Tonon: Lecture IV Flashcards
Pseudogenes and Fragile Sites
What is a pseudogene?
a construct that is transduced into RNA but not a protein
What is the difference between non-coding RNA and pseudogenes?
pseudogenes resemble real genes except the stop codon is either in the beginning or middle of the sequence
What are pseudogenes derived from?
genetic duplication or retro-transposons
What do pseudogenes share with ancestral genes?
5’ and 3’ untranslated regions (UTRs)
List 3 characteristics related to pseudogenes
- almost as numerous/abundant as coding genes (∼19,000)
- represent a significant proportion of the ‘transcriptome’ (actively transcribed
- 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
What is PTEN?
central gene in chromosome 10 that is involved in a central pathway that is activated by cancer
What is the PI3K pathway?
GF binds to cell surface → PI3K & AKT activated → apoptosis is prevented → mTOR activated
Why would a tumor eliminate PTEN?
PTEN is a tumor suppressor because it blocks AKT, so many tumors eliminate PTEN to activate the AKT pathway and induce cancer
What is a ceRNA?
competing endogenous RNA: regulate other RNA transcripts by competing for shared microRNAs
What is the pseudogene hypothesis?
pseudogenes can block the transcription of corresponding genes
How can pseudogenes block the transcription?
the pseduogenes and normal genes both have the same 3’ UTR sequence, so it attracts miRNAs as if it were a normal gene
What are the 2 functions of a miRNA?
reduce levels of RNA by inducing the catabolism of mRNA (degradation)
block translation (may be the more important function)
What is a consequence of removing pseudogenes?
decrease in PTEN expression
What do pseudogenes behave like?
oncogenes
Describe an oncogenic pseudogene:
behaves like an oncogene: copy number is increased
Describe a tumor supressor pseudogene:
behaves like a tumor supressor
What is non-coding RNA?
RNA that is not translated into a protein
What are fragile sites?
portion of the genome that seems to be more breakable than others
What occurs during mitosis if there is a breakage at the fragile sites?
small deletions and small amplifications
What occurs during replication if there is a breakage at the fragile site?
cells try to repair damage, but they introduce errors
What are the main DNA repair pathways in cells?
homologous recombination and non-homologous recombination
What DNA repair is involved during mitosis?
usually homologous except in G1 it is non-homologous
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?
the loss of a portion of a gene could result in a gene being activated and expressed
What happens when CRISPR-Cas9 is bound to a KRAB domain?
gene expression is silenced
if done in the presence of a pseudogene, pseudogene expression can be silenced and corresponding gene expression can be enhanced
What are the 2 experiments done with pseudogenes?
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
What was the aim of the 2 experiments done with pseudogenes?
to know if there is transcriptional regulation of pseudogenes
What are the 2 groups of ncRNA?
below 200 nt: siRNA, miRNA, piRNA
above 200 nt: lncRNA and long non-coding intergenic RNA (lincRNA)
What are some lncRNA characteristics?
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
Describe PANDA and p53:
compensates the action of p53 and induces apoptosis and acts as a gene repressor
Describe DINO and p21:
stabilizes p53 and modulates its activity on target genes
if DINO is not present, p53 is downregulated
What do lncDNA act in?
chromatin interaction: they can form or contribute to form loops within different portions of DNA
protein interactions
RNA interactions
What mediates the interaction between the 2 proteins: EZH2 and LSD1?
HOTAIR
