Tonon: Lecture IV

Question 1

What is a pseudogene?

Answer 1

a construct that is transduced into RNA but not a protein

Question 2

What is the difference between non-coding RNA and pseudogenes?

Answer 2

pseudogenes resemble real genes except the stop codon is either in the beginning or middle of the sequence

Question 3

What are pseudogenes derived from?

Answer 3

genetic duplication or retro-transposons

Question 4

What do pseudogenes share with ancestral genes?

Answer 4

5’ and 3’ untranslated regions (UTRs)

Question 5

List 3 characteristics related to pseudogenes

Answer 5

1. almost as numerous/abundant as coding genes (∼19,000)
2. represent a significant proportion of the ‘transcriptome’ (actively transcribed
3. lack canonical promoters and use proximal regulatory elements to mediate transcription
   transcription exhibits tissue-specificity that is aberrantly activated in cancer

this leads to the hypothesis that they could have a functionality in cancer

Question 6

What is PTEN?

Answer 6

central gene in chromosome 10 that is involved in a central pathway that is activated by cancer

Question 7

What is the PI3K pathway?

Answer 7

GF binds to cell surface → PI3K & AKT activated → apoptosis is prevented → mTOR activated

Question 8

Why would a tumor eliminate PTEN?

Answer 8

PTEN is a tumor suppressor because it blocks AKT, so many tumors eliminate PTEN to activate the AKT pathway and induce cancer

Question 9

What is a ceRNA?

Answer 9

competing endogenous RNA: regulate other RNA transcripts by competing for shared microRNAs

Question 10

What is the pseudogene hypothesis?

Answer 10

pseudogenes can block the transcription of corresponding genes

Question 11

How can pseudogenes block the transcription?

Answer 11

the pseduogenes and normal genes both have the same 3’ UTR sequence, so it attracts miRNAs as if it were a normal gene

Question 12

What are the 2 functions of a miRNA?

Answer 12

reduce levels of RNA by inducing the catabolism of mRNA (degradation)

block translation (may be the more important function)

Question 13

What is a consequence of removing pseudogenes?

Answer 13

decrease in PTEN expression

Question 14

What do pseudogenes behave like?

Answer 14

oncogenes

Question 15

Describe an oncogenic pseudogene:

Answer 15

behaves like an oncogene: copy number is increased

Question 16

Describe a tumor supressor pseudogene:

Answer 16

behaves like a tumor supressor

Question 17

What is non-coding RNA?

Answer 17

RNA that is not translated into a protein

Question 18

What are fragile sites?

Answer 18

portion of the genome that seems to be more breakable than others

Question 19

What occurs during mitosis if there is a breakage at the fragile sites?

Answer 19

small deletions and small amplifications

Question 20

What occurs during replication if there is a breakage at the fragile site?

Answer 20

cells try to repair damage, but they introduce errors

Question 21

What are the main DNA repair pathways in cells?

Answer 21

homologous recombination and non-homologous recombination

Question 22

What DNA repair is involved during mitosis?

Answer 22

usually homologous except in G1 it is non-homologous

Question 23

In terms of the entire genome, genes in fragile sites are usually down-regulated…why would there be increased expression in some circumstances at fragile sites like CCSER1?

Answer 23

the loss of a portion of a gene could result in a gene being activated and expressed

Question 24

What happens when CRISPR-Cas9 is bound to a KRAB domain?

Answer 24

gene expression is silenced

if done in the presence of a pseudogene, pseudogene expression can be silenced and corresponding gene expression can be enhanced

Question 25

What are the 2 experiments done with pseudogenes?

Answer 25

cut only the intron sequence so that the pseudogene is free and shuts down the expressio of CCSER1

KRAB-CrisprCas9 targets intron sequence and pseudogene expression is silenced

Question 26

What was the aim of the 2 experiments done with pseudogenes?

Answer 26

to know if there is transcriptional regulation of pseudogenes

Question 27

What are the 2 groups of ncRNA?

Answer 27

below 200 nt: siRNA, miRNA, piRNA

above 200 nt: lncRNA and long non-coding intergenic RNA (lincRNA)

Question 28

What are some lncRNA characteristics?

Answer 28

transcribed by Pol II
5’ capped
spliced
poly-adenylated
protein is not generated
shorter than mRNA
fewer but longer exons
expressed at relatively low levels
poor primary sequence conservation

Question 29

Describe PANDA and p53:

Answer 29

compensates the action of p53 and induces apoptosis and acts as a gene repressor

Question 30

Describe DINO and p21:

Answer 30

stabilizes p53 and modulates its activity on target genes

if DINO is not present, p53 is downregulated

Question 31

What do lncDNA act in?

Answer 31

chromatin interaction: they can form or contribute to form loops within different portions of DNA

protein interactions

RNA interactions

Question 32

What mediates the interaction between the 2 proteins: EZH2 and LSD1?

Answer 32

HOTAIR