13. cancer epigentics 2 Flashcards
how thick is chromatin fibre? and how does this differ from beads on a string?
30 nm
10 nm
name the chromatin remodeller that opens up chromatin and what does this require?
SWI/SNF
this requires ATP to move nucleosomes around
name the chromatin remodellers than condenses chromatin
NURD complex
this is also ATP dependent
what is the catalytic core of SWI/SNF?
BRM - ATPase
describe the subunits of SWI/SNF
many subunits are inter-changeable, giving the complex different specificities - dependent on cells type and how the cell needs to be regulated
how does SWI/SNF remodel nucleosomes?
> SWI/SNF binds nucleosome
energy of binding disrupts histone DNA contact
SWI/SNF bound to histone has 5’ to 3’ translocase activity
loop propagation allows complex to slide along DNA
can also lead to ejection of adjacent nucleosome from DNA
SWI/SNF can open up chromatin to allow TF to bind and promote expression, how can it also repress gene expression?
opening up chromatin and allowing repressors to bind
what has GWAS shown in terms of SWI/SNF and cancer?
lots of SWI/SNF subunits have been implication in cancer e.g. BRM TS
what type of gene is BRM?
a tumour suppresser
what do BRM mutants have?
defect in G1 checkpoint control - they ignore UV damage and keep dividing, going past checkpoint means cancer will divide faster
name another subunit of SWI/SNF that is implicated in cancer and what does it do? and what can rescue this cancer prone phenotype?
SNF5 is a tumour suppresser that represses cyclin D expression to allow for correct levels of G1 to S phase transition
>KO cyclin D
SNF/SWI regulates lots of pathways that are implicated in cancer. when certain subunits are mutated (inactivating mutations) what might this lead to? (3)
- promotes cell migration
- inhibits RB pathway
- promote proliferation
name the 2 core subunits of NurD
- chromodomain helicase DNA binding proteins 3 and 4 (CHD3 and CHD4)
- HDAC1 and HDAC2
which subunit of NurD catalyses ATP-dependent chromatin remodelling?
CHD3 and CHD4
>provides energy to remodel chromatin by displacement of histones of histone sliding
what do HDAC1 and HDAC2 do in NurD?
they mediate the deacetylation of proteins such as TFs and other proteins
name another subunit in the NurD comples
MBD - methyl binding domain - proteins for recruitment of methylated DNA
how is the Nurd complex recruited to DNA?
transcription factors and methylated DNA
what does Nurd complex do to TF that its recruited by? and how is this implicated in cancer?
PTM modifys them to modulate downstream activities
>oncogenes can recruit Nurd to supress transcription of TS
what can the NurD complex deacetlyate and what implications does this have?
p53 inactivation - cell resistant to arrest and apoptosis
when NurD complex contains MBD what can it do?
bind hypermethyalted promoter of TS and mediate transcriptional silencing
what subunit of the Nurd complex is associated with epithelial to mesenchymal transition?
MTA - metastatic associated protein
promotes metastasis when over expressed
- this can function independent of the Nurd complex when activated by myc
what are also involved in epigenetic changes?
non-coding RNAs
what are the two classes of non-coding RNAs?
miRNA and lncRNA
describe miRNA
20-24nc
generated by Drosha and dicer complex
how do miRNA function
target mRNA for degradation or inhibit translation
describe lncRNA
> 200bp up to 100kbp
how do lncRNA function
many different models of function >chromatin remodelling >transcriptional co-activation and co-repression >protein inhibition >splicing regulation
when the sequenced the genome and didn’t find that many genes they suggested lots of DNA is junk DNA - and many non coding RNAs are just transcriptional slop. what was controversially suggested in 2000?
non-coding RNAs interact with each other, mRNA, DNA and proteins to form networks that can regulate gene activity with almost infinite potential complexity - lncRNAs could impact on the genome activity and provide diversity
what was the nobel prize for in 2006
RNA interference – gene silencing by double-stranded RNA’ i.e. miRNA
what is now well excepted by the year 2014?
