Epigenetics

What is a chromatin?

• DNA assoicated with proteins that coils/uncoils to regulate gene expression

• made of nucleosome with 8 histone proteins

• DNA wraps around nucleosome

What is epigenetics?

• heritable changes in gene expression that do involve changes to the nucleotide sequence of DNA

• dynamic and reversible

• influenced by environment

What overall effects do marks have?

• change protein expression and phenotypes

• allows for response to environment

• contributes to variable expressivity and incomplete penetrance

How does a tightly coiled, or heterochromatin, prevent gene expression?

• DNA tightly wrapped around nucleosome

• nucleosome blocks TFs and RNA pol2 from binding to promoter

Describe how DNA is unwound from histones (heterochromatin → euchromatin)

remodeling proteins unwind DNA from histones to make accessible to RNA pol 2 and Tfs

What is a euchromatin?

• loose/open chromatin

• histones have high acetylation and methylation at H3K4

• DNA hypomethelated

• accessible for transcription

• gene expression

What is a heterochromatin?

• tight/closed chromatin

• histones have low acetylation and methylation at H3K9 OR H3K27

• DNA HYPERmethylated

• not accessible for transcription

• gene silencing

Does acetylation increase or decrease transcription of DNA?

acetylation increases transcription

Describe histone tails and their purpose

• stick off of histones

• lysine rich tails (positive) interact with negatively charged DNA backbone to hold tightly to DNA

• can be aceytlated (increase transcription) or methylated (modify transcription)

In histone nomenclature, what does H3K4ac mean?

• H3 - H3 histone subunit

• K4 - 4th lysine

• ac - 1 acetyl group added

Describe the process of histone acetylation and deacetylation, including the enzymes and purpose

• non acetylated lysine has positive charge, attaches to DNA backbone, high expression (euchromatin)

• acetyl group added to lysine by HAT, neutralizing charge and changing DNA shape (heterochromatin)

• acetyl group removed by HDAC, back to euchromatin

What are HAT and HDAC?

• HAT - histone acetyltransferase - add acetyl group to lysine on histone tails - increase expression (euchromatin)

• HDAC - histone deacetylase - remove acetyl group from lysine on histone tails - decrease expression (heterochromatin)

How would a LOF mutation in HDAC affect gene expression ? How would a GOF?

• LOF - increase gene expression (can’t remove acetyl groups)

• GOF - decrease gene expression (acetly groups keep getting removed)

What is methylation?

• adding methyl groups to histone tails or CpG sites on DA

• can either active or repress genes

Describe histone methylation

• added to lysine of histone tails

• recruits regulatory proteins (chromatin remodelers or repressors/activators)

• can activate/repress gene expression

• does not affect lysine charge

• can add 1, 2, or 3 methyl groups

What impacts DNA methylation throughout life?

environment

Describe DNA methylation

• changes conformation of DNA to Z form to reduce gene expression

• methylated on the C of CpG dinucleotides (on same strand right beside each other)

• can occur inside a promoter or enhancer region to control gene expression

What is the Z and B form of DNA? What causes this?

• B-form, standard double helix, available for transcription, unmethylated DNA

• Z-form - twisted double helix, unavailable for transcription, methylated DNA

Where does DNA methylation occur?

At CpG dinucleotides on the same strand

How are epigenetics inherited?

• after DNA replication, old histones on parent strand act as a template for daughter strand to tell what modifcatins should be made to histones

• for histones: can recruit enzymes to mark daughter histone tails after replication

• for DNA methylation: methyltransferase adds methyl group to daughter strand to match original pattern in pattern

What is epigenetic inheritance?

passing along chromatin state through division

Why are epigenetics inherited?

• to maintain cell identity

• to maintain gene expression patterns

What is hemimethylation?

• one strand methylated

• refers to before daughter strand has been methylated during epigenetic inheritance

What is epigenetic imprinting? What is it used for?

• certain maternal and paternal genes are always silenced

• only 1 allele for a gene expressed

• for proper gene dosing

• ex. SMN1 - on in mom, silent in dad. only display allele from mom

Explain the roles of histones

• small positively charged proteins that DNA wrap around to help neutralize the charge and compact the DNA into the nucleus

• help regulate gene activity through modifications to histone tails through acetlyation and methylation

Explain the roles of nucleosomes

• basic unit of chromatin, made of DNA wrapped around 8 histone proteins

• helps package DNA inside the nucleus and control access to transcription