA methylation signatures with disease or cellular phenotypes

case control studies

Episign

clinical methylation assay designed to identify epigenetic signatures associated with specific genetic disease

What have been associated with several single-gene disorders

Unique methylation patterns (epigenetics signatures) have been associated with several single-gene disorders

Genomic imprinting

process by which only one copy of a gene in an individual (either from their mother or their father) is expressed, while the other copy is suppressed

What is the primary mechanism that drives genomic imprinting

DNA methylation

Gynogenetic lethal

gamete with paternally-expressed genes absent- maternal allele expression doubled

Androgenetic lethal

gamete with maternally-expressed genes absent- paternal allele expression doubled

What was the first indication that parental origin was important in the context of gene expression

nuclear transplantation experiments in mice

What are the four mechanisms of disease in genomic imprinting

1. Deletion

2. Uniparental disomy

3. Imprinting defect

4. Gene mutation

Which chromosome is MAGEL 2 expressed from and which chromosome is it imprinted on

MAGEL2 is paternally expressed and imprinted on the maternal chromosome

Methylation-dependent restriction enzyme mechanism for finding variant of interest in imprinted gene

1. Digest DNA from the affected patient with Dpn1 (or another methylation-dependent restriction enzyme)

2. Imprinted allele will be fragmented

3. Not imprinted allele will remain intact

4. Not imprinted allele can be amplified and tested for variant of interest

Linked genetic variants method for determining parental origin of imprinted variant

another nearby DNA variant inherited together with the variant of interest. Test the parents to determine which parent carries the pathogenic variant in cis with the same linked marker found in the offspring

Methylation status method of determining parental origin of an imprinted variant

pacbio or oxford nanopore

How does Prader-Willi Syndrome work

The PWS region on Chromosome 15 is paternally expressed and maternally imprinted

How does Angelman Syndrome work

The AS region on Chromosome 15 is maternally expressed and paternally imprinted

Prader-willi syndrome main symptoms

mild intellectual disability, poor feeding in infancy, small genitalia

Angelman syndrome main symptoms

Sever speech issues, severe intellectual disability, and distinct happy demeanor

What kinds of pedigrees result from imprinting

Unusual pedigrees

Uniparental disomy (UPD)

genetic condition where a person receives both copies of a chromosome from one parent and no copies from the other

What is the primary mechanism for UPD

trisomy rescue

What does trisomy rescue result from

anaphase lag in early embryo mitotic divisions; one of the chromosomes is lost and is not passed into the daughter cell

Isodisomic UPD

two identical copies of a chromosome from one parent

Heterodisomic UPD

two different copies of a chromosome from one parent

What genomic techniques are used to detect Isodisomic and Heterodisomic UPD

Detect via exome/genome sequencing or chromosomal microarray

What must be identified for Isodisomic UPD

regions of homozygosity that span an entire chromosome

What must be identified for Heterodisomic UPD

chromosome regions with mendelian inheritance errors

Are parental samples needed for Isodisomic UPD detection

no

Are parental samples needed for Heterodisomic UPD detection

yes

Why is maternal UPD more common

eggs are arrested in female body leading to higher risk for nondisjunction

How frequent is uniparental disomy

0.02%