Clock genes Flashcards
How many clock genes are present between species?
Many many many
True/False? Even though clock genes have different names, their functions are all similar
True
“the actors are different but the plot is the same”
What are the two conserved features of clock genes?
Oscillating mRNAs, proteins or activity
Autoregulatory feedback loops
Describe the basic mammalian clock and when Period protein is expressed the most
CLOCK and BMAL1 proteins associate and activate transcription of Per1,2,3 and Cry1,2, PER1,2,3 and CRY1,2 proteins inhibit CLOCK-BMAL1 complex leading to inhibition of Per123/cry12 transcription
Per1 RNA is most concentrated during the day, and PER protein is most expressed at CT 12`
Why is CLOCK/BMAL1 called a negative autoregulatory loop?
Because CRY/PER INHIBIT further synthesis
How do drosophila differ from mammals in terms of their clock genes?
CLOCK-CYCLE instead of CLOCK-BMAL1
just PER instead of PER1,2,3
TIM instead of CRY1,2
How was the period gene determined to affect circadian rhythm in drosophila?
“period mutants” would hatch at irregular periods
Can Per function without Tim in drosophila?
No, Per needs Tim to enter the nucleus and to be stabilized
What is interesting about the PAS domain in the mammalian clock gene?
It shares homology with Per (in drosophila)
How was clock deduced to be a transcription factor?
Q-rich region, a hallmark of many TFs
Do humans have Per gene?
Yes! 3 of them
How are Per genes controlled?
Via CLOCK-BMAL1 complex
What are cryptochromes?
A group of light-sensitive flavoproteins (FAD binding proteins), similar to photolyases (light-sensitive DNA repair)
Are Cryptochromes transcription factors?
Yes and no
They don’t bind DNA themselves, but they bind to Transcription Factors and prevent them from activating transcription
What happens if Cry1 is knocked out? Cry2? Both?
Cry1 KO: FRP is shorter
Cry2 KO: FRP is longer
Both: No clock present
True/False? Activity of a protein is roughly proportional to the expression of its gene
FALSE
How is REV-ERBalpha involved in circadian rhythms?
Rhythmically represses Bmal1 gene and its absence alters circadian rhythms
How is REV-ERBalpha expression regulated?
By BMAL1-CLOCK
What is ROR protein and?
Activates Bmal1 gene and opposes REV-ERB
Is there more to it than what we’ve seen in class?
Yes, lost more proteins and enzymes and co-activators etc
Of the crazy list of other proteins seen in class, what else should we know about?
BMAL2 (like BMAL1) and NPAS2 (like CLOCK)
What’s another layer of complexity on top of the typical mammalian rhythm seen in class?
Post-translational modifications
What is the most common Post translational modification? Second most?
What do they do?
Phosphorylation (regulation of clock protein stability, activity, intra-cellular localization)
Ubiquitination (Regulation of clock protein stability and more)
What enzyme phosphorylates most circadian rhythm proteins?
Casein Kinase 1 epsilon
Affects how much Per is degraded and how fast they can transit in/out of nucleus
What is the purpose of Glycogene Synthase Kinase 3 beta (GSK3B)?
Phosphorylation and stabilization of REV-ERB alpha
How does lithium affect circadian rhythms?
Li inhibits GSK3B, thus preventing REV-ERB alpha from being phosphorylated, and is thus degraded
How does Casein Kinase 1 Delta/Epsilon lead to degredation of PER 1/2 in mammals?
CK1 phosphorylates PER, Phosphorylated PER is then ubiquilated by B-TRCP1/2, leading to proteasomal degradation
