Lesson 4

Question 1

What is a psendogene?

Answer 1

A genomic locus that resembles real genes but do not have biological relevance / consequence → transduced into RNA but not translated into a protein

Question 2

How prevalent are pseudogenes?

Answer 2

Are almost as numerous as coding genes

Question 3

Although they lack canonical promoters, what do pseudogenes use to regulate their transcription?

Answer 3

Proximal regulatory elements

Question 4

Describe psendogene transcription in regards to location and presentation:

Answer 4

Exhibits tissue-specificity and is aberrantly activated in cancer

Question 5

What is PTEN?

Answer 5

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

Question 6

Why is PTEN an important tumor suppressor?

Answer 6

It blocks AKT→ many tumors eliminate PTEN to activate AKT pathway to induce cancer

Question 7

What are the 2 main functions of miRNAs?

Answer 7

Reduce the levels of RNAs by inducing degradation (catabolism) and to block translation

Question 8

What is the “sponge effect”?

Answer 8

When the psendgogene and the gene go in the same direction → shutting down 1 leads to the reduction of the other

Question 9

What is the competitive endogenous RNA (ceRNA) hypothesis?

Answer 9

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

Question 10

What are the 2 main DNA repair pathways?

Answer 10

Homologous and nonhomologous recombination

Question 11

Which method of DNA repair is more error-prone?

Answer 11

Non-homologous DNA repair

Question 12

Tumor suppressor genes often have what type of deletions?

Answer 12

Heterozygous deletions→ but remaining copy is mutated

Question 13

How is the expression of a gene effected when a deletion is present?

Answer 13

The gene has increased expression

Question 14

Name four characteristics of pseudogenes:

Answer 14

1. almost as numerous as coding genes
2. represent a significant portion of the transcriptome
3. processed pseudogenes use proximal regulator elements to mediate transcription
4. exhibit tissue-specificity and is aberrantly activated in cancer

Question 15

What can miRNAs bind to?

Answer 15

both the gene itself at the 3’ end and the pseudogene

Question 16

What must happen in cancer in order to shut down the effect of the tumor suppressor?

Answer 16

the elimination of the pseudogene lets the miRNA target PTEN causing PTEN to go down - cancer cell losses PTEN

Question 17

Describe the sponge effect in regards to PTEN and miRNA in cancer:

Answer 17

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

Question 18

In the case of cancer and PTEN, what will happen if the pseudogene is increased?

Answer 18

this means increasing the expression of PTEN meaning the cells will grow more slowly (since it is a tumor suppressor)

Question 19

In what way does the ceRNA hypothesis suppose that passive players become active players?

Answer 19

microRNA from active become passive because pseudogenes become sponges for the microRNA and they are trapped by the pseudogene

Question 20

What do pseudogenes behave like?

Answer 20

tumor suppressors and oncogenes

Question 21

How do pseudogenes behave like oncogenes?

Answer 21

increase in copy numbers

Question 22

how do pseudogenes behave like tumor suppressors?

Answer 22

loss of genome

Question 23

what are fragile site?

Answer 23

portions of the genome on which there are some parts that seem to be more fragile than others

Question 24

what happens at fragile sites during mitosis?

Answer 24

breakage of these sites of a genome causes small deletions and small amplifications inducing errors

Question 25

what type of DNA repair occurs at fragile sites?

Answer 25

non-homologous repair

Question 26

looking at the entire genome, genes residing in fragile sites tend to have what type of expression?

Answer 26

downregulated

Question 27

what is the outcome of a focal deletion?

Answer 27

a shorter over expressed protein

Question 28

what occurs when a pseudogene is cut out using CRISPR-Cas?

Answer 28

losing the pseudogene, the silencer is removed and there is an increase in expression of the corresponding gene → deletion induces expression of a gene

Question 29

what occurs when CRISPR-Cas is bound to the KRAB domain?

Answer 29

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

Question 30

describe the "leaking effect" in CRISPR-Cas 9 domains

Answer 30

methylation domains are deposited but the methylation is spread and effects the pseudogene

Question 31

overall, what is a pseudogene?

Answer 31

a silencer

Question 32

what effect has been suggested that a pseudogene has on polymerase?

Answer 32

RNA polymerase stops when it finds a pseudogene

Question 33

experiments show that during mitosis there is genomic instability and chromosomic instability in patients, how could we treat this issue?

Answer 33

with kinase inhibitors

Question 34

what two groups are non-coding RNAs divided into?

Answer 34

below 200 nt and above 200 nt

Question 35

what are non-coding RNAs above 200 nt called?

Answer 35

long non-coding RNAs (lncRNA) or long non-coding intergenic RNAs (lincRNA)

Question 36

describe the differences between mRNA and lncRNAs:

Answer 36

1. tend to be shorter 2. fewer but longer exons 3. expressed at relatively low levels 4. have poorer primary sequence conservation

Question 37

what two histone markers can be used to find lncRNA?

Answer 37

H3K4me3 and H3K36me3

Question 38

where are lncRNA expressed?

Answer 38

each tissue has a very specific set of lncRNA that is only expressed in that specific tissue

Question 39

where are encoding genes expressed?

Answer 39

all tissues

Question 40

compare the expression of lncRNAs and encoding genes:

Answer 40

lncRNAs present a lower median expression but they have much higher tissue specificity

Question 41

where do pseudogenes tend to be located?

Answer 41

in the nucleus

Question 42

what are the two phenotypic outcomes of the activation of the p53 pathway?

Answer 42

growth arrest and apoptosis - suggesting that lincRNAs can mediate this pathway

Question 43

what happens in tumors, sarcomas and lymphoma if we put back p53?

Answer 43

there is a lot of increase on the RNA level of p21

Question 44

what is PANDA?

Answer 44

a gene repressor that induces apoptosis and compensates the action of p53

Question 45

what is the function of DINOL?

Answer 45

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

Question 46

what do lncRNAs act in?

Answer 46

chromatin interactions (can form a loop with different portions of the DNA), protein interactions, and RNA interactions

Question 47

What is the target of p53 when it is activated?

Answer 47

p21

Question 48

when is p53 activated?

Answer 48

after DNA damage