- miRNA are everywhere and regulate just about everything
- lncRNA are appearing to have a diverse array of functions - interact with other RNA, proteins and DNA
where are many cancer related SNPs seen in cancer? and what does this suggest?
non-coding regions of the genome (intergenic or intronic) and only a small number are found in coding regions
- either in regulatory regions or non-coding RNA
- non coding RNA have important role
describe how miRNA are produced
> pre-miRNA transcript is expressed in nucleus
Drosha cuts to 70nc
pre-miRNA exported from the nucleus
dicer cuts the pre-miRNA up into 20-24bp
miRNA RISC complex either binds DNA and prevents translation
or the mRNA that miRNA binds is exactly complementary then then the mRNA is cleaved
what have miRNAs been implicated in?
tumour survival and metastasis - groups of miRNA involved in migration and invasion, involved in angiogenesis, proliferation and involved in apoptosis
>can act as oncogenes or TS
give one example of an miRNA and how it is implicated in cancer
miR-21
affects pathways in cells survival and metastasis - inhibits aspects of tumourigenesis
what uses miRNA to repress genes and what sort of genes are repressed?
p53 produces miRNA that repress genes and give an anti-proliferative effect
is p53 itself is the target of multiple miRNAs?
yes, this reduces the p53 response
some of these miRNAs might be upregulated in cancer to reduce the p53 response
how is miRNA a unique candidate for targeting therapeutically?
> they can simultaneously affect multiple molecules in the same pathway
could use miRNA to target and reduce multiple transcripts in tumour
one problem would be getting these miRNA into cells e.g. miR-21 inhibits some aspects of tumourigenesis
name another type of non coding RNA that is implicated in cancer? and what can this do? how might these have a therapeutic affect?
circular RNA >can act as miRNA sponge >can act as miRNA buffer >can act as miRNA reservoir - preventing these from forming may have a therapeutic effect
name a lncRNA associated with cancer
ANRIL
describe ANRIL
100kb
polymorphisms associated with it - associated with breast and prostate cancer
what are lncRNA often associated with? and what can this lead to?
they form specific secondary structure to interact with chromatin remodelling complexes and are recruited to specific sites in the genome
>this can lead to activation or repression
HOTAIR is an oncogenic lncRNA, describe it and where is this found in increased levels?
recruits PCR2 (part of polycomb) to specific gene promoters
>resulting in methylation of H3K17
>breast cancer - promotes metastasis
describe where a lncRNA is expressed antisense of its target gene
lncRNA transcribed antisense of the p21
binds protein and mediates epigenetic silencing of p21 through histone methylation
what is ANRIL transcribe antisense of?
ARF and p16
how does ANRIL silence genes?
binds component of PRC1 complex and silences locus
what affect does ANRIL have? (3)
increases G1/S transition
increases ribosomal biogenesis
decreases level of p53
describe a TS lncRNA
> DNA damage induces expression of lncRNA from the 5’ of the cyclin D1 gene
this interacts with a protein and allows it to bind cyclin D promoter
blocks promoters and HAT activity
what are sORF proteins?
small open reading frame proteins
>highly prevalent and may have many important regulatory processes
>bind proteins to cause degradation, cleavage and alter function
where might sORF proteins be encoded?
encoded by what were thought to be lcRNAs, and embedded in protein coding genes
what has been identified that binds to the tumour suppresser BRAC1 ?
a sORF
why could sORFs have the potential to be very efficient therapeutic molecules ? (3)
they are very stable
easy to make
easy to get in cells
what allows lncRNA to interact with proteins and complexes?
their secondary structure
what is the oncogenic function of lncRNAs
recruiting repressive complexes to tumour suppresser genes (e.g. polycomb)
what is the TS function of lncRNAs
the recruitment of proteins that inhibit the repression complex at a TS gene
when might some lncRNA and miRNA have obvious phenotypes?
when the system is perturbed i.e. can be KO in normal conditions but they might be necessary in a disease state
give example of when lncRNA were though to be homozygous viable
> people found lncRNAs in the brains of mice
mice moved past ambulance and were paralysed
the buffering system in the brain went wrong in some of the neurones and some of the mice were paralysed
there is a lot of cross talk between of these different mechanisms of activation and repression of gene expression, what happens when one is petered?
this will have a knock on affect on others
what does DNA methylation of cytosine recruit?
Nurd complex
HDAC
what can PCR2 recruit?
DMHTs to methylate DNA
what can bind and recruit the polycomb complex?
lncRNA
what do acetylated histones recruit?
SNF/SWI - can remodel the chromatin
what can bind and recruit methyl transferases?
lncRNAs
what is a promising avenue of therapy?
targeting epigenetic mechanism
>drugs that inhibits HDACs, HDMs and DNMTs are already in clinical development
what will understanding more about these mechanisms allow us to do?
tailor therapeutics around them
