L34 Epigenomics in Cancer Flashcards
What is epigenetics
- in addition to the genetics - the study of changes WITHOUT ALTERATION of the genetic code itself
What is epigenomics
the study of the epigenome ALL epigenetic MODIDFICATIONS across an individuals entire genome
% of genome that is protein encoding
1% (the rest is non-coding)
Epi-genetics and genomics is essentially _____
above or in addition to the genetics/the genome
Epigenomics helps to understand…..
- how a genotype gives rise to different phenotypes
- how traits are inheritied
- how structural adaptation of the genome facilitates gene activation or repression
- most epigentic modifications are reversible
- epigentic landscape
- waddington
- how genes are read during embyonic development
- metaphor to a marble; cells take different directions
biological influences on the genome
- either endogenous (interrnal; comes from inside cell) or exogenous (external; environmental factors):
- cell to cell contact (very specific and precise)
- secreted cell factors
- homone signals (which go throughout body)
- environmental factors (can be indirect/direct)
biological signifigance of the epigenome
- turning genes on and off
- structural adaptation of the genome which to register signal or maintain activity states of the DNA
- proteins read,write, or erase these structural changes
covalent modification to genome
- enzyme reaction takes place
- examples:
- post-transational histone modifications (including methylation, acetylation, phosphorylation, ubiquinations, and ADP-ribosylation
*DNA methylation
histone octamer
- two each of histones: H2A, H2B, H3 and H4
- negatively charged DNA wrapped (147bp) (histones are positively charged which allows this interaction)
- separated by linker DNA
- histones H1 compats the string to solenoids
histone tail modifications
- influence how closely DNA is packed
- different amino acids do different things; for example Ardinine can be methylated; K (lysine can be both methylated or aceyltated)
- they have different propoties
phosphorylation adds
negative charge
acetylation adds
positive charge
lysine…..
acetylation and methylation - either or but never both
histone modification nomenclature
counted from end of tail (so as you get closer to the core the number goes up) H3K9me3
how do histone modification impact DNA transcription
- ACTIVE TRANSCRIPTION (Euchromatin)
- weakened electrostatic interactions between DNA and histone
*DNA is not tightly packed and permits transcription - REPRESSED TRANSCRIPTION (heterochromatin)
- strong interactions between DNA andhistones
- DNA is tightly packed, primarily inactive genes
ACTIVE TRANSCRIPTION
- Euchromatin
- weakened electrostatic interactions between DNA and histone
*DNA is not tightly packed and permits transcription - acetylation is mainly associated
REPRESSED TRANSCRIPTION
- Heterochromatin
-strong interactions between DNA andhistones - DNA is tightly packed, primarily inactive genes
- methylation is mainly associated
______ is mainly associated with Euchromatin (active)
acetylation
________ is mainly associated with heterochromatin (repressed)
methylation
histone tail methylation
- in repressed - trimeth of lysine
- whereas when of gylsine; its when in active form
If you have more than one methylation, its asoociated with active
proteins recognize histone modifications
readers, writers, and erasers
bromodomains and Extra-terminal domain (BET)
- recognized acetylated lysine and recuit transciption factors
histone deacetylases (HDACs and histone acetyltransferase (HATs)
histone modifying enzymes
histone demethylases and histone methylases
- specific for lysine and arginine
- balance important in controlling the active/repressed state
histone modifications affect DNA- dependent processes such as:
transcription, splicing, replication, and repair
histone modifications alter DNA accessibility by:
strengthening or weakening interactions between DNA and histones
CpG methylation
- important in transcriptions
- important epigentic mechanism
- happens on a CpG site (a region of DNA where we have a cytoceine followed by a theonine from the 5 to 3 prime direction
- ## cytosine can become methylated to form a different thing (specifically in this lecture 5-methylcytosine)
CpG methylation changes a ______ into a ______
cytosine into a 5-methylcytosine (the fifth base of the human genome)
Why is there CpG deficiency in the human genome?
- there are less sites than we would expect (expect 4.41% but there are actually less than 1%)
- methylated CpG are highly mutated
Why are CpG sites highly mutated?
- spontaneaou deamination of the methylated cytosine
- this leads to thymine
- also to a mutation
- leads to C to T transition
How much % of CpG sites are methylated
- 60-90%
Where are CpG sites located?
