Week 5 - Epigenetic and epigenomic regulation

Question 1

Epigenetics in general

Epigenomics

Answer 1

Epigenetics in general
● heritable changes in gene expression and regulation of non coding sequences without alteration in DNA-sequence

1. changes are stable in cell division
2. changes are reversible
3. crucial epigenetic reprogramming occurs during germ cell development and early
   embryogenesis in mammals

● Epigenomics = epigenetic changes on the level of the whole genom

Question 2

Epigenetics vs Epigenomics

Answer 2

Epigenetics focuses more on processes (chemical modifications) that regulate gene expression and genomic stability

Epigenomics: Epigenome are multiple chemical compounds that can tell the genome “what to do”

BOTH: Provide a programme for gene expression in an organism

Gene expression is influenced by: enviroment, lifestyle, age and disease state.

Question 3

Regulations in eukaryotes

Answer 3

● Epigenetic events provide a more precise and stable control of gene expression and genomic regulation through multiple generations

● Epigenetic marks such as silencing of centromeres, telomeres and transposable elements play a crucial role in genomic stability - they ensure:

1. the correct attachment of microtubules to centromeres
2. decrease in excessive recombination between repetitive elements
3. prevention of transposition of transposable elements

Question 4

Question 5

Picture of lecture 5

Answer 5

Question 6

Epigenator

Answer 6

changes in the environment trigger epigenetic changes in cells. The environmental signal is
considered as epigenator - which will lead to the activation of an initiator.

epigenator could be: differentiation signals, temperature variations, metabolites.

Question 7

Initiator

Answer 7

Initiator:
● translates the epigenator’s signal

● identifies the location on a chromosome where epigenetic marks will be established

● initiators are e.g. DNA binding proteins, noncoding RNAs etc.

● they are DNA sequence specific, epigenetic initiators BINDS to DNA.

Question 8

DNA binding proteins:
Type 1 of initators

Answer 8

DNA binding proteins:

● The ability of DNA-binding proteins to bind on specific DNA sequences results from noncovalent interaction between the alpha-helix in the DNA binding protein domain and:

1. atoms on the edges of he base within a major groove of the DNA
2. DNA sugar-phosphate backbone atoms
3. atoms in a DNA minor groove also contrib. to binding.

Question 9

Noncoding RNAs:
type 2 initiator

Answer 9

Noncoding RNAs

● functional RNA molecule that is transcribed from DNA but not translated into proteins

● epigenetic related ncRNAs are either short or long.

● regulate gene expression at transcriptional or post-transcriptional level.

Question 10

Short ncRNA

Answer 10

short ncRNAs: (< 30 nts)

● microRNAs - bind to a specific target mRNA with a complementary sequence to induce
cleavage/degradation or to block translation in the context of a feedback mechanism that involves chromosome methylation

● short interfering RNAs
- siRNA is designed to target and degrade specific messenger RNA (mRNA) molecules in a cell. → it prevents certain genes from being used to make proteins.

● piwi-interacting RNAs - chromatin regulation and surpression of transposon activity in
germ and somatic cells

Question 11

long ncRNAs: (>200 nt)

Answer 11

● forms complex with chromatin

● modifying proteins and recruit their catalytic activity to specific sites in the genome

→ thereby modifying chromatin states and influencing gene expression

Question 12

ncRNA functions:

Answer 12

● in chromatin remodelling
● in transcriptional regulation
● in post-transcriptional regulation
● as precursor for siRNAs

Question 13

Epigenetic maintainer:

Answer 13

Epigenetic maintainer:

SIMPLE EXPLANATION: The mfs doing all the work. Main the gene expression.

● DNA methylation: addition of methyl-group to the 5-carbon of the pyrimidine base
cytosine in CpG islands - maintained by one of three enzymes called DNA
methyltransferases (DNMTs)

● DNA methylation of a gene’s CpG island represses gene expression; different cell type have different methylation patterns which contribute to the differences in gene
expression in different cell types

● non-CpG cytosine methylation has been identified at a high level in stem cells, indicating
that loss of methylation may be critical for end differentiation of cells

● the total level of global methylation and the degree of non. CpG methylation is inversely proportional to the level of differentiation

Question 14

Histone modification:

Answer 14

● HM and DNA-m. are coordinated and correlated processes

● histone modification is a covalent, post-translational modification (PTM) to histone proteins

● PTM work together to regulate the chromatin structure which affects biological processes
including gene expression, DNA repair and chromosome condensation

Question 15

Histone PTM to histone proteins inculdes:

PTM - post translational modification

Answer 15

1. methylation
2. phosphorylation
3. acteylation
4. ubiquitylation (the addition of ubiquitin proteins to a substrate protein)
5. sumoylation (the addition of Small Ubiquitin like Modifier protein to a substrate protein

Histones consist of a globular histone core and a loosely structured N-terminal tail, which protrudes out of the nucleosome) > majority of histone PTMs occur on the N-terminal tail

-> due to theic chemical properties these epigenetic modification alter the condensation of the chromatin and as a consequence the accessibility of the DNA to the transcriptional machinery

Question 16

Super short about the different Histone PTM

Answer 16

Question 17

Acetylation

Answer 17

Acetylation:

● histones can become acteylated on lysine residues; enzymes regulating histone acetylation consist of the histone acetyltransferases (HATs) and histone deacetylases (HDACs)

● The acetyl group addition neutralizes the positive charge of the amino group of the lysine, leading to decreased affinity between the histone tail and the negatively charged DNA

In simple terms:
AFFINTY = SAMMANHÖRIGHET

Histone acetylation is like loosening the grip of histones on DNA, making the DNA easier to read, and helping activate certain genes.
Without acetylation, the DNA stays tightly wrapped, and the genes are harder to access, meaning they’re turned off or less active.

baxare

Question 18

Methylation

Answer 18

Methylation
● Histone methylation occurs on both lysine and arginine residues. This epigenetic modification is associated with both transcribed and silences genes

● Arginine residues can be both mono- and di-methylated and lysine residues can be mono-, di-, and tri-methylated. These degrees of histone methylation can have differing roles on the regulation of gene expression

● Enzymatically, histone methylation is controlled by histone methyltransferases and by
histone demethylases

Question 19

Phosphorylation

Answer 19

Phosphorylation:

● histone phosphorylation occurs on serine, threonine and tyrosine residues and is most commonly associated with transcriptional activation, because the negative charge of the phosphate group creates a repulsive force between the histones and the negatively charged DNA. Phosphorylation is reversible.

