lecture 9 Flashcards
your patient is severely anemic and has essentially no B-globin protein or RNA. There is no mutation within the B-globin gene
What is the defect?
deletion of the B-globin locus control region
B-thalassemia
Cleft palate
sequence variants in the transcription factors IRF6, PVRL1, MSX1
white coat
mutation in a gene on the S locus encoding transcription factor MITF
Canine Burkitt Lymphoma
Cause?
chromosomal translocation of the c-Myc transcription factor gene into the IgH locus causing dysregulation of c-Myc expression
TADs
topological associated domains
organize genome
usually active
regulatory loops
sub-TADs -enhancers and promoters
long distance DNA interactions by architectural loops
subTAD
brings together enhancer that binds transcription factors and bind them to a promoter
histone code terms
histone modification writes
histone modification erasers
histone modification readers
examples of histone modification writers
acteylases (make less + add Ch3-C=0)
methy-transferases (add CH3)
kinases (add phosphate)
examples of histone modification erasers
deacteylases
demethylases
phosphatases
examples of histone modification readers
proteins with bromodomains
-see acetylated histones
proteins with chromodomains
-see methylated histones
activation histone code signals
H3K4me3
H3K9ac
H3K14ac
repression histone mode signals
H3K9me3
H3K27me3
HDAC inhibitors and therapy
histone deacetylase
leads to silencing- turn off gene
inhibiting these will turn on genes
depsipeptide-CLL and T cell lymphoma
MS-275
SAHA
Depudesin (reverses transformation of NIH3T3 cells)
if C followed by a G
CpG
DNA is methylated
transcription is off
involved in DNA imprinting during development- different methylated groups go on and off as organism develops
locus control regions now called ____
super enhancers
super enhancers or locus control regions are
regions of the genome that control very large sections of the genome
example of deletion of an LCR
LCR deleted upstream from B-globin locus.
patients get B-thalassemia
spot on gene that help polymerase to bind
TATA box
what binds to TATA box
general transcription factors attach to TATA
(TBP, TAFs) TF 11D
TF-IIA
TF-IIB
TFIID- binds along with other complexes
TF-IIA stabilizes the complex on DNA
TF-IIB helps position RNA polymerase to the right start site
___ directs RNA Polymerase II to attach
general transcription factors specifically TF-IIB
three types of coactivators
mediators
-bridges activators, GFT, RNA polymerase
Swi/Snf- has ATPase activity that remodels chromatin (makes things move over to allow transcription)
histone modification enzymes
-HAT/HDAC/Methyltransferase
example of mediator coactivators
bridges activators between transcription factors and RNA polymerase
example of Swi/Snf
ATPase that remodels chromatin
example of Histone Modification Enzymes
HAT/HDAC/Methyltransferase
(acetylation, deacetylation, methylation)
(covalently modify histones and other proteins
carboxy terminal Domain
CTD
largest subunit of RNA polymerase II
repeated sequence of specifically amino acids that repeat 27-52 times
(have hydroxyl groups(OH)
sites of phosphorylation (add P with 4 O/phosphate)) tyr-ser-pro-thr-ser-pro-ser
TF-IIH is believed to phosphorylate CTD
TF-IIH
kinase that adds phosphate to CTD and tells RNA polymerase it is time to bind
TF-IIH (XPB and XPD) is from NER
(nucleotide excision repair) that causes unwinding of DNA (helicase)
transcription factors will
bind to specific DNA sequences.
control the level of transcription either activate or repress expression.
can be thousands of base pairs away
there are 1000s of transcription factors
there are two parts of transcription factors
DNA binding domain- bind to DNA and interact with the basal complex to stabilize TFIID binding to the TATA
transcriptional activation domain
-interact with coactivators to increase TFIID binding and RNA polymerase recruitment.
types of DNA binding domains
zinc fingers homeodomains leucine zipper and basic region helix-loop helix and basic region Ets domain Fork head Rel
leucine zippers deal with
dimerization domains
control bone formation, cell growth
homeodomains deal with
development
can create bithorax (double wings)
type os activation domains
acid blobs
proline rich
glutamine
HAT vs HDACs
there are retinoic acid receptors in the cell
if RAR bind with retinoic acid(RA) then RAR binds with HAT- transcription on
if RAR does not bind with RA then RAR binds with HDAC- transcription off
histone acetyltransferase activity (HAT)
bind with retinoic acid and add histone acetyl marks which activates transcription
histone deacetylase (HDACs) separate from retinoic acid and removes histone acetyl marks and represses transcription
HAT
type of coactivators
histone acetyltransferase activity (HAT)
bind with retinoic acid and add histone acetyl marks which activates transcription
HDACs
histone deacetylase (HDACs)
separate from retinoic acid and removes histone acetyl marks and represses transcription
Swi/Snf
type of coactivators
push nucleosomes
this allows TATA to be exposed
allows transcription
mediator
type of coactivators
acts as bridge between transcription factors and RNA polymerase
this stabilizes everything at promotor so gene expression can go on
how are gene regulation controlled
regulators can be present in single tissue types
multiple dimerization partners
post-translational modifications
combinatorial assortment of binding proteins
how do flies get stripes
bicoid expresses stripes
hunchback and knirps are repressors of bicoid
when neither hunchback or knirps are expressed then you get a stripe (kruppel)
example of tissue differentiation regulated by dimer formation in muscle development
MyoD-E2A heterodimer= muscle development
MyoD-Id heterodimer= no muscle
cell types can be triggered by transcription factors into another cell type
(change cell into other cell)
explain how gene regulatory networks could be used in medicine
- activate lineage-specific gene regulatory networks
- turn off broken one
- make sure you did the right thing and didn’t change something else accidentally
*** transcription factor activation domains can stimulate transcription. Describe several ways that these domains can function
activation domains such as acid blobs, proline rich or glutamine rich act to bridge information/relay between general transcription factors and DNA binding domain of transcription factors. they can also act to bring proteins to the transcription area. such proteins may act to speed up the initiation or process of transcription. activation domains may also communicate with co-activators such as mediators, swi/snf and HAT. Activation domains may also function to specifically expedite the entrance of RNA polymerase to the TFIID or even to expedite the binding of TFIID to DNA
Bind to DNA and interact with the basal complex to stablilize GFTs (TFIID) binding.
interact with coactivator (mediators, Swi.Snf and HAT/HDAC/Methyltransferase) to increase TFIID binding and RNA polymerase II recruitment
