what are cis regulatory elements
proteins that bind to DNA itself - enhancer sequence, basal promoter sequence, proximal control region
what are trans regulatory elements
proteins that bind to the cis regulatory elements - enhancers, transcription factors
what does the basal promoter sequence consist of
TATA box and CAAT box
what is promoter region responsible for
interaction of RNA pol II with its associated factors
whats the point of having both a basal and upstream promoters
allow for tight regulation
what do transcription factors do
help to grant specificity to RNA pol II regulated transcription
what promotes high levels of transcription?
enhancer, proximal promoters
level of expression with just the basal transcription machinery
low
where can enhancer be found
before gene, introns, or after gene
examples of eukaryotic transcription factors that must dimerize to function
leucine zipper, helix-turn-helix, zinc finger
what are DNA binding domain
part of transcription factors that only bind to certain DNA sequences
advantages of forming a dimer
adds an element of complexity and versatility
what does enhancer do to basal transcription apparatus
it stabilizes it thus increasing transcription levels
three modes of repressor action for transcription factors
quenching, blocking, competition
when does quenching occur with repressor proteins
repressor protein binds directly to the activator and hence can’t bind enhancer
when does competition occur with repressor protein
activator and repressor compete for binding to the enhancer
when does blocking occur with repressor protein
repressor binds to activation domain of the activator and now cant interact with basal transcriptional machinery
if repressor protein binds to the activation domain of the activator, can it still bind to the DNA
yeah but it is non functional
advantage of different genes having the same cis regulatory sequence
multiple genes can be regulated together - turned on and off at same time etc
short sequences of DNA within a gene promoter region that are able to bind a specific transcription factor and regulate transcription of genes
response elements
what allows the hypoxia inducible factors to bind and regulate transcription of genes
short DNA sequences (HREs) in the promoter of the genes
how do hypoxia element factors work
they (HIF alpha and HIF beta) must dimerize before they can bind to DNA sequences and regulate expression
what type of elements are the hypoxia inducible factors
cis regulatory elements
most oxygen breathing species express what highly conserved transcriptional complex
HIF-1
what does HIF do
allows for coordinated cellular response to low oxygen tension
name giving to normal cells with oxygen stress
normoxia
fate of HIF-1 alpha under normal oxygen conditions
they are degraded by proteasomes in the cytoplasm and genes for hypoxia response are not expressed
fate of HIF-1 alpha under low oxygen state
HIF-1 alpha is not degraded and it enters cell nucleus where it forms dimer with HIF-1 beta allowing it to bind to DNA of target genes carrying hypoxia response element (HRE)
Induction of expression of a family of genes by transcription factor binding to a common enhancer sequence of many different genes is an example of?
cells in hypoxia state
what happens inside a tumor that causes it to grow
so there is no oxygen inside a tumor hence HIF-1 alpha is not degraded. HIF-1 alpha stimulates angiogenesis (development of new blood vessels) hence giving supply for tumor to grow
reason why we learn about hypoxia in relation to how we should treat tumor
if we could find a way to inhibit HIF-1 alpha and beta inside tumors we can stop its growth
glucocorticoid receptors is what type of transcription factor
zinc finger TF
What does activated glucocorticoids receptor do in nucleus and cytosol
upregulates expression of anti inflammatory genes in nucleus
represses expression of pro inflammatory proteins in cytosol
glucocorticoids is used as treatment for
glucocorticoid deficiency and to suppress the immune system
key thing to note about glucocorticoid response elements DNA sequence
they are inverted repeats
what happens to glucocorticoid receptors in cytoplasm in absence of glucocorticoids
become part of an inactive multi-protein complex
when happens when cortisol (glucocorticoids) is present in cytoplasm
its receptors dissociate from the multi protein complex, dimerizes, and moves to the nucleus
what do glucocorticoids receptors do in nucleus
induce or repress target genes
also bind response element DNA in the promoter regions of glucocorticoid-responsive genes
what is the myc/max system
regulatory mechanism that switches between gene activation and repression
in absence of myc, what does max do
max dimers with itself (homodimer) and represses gene transcription
what does myc do with its transcriptional regulation domain
it has to dimer with max first before it can bind to DNA then regulates expression of genes involved in cell cycle progression
when is max expressed and myc not
in non proliferating cells
in presence of myc what happens
myc and max dimerize (heterodimer) and activate gene expression
difference between myc/max heterodimer and max homodimer
myc/max - gene expression (more favorable)
max/max - gene suppression
problem with myc over expression in tumors/cancers
it will favor forming the heterodimer with max and will promote cell proliferation
Processes long primary- miRNAs to pre-miRNA hairpin structures
Drosha
Base pairing between miRNA and target mRNA give what
target specificity
what happens if specificity is not complete with miRNA
one miRNA can silence many mRNA
what further processes pre-miRNA to single stranded RNA and initiates the formation of the RNA-induced silencing complex (RISC)
dicer
is it common in human for mRNA to be regulated by miRNA
yeah
how does miRNA regulate gene expression in mRNA
it binds to the 3’ UTR and base pairs to it preventing interaction of translational machinery with the 5’ cap structure
basically prevents mRNA from getting translated
miRNA are normally involved in what type of regulation
cell proliferation
what happens to the genes that code for miRNA in tumor cells
amplified so they proliferate uncontrollably
short interfering RNA (siRNA) is processed by what type of enzyme
dicer
Double stranded RNA Often transcribed of two opposable promoters in a gene delivery vector
siRNA