Epigenetics

Question 1

What is epigenetics?

Answer 1

The study of changes in gene expression that do not result from changes in DNA sequence

Epigenetic changes silence or activate chromosomal regions

Question 2

What are the ways that epigenetic changes silence or activate chromosomal regions?

Answer 2

1. Chromatin remodeling (rearranging histones)
2. DNA methylation and demethylation
3. Histone acetylation and deacetylation
4. Non-coding RNA

Changes are perserved through mitosis and can persist through life of individual

Question 3

How are chromatins remodeled via histones?

Answer 3

Histones can be repositioned on DNA to facilitate or impede transcription

Question 4

What are the 2 most important types of chromatin remodeling protein complexes?

Answer 4

SWI/SNF remodelers reposition or slide histones - repositioning exposes sites for DNA binding proteins and facilitate transcription

ISWI, CHD remodelers load histones onto DNA - histones can occlude sites for DNA binding proteins and so histone loading inhibits transcription

Question 5

What are chromatin remodeling disorders and examples?

Answer 5

Mutations in components of the SWI/SNF complex affect chromatin remodeling - 20% of cancers and produces cancer vulnerability

Another example is SMARCA4 (BRG) mutations cause dominant tumor susceptibility

Question 6

How does DNA Methylation work in epigenetic regulation?

Answer 6

Cytosine bases in CpG DNA sequences can be methylated by DNA methyltransferases (DNMT)

DNA methylation does not affect base pairing during replication or transcription, but does affect binding of methylation sensitive DNA binding proteins

DNA methylation silences a genomic region

Question 7

How does methylation of cytosine affect the binding of critical DNA binding proteins?

Answer 7

Prevents binding of methylation sensitive transcriptional activators - prevents the transcription of methylated region

Promotes binding of chromatin silencing factors (histone modifiers)

Question 8

Where are methylated regions in the genome?

Answer 8

Found in repetitive DNA - CpG sequences take up about 40-50% of genome and encode retroviral DNA that must be silenced to prevent harm via methylation

Found in promoter region - CpG islands, shores, and shelves. Regulatory elements have methylation shutting down gene expression. Unmethylated in transcribed regions and methylated in silent regions

Question 9

What are the effects of methylation on gene expression?

Answer 9

Hypermethylation of the genome will shut down expression of genes so if the gene being shut down is tumor suppressor than cancer will be promoted. Silencing important genes

Hypomethylation of the genome leads to expression of genes in normally silent regions of the genome and will reactivate transposable elements in normally silent regions. So if oncogene is normally repressed, it will now not be repressed and produce cancer. Activating wrong genes and causes genome instability

Question 10

What does methylation do?

Answer 10

Methylation mutes and shuts down gene expression

Silences inappropriate genes (wrong developmental stage), adjust gene dosage for monoallelic expression (X-chromosome, IGF2), and silence repetitive DNA (retrotransposons)

Question 11

How is methylation established and maintained through DNA replication and cell division?

Answer 11

Writing on unmethylated DNA via the action of De novo DNA methyltransferase DNMT3 and maintenance methyltransferase DNMT1

Copying after DNA replication via maintenance methyltransferase DNMT1 - allows DNA repair ensymes to determine which strand is original and which one is copy

Question 12

How are methylation patterns erased?

Answer 12

Active mechanism - alphaKG-dependent dioxygenases (TET) followed by base excision repair

Passive mechanism - Inhibition of DNMT1 which leads to passive demethylation

Question 13

How are the TET Oncogenes linked to metabolism and tumor progression?

Answer 13

TET proteins erase methylation patterns

TET catalyze stepwise demethylation of cytosine and demethylation progresses via hydroxymethylcytosine, formylcytosine to carboxylcytosine

DNA glycosylase removes and replaces products with fresh cytosine

TET enzymes require alpha-ketoglutarate from metabolism - link DNA methylation and metabolism

Increased tumor risk in individuals with TET mutations

Question 14

How are histones regulated?

