Lesson 4 Flashcards
What is a psendogene?
A genomic locus that resembles real genes but do not have biological relevance / consequence → transduced into RNA but not translated into a protein
How prevalent are pseudogenes?
Are almost as numerous as coding genes
Although they lack canonical promoters, what do pseudogenes use to regulate their transcription?
Proximal regulatory elements
Describe psendogene transcription in regards to location and presentation:
Exhibits tissue-specificity and is aberrantly activated in cancer
What is PTEN?
A central gene which is involved in one of the central pathways that is activated in cancer→ resides in the short arm of chromosome 10
Why is PTEN an important tumor suppressor?
It blocks AKT→ many tumors eliminate PTEN to activate AKT pathway to induce cancer
What are the 2 main functions of miRNAs?
Reduce the levels of RNAs by inducing degradation (catabolism) and to block translation
What is the “sponge effect”?
When the psendgogene and the gene go in the same direction → shutting down 1 leads to the reduction of the other
What is the competitive endogenous RNA (ceRNA) hypothesis?
Passive players become active players →microRNA from active genes become passive because pseudogenes become sponges for the microRNA and they are trapped in the pseudogene
What are the 2 main DNA repair pathways?
Homologous and nonhomologous recombination
Which method of DNA repair is more error-prone?
Non-homologous DNA repair
Tumor suppressor genes often have what type of deletions?
Heterozygous deletions→ but remaining copy is mutated
How is the expression of a gene effected when a deletion is present?
The gene has increased expression
Name four characteristics of pseudogenes:
- almost as numerous as coding genes
- represent a significant portion of the transcriptome
- processed pseudogenes use proximal regulator elements to mediate transcription
- exhibit tissue-specificity and is aberrantly activated in cancer
What can miRNAs bind to?
both the gene itself at the 3’ end and the pseudogene
What must happen in cancer in order to shut down the effect of the tumor suppressor?
the elimination of the pseudogene lets the miRNA target PTEN causing PTEN to go down - cancer cell losses PTEN
Describe the sponge effect in regards to PTEN and miRNA in cancer:
the pseudogene and the gene go in the same direction → by shutting down one we get the reduction of the other - losing the endogenous sponge the target gene is free to be targeted
In the case of cancer and PTEN, what will happen if the pseudogene is increased?
this means increasing the expression of PTEN meaning the cells will grow more slowly (since it is a tumor suppressor)
In what way does the ceRNA hypothesis suppose that passive players become active players?
microRNA from active become passive because pseudogenes become sponges for the microRNA and they are trapped by the pseudogene
What do pseudogenes behave like?
tumor suppressors and oncogenes
How do pseudogenes behave like oncogenes?
increase in copy numbers
how do pseudogenes behave like tumor suppressors?
loss of genome
what are fragile site?
portions of the genome on which there are some parts that seem to be more fragile than others
what happens at fragile sites during mitosis?
breakage of these sites of a genome causes small deletions and small amplifications inducing errors
what type of DNA repair occurs at fragile sites?
non-homologous repair
looking at the entire genome, genes residing in fragile sites tend to have what type of expression?
downregulated
what is the outcome of a focal deletion?
a shorter over expressed protein
what occurs when a pseudogene is cut out using CRISPR-Cas?
losing the pseudogene, the silencer is removed and there is an increase in expression of the corresponding gene → deletion induces expression of a gene
what occurs when CRISPR-Cas is bound to the KRAB domain?
inactive Cas9 binds in proximity to the promoter and KRAB shuts down the expression of the pseudogene → thus we obtain in increase of the corresponding gene
describe the “leaking effect” in CRISPR-Cas 9 domains
methylation domains are deposited but the methylation is spread and effects the pseudogene
overall, what is a pseudogene?
a silencer
what effect has been suggested that a pseudogene has on polymerase?
RNA polymerase stops when it finds a pseudogene
experiments show that during mitosis there is genomic instability and chromosomic instability in patients, how could we treat this issue?
with kinase inhibitors
what two groups are non-coding RNAs divided into?
below 200 nt and above 200 nt
what are non-coding RNAs above 200 nt called?
long non-coding RNAs (lncRNA) or long non-coding intergenic RNAs (lincRNA)
describe the differences between mRNA and lncRNAs:
- tend to be shorter
- fewer but longer exons
- expressed at relatively low levels
- have poorer primary sequence conservation
what two histone markers can be used to find lncRNA?
H3K4me3 and H3K36me3
where are lncRNA expressed?
each tissue has a very specific set of lncRNA that is only expressed in that specific tissue
where are encoding genes expressed?
all tissues
compare the expression of lncRNAs and encoding genes:
lncRNAs present a lower median expression but they have much higher tissue specificity
where do pseudogenes tend to be located?
in the nucleus
what are the two phenotypic outcomes of the activation of the p53 pathway?
growth arrest and apoptosis - suggesting that lincRNAs can mediate this pathway
what happens in tumors, sarcomas and lymphoma if we put back p53?
there is a lot of increase on the RNA level of p21
what is PANDA?
a gene repressor that induces apoptosis and compensates the action of p53
what is the function of DINOL?
close to p21, stabilized p53 and modulates the activity of its target genes - if there isn’t DINOL we have a down-regulation of p53
what do lncRNAs act in?
chromatin interactions (can form a loop with different portions of the DNA), protein interactions, and RNA interactions
What is the target of p53 when it is activated?
p21
when is p53 activated?
after DNA damage
