Clock Genes

Question 1

What features are conserved in the clock genes in all Kindgoms?

Answer 1

Oscillating mRNAs, proteins, or activity

Autoregulatory feedback loops

Question 2

What hallmark of activating TFs was found in Clock?

Answer 2

Q-Rich domain

Question 3

What are the roles of cryptochromes Cry1 and Cry2?

Answer 3

Bind BMAL1 and prevent it from activating transcription

Cry1 KO has shorter FRP

Cry2 KO has longer FRP

CRY1/CRY2 KO has no clock

Question 4

What is the (simplified) mammalian feedback loop learned in class?

What’s missing?

Answer 4

BMAL1:CLOCK induce transcription of REV-ERB alpha and Per1, Per2, Cry1, Cry2

PER:CRY inhibits CLOCK

REVERB A inhibits BMAL1

many post translational modifications modify these steps further

Question 5

Name the enzyme mutate in Tau hamsters and the end result on the clock

Answer 5

Casein Kinase 1Epsilon

CK1E phosphorylates many things and regulates essentially every process
Affects how much Per is degraded and how it exits the nucleus

Unstable PER proteins that can’t enter/exit nucleus easily and lead to decreased duration of CLOCK:BMAL1 inhibition

SHORTER PERIOD

Question 6

Name the enzyme that phosphorylates REVERB alpha and the effect of this phosphorylation

Answer 6

Glycogene Synthase Kindase 3Beta (GSK3B)

Stabilizes and prevents degradation

Question 7

How is phosphorylated Per signalled for degradation? What enzyme does this? What happens when this enzyme is KOed?

Answer 7

Ubiquitination by Beta-Trcp ubiquitin ligase

Knowkout leads to a lengthening of FRP

Question 8

What interesting feature makes CLOCK unique as a TF? How does it use this property?

Answer 8

It has its own HAT domain (instead of needing to requit HATs)

Acetylates BMAL1, necessary for proper clock function

Question 9

What is the difference between clock genes and clock controlled genes?

Answer 9

Clock genes: per 1/2, cry1/2, bmal1/clock, etc

Clock controlled genes: Any gene that is affected by BMAL1:CLOCK