Epigenetics Flashcards
What is epigenetics?
The study of changes in gene expression that do not result from changes in DNA sequence
Epigenetic changes silence or activate chromosomal regions
What are the ways that epigenetic changes silence or activate chromosomal regions?
- Chromatin remodeling (rearranging histones)
- DNA methylation and demethylation
- Histone acetylation and deacetylation
- Non-coding RNA
Changes are perserved through mitosis and can persist through life of individual
How are chromatins remodeled via histones?
Histones can be repositioned on DNA to facilitate or impede transcription
What are the 2 most important types of chromatin remodeling protein complexes?
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
What are chromatin remodeling disorders and examples?
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
How does DNA Methylation work in epigenetic regulation?
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
How does methylation of cytosine affect the binding of critical DNA binding proteins?
Prevents binding of methylation sensitive transcriptional activators - prevents the transcription of methylated region
Promotes binding of chromatin silencing factors (histone modifiers)
Where are methylated regions in the genome?
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
What are the effects of methylation on gene expression?
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
What does methylation do?
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)
How is methylation established and maintained through DNA replication and cell division?
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
How are methylation patterns erased?
Active mechanism - alphaKG-dependent dioxygenases (TET) followed by base excision repair
Passive mechanism - Inhibition of DNMT1 which leads to passive demethylation
How are the TET Oncogenes linked to metabolism and tumor progression?
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
How are histones regulated?
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
How are histone modifications placed into a histone code?
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
How are metabolism and epigenetics linked together?
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
What is self-propagating silencing?
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
What is Rett Syndrome?
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
What should we know about epigenetic disorders?
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)
What is the parent of origin effect?
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
What are two examples of parent of origin effects?
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
What is Beckwith-Wiedemann Syndrome?
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)
How is methylation tie to cancer?
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
What are histone deacetylase (HDAC) inhibitors?
Promote histone hyperacetylation and gene re-expression in chronic lymphocytic leukemia
HDAC inhibitors are also in use for treatment of depression and mood stabilizers
What are DNA methyltransferase (DNMT) inhibitors?
Promote hypomethylation of the genome. Have potential to counteract malignancies associate with hypermethylation and have been approved for the therapy of myelodysplastic syndrome
