Lecture 25 & 26 Flashcards
describe the feedback loops seen in histones
To allow for the heritability of chromatin after DNA replication, histones will reassociate with the same local region & new histones will be modified to reinforce the previous modifications (FEEDBACK LOOPS)
Describe retinal opsin expression, describe the signal cascade
cone and rod cells in the retina express opsins
opsin + 11-cis retinal = rhodopsin
Rhodopsin + light converts 11-cis to all-trans retinal
all-trans retinal activates transducin, which activates phosphodiesterase-6 which hydrolyzes the messenger molecule cGMP whic prevents ion channels opening, which prevents neurotransmitter release which signals the connected neuron that light is detected
Describe CRX(what kind of TF), what happens in a k.o. mouse
CRX is a helix-turn-helix transcription factor
The consensus sequence is an enhancer located in the control region of several opsin genes
Crx k.o. mouse develops normally, except they are totally blind, also lack a circadian rhythm because opsins are in the pineal
When can expression of crx first be detected
around 12 days after fertilization
expression remains active for the lifetime of the mouse in the cone and rod cells
How does CRX regulate opsin expression? What are the 3 HATs?
Through chromatin remodelling
Crx recruits at least 3 specific HATS
Interactions with two other transcription factors Nrl and Nr2e3 which determine whether rods or cones will develop
3 HATs: Gcn5, CBP & AcH3
H3K9 and H3K14 acetylation
what condition comes from mutation Crx? What kind of mutation? What domain does it affect?
Leber Congenital Amaurosis is a group of vision-loss phenotypes with no apparent deformity in the eye
LCA7 is an especially devastating form of LCA due to the dominant inheritance pattern
Frameshift which causes an early stop codon which affects the activation domain but the DNA binding domain is still fine
what is CpG island
a cluster of CG dinucleotides
What can cytosine undergo? How is it repaired
can undergo deamination to become uracil
Uracil shouldn’t be in DNA so Base Excision Repair utilizes a uracil DNA glycsosylase to remove the uracil
U:G –> abasic:G –> C:G
What is the most frequently modified nucleotide in eukaryotes
5-methyl-cytosine but is is deaminated into thymine instead of uracil which is still fixed used BER
T:T –> abasic:G –> C:G
Which dinucleotide is seen the least
CG
CpG are seen only 1% of the time
What happened to CpG? Process? At promoters?
lost to mutation
Methylated CpG’s will degrade over evolutionary time and the lack of CpG’s can be explained because methylated cytosines caused CpG’s to become TpG’s and there was no selection against this process
At promoters, the degradation is slower, because selection has required those CpG’s to be there for some reason, CpG’s are less methylated at promoters, or both
Describe DNA silencing by CpG methylation?What enzyme? Chromatin state?
Vertebrates have DNA methyltransferases (DNMT’s) that target CpG dinucleotides
outside of CpG islands, 80% of CpG’s are methylated
5-meCpG’s are associated with heterochromatin and are off
Unmethylated CpG’s recruit HAT’s and HMT’s which turn it on
What are the 4 ways DNMT’s methylate CpG islands
Specifically – by association with a DNA binding protein
* Unspecifically – by association with a chromatin state
* Maintaining – requires the “old” strand to be 5-meCpG
* De novo – can methylate a new CpG
What is a bistable switch? What is it caused by?
Bistable switches control gene expression are either stably On or Off with no in between
They have a threshold which cause the gene to switch on or off
Epigenetic feedback loops create these stable on/off states
describe demethylation in embryogenesis
By 4-cell stage they have no methylation but when they become blastocysts they start to have methylation again
Passive demethylation of maternal DNA
Active demethylation of paternal DNA
