regulation of gene expression

Question 1

what role does the upstream activating sequence (UAS) and/or enhancer region play in transcription?

Answer 1

UAS and enhancer make up the promotor regions upstream of TATA-box, when the activator binds the UAS or enhancer it promotes assembly of the general transcription factors (GTFs) by interacting with the co-activator/target (T) to form the pre-initiation complex (PIC) at the core promoter/TATA-box for transcriptional initiation

Question 2

two domains on an activator

Answer 2

DNA binding domain which binds to specific UAS/enhancer region of DNA

activation domain: interacts with co-activator/target (T) on general transcription factor (GTF)

Question 3

differentiate enhancer vs promotor

Answer 3

enhancer can be however far up or downstream of the gene. function: bind transcription factors and bend the DNA to bring the transcription factor to the promotor region resulting in increased speed, can affect multiple various genes

promotors must be proximal to the TATA-box. Both transcription factors and RNA polymerase bind here in order to initiate transcription. promotors are unique to each gene

Question 4

define nucleosome

Answer 4

DNA wrapped around a histone ovtamer that is composed of histones H2A, H2B, H3, and H4

Question 5

define chromatin

Answer 5

array of nucleosomes

Question 6

histone acetylation: how and result

Answer 6

acetyl is added to histone by histone acetyltransferase (HAT) and is generally associated with transcription activation

Question 7

histone deacetylation: how and result

Answer 7

histone deacetylase (HDAC) removes acetyl from histone which usually is associated with transcriptional repression

Question 8

histone methylation: how and result

Answer 8

histone methyltransferase (HMT) adds methyl to histone which results in transcriptional stimulation if occurs at H3 K4 and results in transcription repression if at H3 K9, H3 K27, and H4K20

Question 9

Swi/Snf complex

Answer 9

an ATP-dependent chromatin remodeling factor which alter structure to regulate transcription, this complex is generally associated with transcriptional activation

Question 10

CpG islands

Answer 10

CG-rich regions upstream of many genes in humans
if methylated they repress transcription
by inhibiting DNA methyltransferase trancription is promoted

(mechanism of expressing HbF in SCD. by inhibiting DNA methyltransferase in order to promote expression of HbF)

Question 11

location of each of the hemoglobin genes

Answer 11

chromosome 11: beta chromosomes (epsilon, gamma (A and B), delta, beta)
chromosome 16: alpha- globin genes (zeta, alpha 1, alpha 2)

Question 12

structures of embryonic, fetal and adult Hb

Answer 12

embryonic: zeta2epsilon2 (HbGowerI), alpha2epsilon2 (HbGowerII)
fetal: alpha2gamma2 (HbF)
Adult: alpha2beta2 (HbA), alpha2delta2 (HbA2)

Question 13

what mechanism alters the expression of the gamma Hb gene

Answer 13

DNA methylation is absent in the gamma gene in the embryonic stage, and therefore it is expressed. methylation of the CpGs in later life stages causes its suppression.

Question 14

5-azacytidine

Answer 14

the first epigenetic modification pharmacological agent, was used to block DNA methyl-transferase thus promoting gamma gene expression and hence HbF, was used to treat SCD and Beta thalassemia

Question 15

silence sequences

Answer 15

included in proximal regulatory elements of the gene
autonomous (does not happen due to competition with other globins being expressed)
they disrupt the interaction between the LCR and the gene resulting in turning off gene expression

Question 16

list the factors that have been shown to have enhancer functions for beta LCR

Answer 16

MARE (Maf-response element)
NEF2 & LCRF1/Nrf1 (AP1 related proteins)
GATA1 (binds GATA)
ELKF (binds to CACC motif)

Question 17

What two binding sites do promotors of Beta globin have in common

Answer 17

TATA and CCAAT

Question 18

BCL11A

Answer 18

silences gamma globin genes by interacting with NuRD (a chromatin remodeling and repressor complex) and the erythroid transcription factors GATA-1 and FOG-1

Question 19

KLF1

Answer 19

promotes BCL11A which silences gamma globin
stimulates beta globin expression by binding to its promotor region with high affinity
also known as ELKF

Question 20

how does BCL11A knockout affect globin expression

how does KLF1 knockout affect globin expression

Answer 20

BCL11A knockout results in gamma globin repression

KLF1 knockout results in beta globin repression

Question 21

how does alpha globin gene expression differ from beta globin gene expression

Answer 21

alpha globin is constitutively active (always active) because its chromatin is always opne due to its highly G+C clusters and multiple CpG islands; alternatively, beta globin genes are A +T rich with no CpG islands
LCR is required for opening in Beta globin and distal regulatory elements are much larger with more hypersenesitive sites since they are required to open the chromatin (as opposed to alpha globin already being open)

Question 22

hydroxy urea

Answer 22

promotes gamma globin gene expression (HbF) via NO/cGMP pathway
NO activates sGC which promotes AP1 to bind to DNA thus promoting expression of gamma globin