regulation of gene expression Flashcards
what role does the upstream activating sequence (UAS) and/or enhancer region play in transcription?
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
two domains on an activator
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)
differentiate enhancer vs promotor
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
define nucleosome
DNA wrapped around a histone ovtamer that is composed of histones H2A, H2B, H3, and H4
define chromatin
array of nucleosomes
histone acetylation: how and result
acetyl is added to histone by histone acetyltransferase (HAT) and is generally associated with transcription activation
histone deacetylation: how and result
histone deacetylase (HDAC) removes acetyl from histone which usually is associated with transcriptional repression
histone methylation: how and result
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
Swi/Snf complex
an ATP-dependent chromatin remodeling factor which alter structure to regulate transcription, this complex is generally associated with transcriptional activation
CpG islands
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)
location of each of the hemoglobin genes
chromosome 11: beta chromosomes (epsilon, gamma (A and B), delta, beta)
chromosome 16: alpha- globin genes (zeta, alpha 1, alpha 2)
structures of embryonic, fetal and adult Hb
embryonic: zeta2epsilon2 (HbGowerI), alpha2epsilon2 (HbGowerII)
fetal: alpha2gamma2 (HbF)
Adult: alpha2beta2 (HbA), alpha2delta2 (HbA2)
what mechanism alters the expression of the gamma Hb gene
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.
5-azacytidine
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
silence sequences
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
list the factors that have been shown to have enhancer functions for beta LCR
MARE (Maf-response element)
NEF2 & LCRF1/Nrf1 (AP1 related proteins)
GATA1 (binds GATA)
ELKF (binds to CACC motif)
What two binding sites do promotors of Beta globin have in common
TATA and CCAAT
BCL11A
silences gamma globin genes by interacting with NuRD (a chromatin remodeling and repressor complex) and the erythroid transcription factors GATA-1 and FOG-1
KLF1
promotes BCL11A which silences gamma globin
stimulates beta globin expression by binding to its promotor region with high affinity
also known as ELKF
how does BCL11A knockout affect globin expression
how does KLF1 knockout affect globin expression
BCL11A knockout results in gamma globin repression
KLF1 knockout results in beta globin repression
how does alpha globin gene expression differ from beta globin gene expression
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)
hydroxy urea
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