> 80% total CpG content are in repetitive sequences; e.g. centromeres, telomeres, LINE, SINE elements
- 1-2% of CpG sites are in ‘CpG islands’
CpG islands
- regions in the DNA with a higher frequency of CpG sites
- 500-3000bp long with 55% CpG content
-associated with promoters of 70% human protein encoding genes - normally hypomethylated in Cancer
What do CpG islands do?
- when not methylated, enable transcription
- when methylated, they supress gene expresion
- often seen in cancer (when the hypermethylated islands become HYPO)
DNA methylation
- euchrmatin (active)= unmethylated cytosines
- in heterochromatin (repressed) = methylated cytosines
meCpG writers, readers, and erasers
Writers: DNMT1 DNMT3a and DNMT3b
Reader: Methyl-CpG Binding Domain (MBD) proteins
Eraser: Ten-Eleven-Translocation (TET) proteins
DNMT1
- me CpG writer
- maintains DNA methylated of one strand
- adds methylatioin to copied strand during transpcription
DNMT3a and DNMT3b
- me CpG writer
- methylation of CpG sites that were previously unmethylated
- imporantant in embryiogenesis
Methyl-CpG Binding Domain (MBD) proteins
- meCpG reader
- recognize methylated CpG sites and typically cause gene repression by histone modification, nucleosome remodeling, and chromatin organization
Ten-Eleven-Translocation (TET) proteins
- meCpG eraser
- role is to demethylate the methylated DNA
Global CpG ______methylation; mainly occuring in __________ (cancer epigenetic dysregulation)
hypo; non-coding regions and repetitive elements
- means lower methylation than in regular cells
Local CpG ______ methylation; mainly occurring in______ (cancer epigenetic dysregulation)
hyper; promoters and CpG islands
- happens early in tumorogenesis
- associated with gene silencing
Effects of Global CpG hyp-methylation in cancer
- increases genomic instability, activates ocnogenes and repetitive elements
effects of Local CpG hyper-methylation in cancer
- associated with gene silencing
- hypermethylated tumour supressor genes (inhibits them)
Colon Cancer Local CpG hyper-methylation Example
MLH1
Breast Cancer Local CpG hyper-methylation Example
BRCA1
Brain and thyroid Cancer Local CpG hyper-methylation Example
PTEN
head and neck and lung Cancer Local CpG hyper-methylation Example
CDKN2A (p16 ink4a)
DNA methyltransferase inhibitors DNMTi
prevent aberrant DNA hypermethylation of tumor supressor genes
histone methyltransferase inhibitors
inhibition of EZH2 - a histone methylatransferates that associated with gene repression
histone deacetylase inhibitors (HDACi)
prevents aberrant gene expression by inhibiting acetylation of histone tails leading to chromatin condensation
(so they keep the gene expression)
bromodomain and extraterminal domain proteins hihibitors (BETi)
inhibition of epigenetic readers which activates gene expression
myelodysplastic syndrome treatment is possible with __________ by using __________ which _____________
- reversing CpG methylation
- DNA methyltransferase inhibitors (DNMTi)
- rexpressed the genes that were silenced
myelodysplastic syndrome
- group of bone cancers that mean that bone marrow does not make enough healthy blood cells
- pathogenesis includes epigenetic dysregulation, or the hypermethylation of specific genes and promotor-associated CpG island
- and histone modidications
- can be treated with DNMTi
EZH2 methyltransferase is a ______ _______ that trimethylates _________
histone methyltransferase; H3K27
H3K27me3 is associated with
gene silencing
EZH2 is _______ in solid tumors and _______ and lymphomas
overexpressed; mutated (gain of function)
inhibitors of histone deacetylation
- HDAC and BET inhibitors
HDAC inhibitors
- inhibit histone deacetylation associated with active transcription
- considered as key epigenetic cancer therapy owing to their ability to express genes that were silenced
- haematological malignanicy treatment (approved and in clinic)
BET inhibitors
- BET proteins recognize acetylated lysine and interact with the chromatin to change histones and transcription to infleunce gene expression
- decrease expression of many oncogenes
- only in trials, not yet in clinic
somatic alteration in histones
oncohistones
An oncohistone can be in _____ and they ______
- both in the N-terminal tails and globular histone fold domains
- affect function ofpolycomb repressor complex 1 and 2 (PRC1 and 2) - responsible for the trimethylation of H3K27
PRC1 and PRC2
- polycomb repressor complex 1 and 2
- function effected by oncohistones or somatic alterations in histones
