Cycle 11: Epigenetics

LECTURE 1: EPIGENETICS I
epigenetic markers can be viewed as punctuations

  • their placements can change the meaning (or interpretation) of the same words

epi = genetics

genetics = genomic sequence

epigenetics refers to all of the tags on top of the DNA

  • tags = methyl groups & acetyl groups

purple proteins = histones

  • histones wrap DNA around themselves so DNA can be compacted

DNA has an overall negative charge because of the phosphate backbone

overall charge of histones is positive

  • have amino acids (they are proteins!)

  • has tails — part of protein but not part of tertiary structure

    • tags are part of the histone protein — like a tail

lysine + = K

  • lysine amino acid is positively charged

lysine (present in histone + tail) gives the overall positive charge

methyl: CH3 — when added, methylation, when removed, demethylation

  • goes on cytosine nucleotide (no other nucleotide gets methylated)

acetyl: Ac — when added, acetylation, when removed, de acetylation

  • goes on lysine amino acid of histone

dynamic: tags go on and off

all the sequences for the tags are the epigenome

  • have an epigenomic sequence

epigenome controls gene expression

what determines when? where? how? life decisions

  • gun + bullet = genome

  • epigenome pulls the trigger (when parts are allowed to do transcription)

    • master regulator


studies on monozygotic twins — born with same genetic + epigenetic sequence

  • by the age of 2, epigenome changes

  • old age: many epigenomic changes

  • everyone is born with epigenome

  • epigenome plays important part as embryo, disease, normal processes

behavioural epigenetics (could also do aging) — controls all genetics

similar experience — similar epigenome

  • traumatic experience → can see similarities

  • can see epigenomic patterns in people who were sexually abused

using CRISPR-Cas9 to edit epigenome

  • catalytically inactive Cas — not cutting anything

  • adds methyl, removes method, adds acetyl, removes acetyl

huge correlation between psych disorders + epigenome

  • most drugs treat symptoms not cause

  • epigenetic editing treats cause


Epigenetic Modulation

epigenomes 100% look different later than at birth

these factors can affect genes through mutations (but not that different)

  • social interactions

  • psychological state

by happy and eat everything in moderation — don’t need to fixate on it


Molecular Mechanism of Epigenetics

signal transductions — overall mechanism is very straightforward

if supposed to be unmethylated + becomes methylated → counts as mutations (and vice versa)

epigenetics: the study of changes in gene expression caused by mechanisms other than changes in the underlying DNA sequence

genes can be “tagged” by our experiences — this is a dynamic process that is not random

tags can be inherited by the offspring (transgenerational epigenetic inheritance)

  • partially inherited by parents

  • partially accumulated → passed on to your offspring

done through sequencing of totipotent zygote

depends on type of experience, severity, we don’t know

DNA Methylation

DNA methyltransferase (DNMT): enzyme that METHYLATES DNA

  • transfers methyl groups to DNA

happens in CpG: (p is for phosphate)

5’ — CpG — 3’

3’ — GpC — 5’

both cytosines get methylated (somewhat across from each other)

hypermethylation: a lot of methylation → gene transcription is OFF

hypomethylation: very little methylation → gene transcription is ON


without acetyl group → histones are tightly wound together

  • lysine is not acetylated (still has its positive charge)

  • makes a structure called heterochromatin

  • gene is embedded in structure (inaccessible to transcription factors, RNA polymerase)

    • INACTIVE

when add acetyl, opens up → gene is accessible therefore ACTIVE

  • loose conformation called euchromatin

  • acetyl group makes the lysine neutral


Methylation and Demethylation

de novo — from scratch (new)

DNMT3A, DNMT3B does methylation

  • programmed in cell

  • there is signal transduction that guides DNMT where to go

Replication — same methylation

  • DNA methylation of maintenance

  • DNMT1 methylates cytosine on other strand

  • DNMT1 recognizes hemimethylated strands (methylates other strand)

evolved to have CpG so it can copy methyl groups over during replication

TET can remove methyl groups

  • active demethylation

TET: ten-eleven Translocation Enzyme removes methyl group from cytosine

DNMT: DNA Methyltransferase; converts cytosine (C) to 5-methylcystosine (5-mC)


Octamer of core histones

core histones: H2A, H2B, H3, H4 (each one x2) — blue

histone H1 — green

  • DNA wraps around

N-terminal tail is a bunch of lysines (K) for #5, 8, 12, 16

lysine (K) → acetylation → acetyl lysine

  • adds acetyl group

  • turns from positive charge to neutral charge

deacetylation makes lysine positive again (wound tighter — heterochromatin)


Histone Acetyltransferase and Histone Deacetylases

HATs: histone acetyltransferases

  • transfer acetyl groups to histones

  • increases transcription

  • euchromatin

HDACs: histone deacetylases

  • remove acetyl groups from histones

  • decreases transcription

  • heterochromatin

residues = another word for amino acid

acetylation of the lysine residues at the N terminus of histone proteins removes positive charges, thereby reducing the affinity between histones and DNA