● Histone phosphorylation is regulated by protein kinases and protein phosphatases

Question 20

Ubiquitination

Answer 20

Ubiquitination:

● refers to the attachment of 76-amino acid protein ubiquitin to the histone core proteins H2A and H2B

addition of ubiquitin protein to:

• on H2A results in repression (inhibition)
• on H2B results in activation + repression.

● H2A and H2B ubiquitination and histone methylation often cross-talk, in particular via H3K4 di- and trimethylation. H2B ubiquitination is thought to be a prerequisite for H3
methylation, but H2A inhibits this methylation.

Question 21

Sumoylation

Answer 21

Sumoylation:

● SUMO Proteins are similar to ubiquitin, roughly 100 amino acids long and added to their targets by specific ligases, the actions of which are reversed by proteases

● histone sumoylation is a mark of transcriptional repression

Question 22

Histone variant

Answer 22

Histone variant: type of epigenetic maintainer

● Histone variants (non allelic) represent one or a few amino acid differences in the histone tails or in the globular central domains

● histone variants have specific expression, localization and distribution patterns

● functionally affecting chromatin, remodelling and histone post translational modifications

Question 23

Nucleosome remodeling:

Answer 23

Nucleosome remodeling:

● refers to the change in the structure of chromatin, requires ATP input
● nucleosome remodelling is carried out by enzymes called ATPases
● Enzyme actions may lead to:
1. complete or partial disassembly of nucleosomes
2. the exchange of histones for variants
3. the assembly of nucleosomes
4. the movement of histone octamers on DNA

Question 24

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Answer 24

Hippocampus - a brain area implicating in stress response

Glucocorticoids - primary stress hormones necessary for life regulate numerous physiological processes to maintain homeostasis DNA methylation in the promotor region of the glucocorticoid receptor gene leads to
decreased GR expression

The transcription factor NGF1-A bind the GR promotor region to initiate gene expression

Epigenetic and gene expression changes persist into adulthood when they lead to heightened stress response at least in the rat model.

Question 25

Allelic imbalance in gene expression

Answer 25

When the ratio of the gene expression levels from each of two alleles in diploid genome genome is not 1 to 1, it is called allelic imbalance.
● 5%-20% of autosomal genes

● Reason: variants in the DNA sequence cause different levels of expression at two gene copies

● Usually early embryogenesis

Question 26

Monoallelic expression

Answer 26

Only one of the two copies of a gene is active while the other is silent. It has four types:
● Somatic rearrangement
● Random allelic silencing or activation
● Genomic imprinting
● X chromosome inactivation

Question 27

Somatic rearrangement

Answer 27

Changes in DNA organization to produce a functional gene at one gene copy, but not another.

Between 0.5% and 15% of autosomal genes exhibit random monoallelic gene
expression, in which different cells express only one allele independently of the underlying genomic sequence, in a cell type-specific manner.
→ Random choice of one gene copy.

Question 28

RAT MODEL

Answer 28

Example of how epigenetic changes can change human pathology

outer enviroment change = epigenator
Lack of love and affection from mother → causes initiator signal to either make noncoding rna or dna binding

Question 29

Random allelic silencing or activation

Answer 29

Expression from only one gene copy at chromosomal localization (locus) due to different epigenetic changes.

Olfactory receptor genes in sensory neurons; other chemosensory or immune system gene; up to 10% of all genes in other cell types.

Question 30

Genomic imprinting

Answer 30

● Epigenetic silencing of gene copy in imprinted regions

● >100 genes known, with developmental functions

● Imprinted region marked epigenetically according to the parental origin

● Parental gametogenesis

NOT RANDOM- allele gene you get from parents

Question 31

X chromosome inactivation

Answer 31

Epigenetic silencing of X chromosomes linked genes on one female chromosome. Most X-linked genes are female. There is a random choice of an X chromosome during the early embryogenesis

Question 32

Sex chromosome inactivation

Answer 32

The epigenetic gene dosage compensation mechanisms of genes located on the sex chromosomes vary with species from simple transcriptional modulation to the entire silencing of one sex chromosome. In humans X chromosome gene dosage between the
sexes is equalized by inactivating one X chromosome in females. The X chromosome is inactivated randomly (paternal or maternal).

Question 33

X-inactivation

Answer 33

The dosage of X-chromosomes will determine whether the escape gene will be active or not.

Females have 2 X chromosomes which is the right dosage of X-chromosomes.

The dosage will activate the escape gene which will induce the XIST gene on the X chromosome to code for the non-coding RNA (ncRNA) that will inactivate the X chromosome.

The DNA will be hypermethylated on cytosine while it will cause hypo-acetylation on the histone H4.

3-7 days in embryonic devolmpent
In somatic cells, reactive in germ cells

Question 34

Phenotype

Answer 34

phenotype is the short-term + long-term outcomes of epigenetic regulation.

short-term = transient outcomes are:
transcription + DNA replication + repair

Long-term outcomes are:
chromatin conformation + heritable markers.