lecture 9

Question 1

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?

Answer 1

deletion of the B-globin locus control region

B-thalassemia

Question 2

Cleft palate

Answer 2

sequence variants in the transcription factors IRF6, PVRL1, MSX1

Question 3

white coat

Answer 3

mutation in a gene on the S locus encoding transcription factor MITF

Question 4

Canine Burkitt Lymphoma

Cause?

Answer 4

chromosomal translocation of the c-Myc transcription factor gene into the IgH locus causing dysregulation of c-Myc expression

Question 5

TADs

Answer 5

topological associated domains

organize genome
usually active

regulatory loops
sub-TADs -enhancers and promoters

long distance DNA interactions by architectural loops

Question 6

subTAD

Answer 6

brings together enhancer that binds transcription factors and bind them to a promoter

Question 7

histone code terms

Answer 7

histone modification writes
histone modification erasers
histone modification readers

Question 8

examples of histone modification writers

Answer 8

acteylases (make less + add Ch3-C=0)
methy-transferases (add CH3)
kinases (add phosphate)

Question 9

examples of histone modification erasers

Answer 9

deacteylases
demethylases
phosphatases

Question 10

examples of histone modification readers

Answer 10

proteins with bromodomains
-see acetylated histones
proteins with chromodomains
-see methylated histones

Question 11

activation histone code signals

Answer 11

H3K4me3
H3K9ac
H3K14ac

Question 12

repression histone mode signals

Answer 12

H3K9me3

H3K27me3

Question 13

HDAC inhibitors and therapy

Answer 13

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)

Question 14

if C followed by a G

CpG

Answer 14

DNA is methylated
transcription is off

involved in DNA imprinting during development- different methylated groups go on and off as organism develops

Question 15

locus control regions now called ____

Answer 15

super enhancers

Question 16

super enhancers or locus control regions are

Answer 16

regions of the genome that control very large sections of the genome

Question 17

example of deletion of an LCR

Answer 17

LCR deleted upstream from B-globin locus.

patients get B-thalassemia

Question 18

spot on gene that help polymerase to bind

Answer 18

TATA box

Question 19

what binds to TATA box

Answer 19

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

Question 20

___ directs RNA Polymerase II to attach

Answer 20

general transcription factors specifically TF-IIB

Question 21

three types of coactivators

Answer 21

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

Question 22

example of mediator coactivators

Answer 22

bridges activators between transcription factors and RNA polymerase

Question 23

example of Swi/Snf

Answer 23

ATPase that remodels chromatin

Question 24

example of Histone Modification Enzymes

Answer 24

HAT/HDAC/Methyltransferase
(acetylation, deacetylation, methylation)

(covalently modify histones and other proteins

Question 25

carboxy terminal Domain

Answer 25

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

Question 26

TF-IIH

Answer 26

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)

Question 27

transcription factors will

Answer 27

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

Question 28

there are two parts of transcription factors

Answer 28

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.

Question 29

types of DNA binding domains

Answer 29

``` zinc fingers homeodomains leucine zipper and basic region helix-loop helix and basic region Ets domain Fork head Rel ```

Question 30

leucine zippers deal with

Answer 30

dimerization domains control bone formation, cell growth

Question 31

homeodomains deal with

Answer 31

development can create bithorax (double wings)

Question 32

type os activation domains

Answer 32

acid blobs proline rich glutamine

Question 33

HAT vs HDACs

Answer 33

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 ```

Question 34

HAT

Answer 34

type of coactivators histone acetyltransferase activity (HAT) bind with retinoic acid and add histone acetyl marks which activates transcription

Question 35

HDACs

Answer 35

histone deacetylase (HDACs) separate from retinoic acid and removes histone acetyl marks and represses transcription

Question 36

Swi/Snf

Answer 36

type of coactivators push nucleosomes this allows TATA to be exposed allows transcription

Question 37

mediator

Answer 37

type of coactivators acts as bridge between transcription factors and RNA polymerase this stabilizes everything at promotor so gene expression can go on

Question 38

how are gene regulation controlled

Answer 38

regulators can be present in single tissue types multiple dimerization partners post-translational modifications combinatorial assortment of binding proteins

Question 39

how do flies get stripes

Answer 39

bicoid expresses stripes hunchback and knirps are repressors of bicoid when neither hunchback or knirps are expressed then you get a stripe (kruppel)

Question 40

example of tissue differentiation regulated by dimer formation in muscle development

Answer 40

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)

Question 41

explain how gene regulatory networks could be used in medicine

Answer 41

1. activate lineage-specific gene regulatory networks 2. turn off broken one 3. make sure you did the right thing and didn't change something else accidentally

Question 42

*** transcription factor activation domains can stimulate transcription. Describe several ways that these domains can function

Answer 42

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