  • makes RNA polymerase and transcription factors easier to access the promoter region


Histone Modification: acetylation or deacetylation

  • acetylation by HATs (euchromatin)

  • deacetylation by HDACs (heterochromatin)

DNA methylation: methylation or demethylation

  • methylation by DNMT (transcription is OFF)

  • demethylation by Ten-eleven Translocation (TET) (transcription is ON)





LECTURE 2: EPIGENETICS II

Epigenome of Twins

epigenetic drift: epigenetic modifications that occur with age

comparative monozygotic twins for methylated DNA

  • drastically change epigenome with age

  • methylation pattern becomes less similar

  • more one-sided hyper and hypomethylation

    • their methylation patterns are mostly similar

Behavioural Epigenetics

how genome gets methylated as you experience a behaviour

behaviour: maternal care

naturally see nurturing + non-nurturing moms

if the pups are not nurtured → difference in genome tagging

non-nurturing: not licking/grooming pups

  • hypermethylation of promoter that codes for Nr3c1

  • Nr3c1 is a gene that codes for glucocorticoid receptor (GR) protein

  • GR is a transcription factor

    • receptor for corticosterone (cortisol in humans)

      • stress hormone

      • good thing — releases it to deal with stressful situation

      • once done it’s job = bad (causes anxiety + other symptoms)

        • targets inflammation

  • GR binds with corticosterone and “gets rid of it”

during stress response (as transcription factor): going into nucleus, binding to promoter, activating genes, controlling moment of stress

  • once stress gone, needs to be taken away

if you don’t have enough GR, won’t take corticosterone away → anxiety + stress

hypermethylation → inactivation

  • cannot make enough GR

  • not getting rid of corticosterone

mice that were not groomed/nurtured were high in anxiety

  • high corticosterone levels in body

nurturing rats had different signal transduction

  • no methylation of promoter → transcription factor NGFI can bind

    • transcription of Nr3c1

    • higher levels of GR

    • GR binds to corticosterone and low anxiety

when pups are switched, epigenetic markers change

female pups raise their offspring the way they were raised

if you inject a drug that adds methyl tags

  • go from relaxed, high-nurtured rat to anxious rat


direct epigenetic proof that maternal care has an effect on epigenome

  • effect translates to a drastically different phenotype


Transgenerational Epigenetic Inheritance
transgenerational epigenetic inheritance: idea that epigenetic marks (i.e. DNA methylation, histone modifications) can be acquired on the DNA of one generation and stably passed on through the gametes (i.e. sperm and eggs) to the next generation

  • experiences and environmental exposures can change the way your DNA works (without changing the DNA itself)

  • this can be passed on to your offspring

early-life experiences exert long-term effects on gene expression which can be inherited by the offspring


signature of maternal care in non-human primates

  • separated from biological mother

  • others raised by human (surrogate nurse)

difference in epigenetic markers

  • normal monkeys

  • surrogate — aggressive + highly anxious

    • alcoholic monkeys

normal monkeys = repulsed by smell

surrogate = drank it, wanted more

Methylone

their epigenetics are the opposite

  • drastic differences in behaviour

methadone of the monkey raised by non-mother monkey looks the same as that of a monkey raised by biological monkey mother

experimental monkeys are different than pets/zoo


Epigenetics has been linked to all these disorders

  • most evidence for schizophrenia, anxiety, depression, drug addiction

epigenome that leads to these changes → can be passed on


epigenetic drugs in the treatment of anxiety disorders

  • acetylation + deacetylation of histones that lead to anxiety

  • drug = valproate (HDAC inhibitors — inhibits histone deacetylase)

tumour suppressor genes are also under epigenetic control

  • hypermethylation of promoter region by DNMT → cancer cells suppress tumour suppressor gene

    • don’t transcribe this because want to form a tumour

treated patients with adjuvant therapy (DNA methylation inhibitor)

  • DNMT no longer methylates promoter

  • methylation targets the promoter

    • hypermethylation → transcription factors don’t bind

need precision for adding these DNA methylation inhibitors

Using CRISPR-Cas9 for Epigenome Editing

use dead Cas9 (dCas9) — not catalytically active

  • don’t want to cut DNA sequence, want to change the epigenomic sequence

dCas9 goes to target (promoter) and sits there

  • linked with DNMT3A — enzyme that does demethylation

hypermethylate: couple Cas9 with DNMT3A

hypomethylate: couple Cas9 with TET

  • TET removes methyl groups


we all have an epigenetic clock

  • look at methylome (DNA methylation pattern)

  • mapped all diseases + healthy cell

biological age

epigenetic age acceleration: biological age is more than chronological age

body parts aren’t all the same age