Answer 14

Acetylation of lysine residues in histone tail decreases affinity to DNA. Acetylation opens up chromatin structure and facilitates transcription

Methylation of lysine residues has regulatory function because it facilitates binding of regulatory proteins and can be activating (H3K4met) or repressing (H3K9met, H3K27met)

Other histone modifications include phosphorylation and ubiquitination

Exhange with non-canonical histone variants provides transcriptional memory

Question 15

How are histone modifications placed into a histone code?

Answer 15

Histone Acetyl-Transferases (HAT) activate transcription and are writers

Histone Methyltransferases (HMT) is also a writer

Methylation-senstivie histone binding proteins (HP1) activate chromatin modifying enzymes and functions as readers of the code

Histone Deacetylases (HDAC) repress transcription and function as erasers of code

Question 16

How are metabolism and epigenetics linked together?

Answer 16

Metabolic activity can influence gene expression by providing substrates for chromatin modification

Acetylation - acetyl-CoA is a substrate for histone acetylation and NAD+ is a cofactor for some histone deacetylases

Methylation - S-adenosylmethionine is a substrate for DNA and histone methyltransferases. alpha ketoglutarate is a cofactor for de-methylases

Question 17

What is self-propagating silencing?

Answer 17

Feature of chromosome inactivation by cytosine methylation and histone deacetylation

Heterochromatin binding protein (HP1) propagates DNA silencing

Boundary elements separate heterochromatin and euchromatin - translocation of methylated fragments can silence adjacent regions and translocations involving the methylated X-chromosome pose risk

Boundary element failure leads to inactivation of adjacent regions and behaves like a mutation

Question 18

What is Rett Syndrome?

Answer 18

Onset at age 6-18 months

Patient presents with autism-like symptoms, repetitive teeth grinding and hand winging, motor problems, and characteristic gait. Stabilizes after initial deterioration

Most patients have mutations in methyl-cytosine binding protein MECP2 gene

Loss of transcriptional silencing

X-linked dominant so affected boys die shortly after birth

Question 19

What should we know about epigenetic disorders?

Answer 19

About 200 genes show parent of origin specific mono-allelic expression - alleles are silenced (imprinted) on either father’s or mother’s contribution

Imprinting explains parent of origin effects - phenotype of a mutation varies depending on which parent contributed mutation. Explain why zygotes with DNA from just one parent are inviable (hydatidiform mole or ovarian teratoma)

Question 20

What is the parent of origin effect?

Answer 20

Genes with parent of origin specific imprint normally produce a balanced amount of protein

Consequences of deletion depend on parent of origin - deletion on paternal or maternal homolog abolishes expression of different genes

Unipaternal disomy upsets monoallelic gene expression balance - overexpression of some genes and lack of expression of others

Question 21

What are two examples of parent of origin effects?

Answer 21

Prader-Willi - Caused by deletion on paternal copy of chromosome 15 or maternal uniparental disomy. Leads to overgrowth and excessive food seeking

Angelman - Caused by deletion on maternal copy of chromosome 15. Leads to autism like features and involvement of UBE3A ubiquitin protein ligase

Question 22

What is Beckwith-Wiedemann Syndrome?

Answer 22

Can be caused by paternal unipaternal disomy of chromosome 11

Leads to microcephaly, macroglossia, and umbilical hernia

Overexpression of insulin-like growth factor 2 (IGF2) and causes multiple organ problems (liver, kidney, hypoglycemia)

Question 23

How is methylation tie to cancer?

Answer 23

Hypomethylation of DNA causes genomic instability - leads to elevated transposon activity, chromosomal abnormalities, and high mutation rate

Hypermethylation of CpG islands shuts down tumor suppressor genes - effect of silencing equals effect of null mutation.

10-15% of non familial breast cancers due to hypermethylation of BRCA1

Question 24

What are histone deacetylase (HDAC) inhibitors?

Answer 24

Promote histone hyperacetylation and gene re-expression in chronic lymphocytic leukemia

HDAC inhibitors are also in use for treatment of depression and mood stabilizers

Question 25

What are DNA methyltransferase (DNMT) inhibitors?

Answer 25

Promote hypomethylation of the genome. Have potential to counteract malignancies associate with hypermethylation and have been approved for the therapy of myelodysplastic syndrome