chapter 13 part 1 Flashcards
what do activator proteins bind & how do they affect transcription
bind regulatory sequences to stimulate transcription
what do repressor proteins bind & how do they affect transcription
bind other (so not regulatory ones)
sequences to hinder transcription
where are regulatory proteins often found?
in large complexes in eukaryotes
-unlike in bacteria, one transcription factor may regulate tens to hundreds of target genes
what are the three regulatory DNA sequences
- core promoter region
- proximal elements
- enhancer/silencer sequences
about the core promoter region!
it contains the TATA Box & other sequences
it is immediately adjacent to the start of transcription
-binds RNA pol II & its associated general transcription factors (GTFs)
tell me about proximal elements!
they are located upstream of the core promoter region & bind additional regulatory proteins
tell me about enhancer/silencer sequences!
they act from greater distances from the core promoter
-the bind regulatory proteins that interact with proteins bound to one another
-enhancers/silencers can be located upstream, downstream, close to, or very far, or even within the genes they regulate
where can enhancers/silencer sequences
can be located upstream, downstream, close to, or very far, or even within the genes they regulate
all three regulatory regions contain ____-_______ regulatory sequences
cis acting
they regulate transcription of genes on the same chromosome as the sequence
what binds the core promoter & are they cis or trans acting?
RNA pol II & various general transcription factors (GTFs)
-trans-acting regulatory proteins which can bind to their target sequence on any chromosome
what are enhanceosomes
when there are aggregations of multiple proteins from large complexes at enhancers
what does the enhanceosome direct
DNA bending/loop formation that allow enhanceosome proteins to interact with RNA pol & transcription factors at the core promoter & proximal promoter elements
what does enhancer activity typically help control
the timing & location of gene transcription
SV80 enhancer
consists of seven adjacent regions that are about 200 bp upstream of the transcription start point
each segment binds specific regulatory proteins
Enhancers and silencers typically contain ___________ _____ (modules) for several transcription factors
binding sites
what are modules
binding sites
what do modules allow silencers/enhancers to do?
integrate activities of different transcription factors to produce different outputs
what are pioneer factors?
are the first to bind regulatory molecules, facilitating the binding of additional transcription factors
can the same sequence act as an enhancer or a silencer?
yes! depending on which regulatory proteins are present & bind to the sequence (often cell type specific)
what is SHH
sonic hedgehog gene
what does SHH gene do?
directs limb formage & is controlled by an enhancer 1 million base pairs away from SHH gene
what type of fashion is SHH expressed in?
tissue-specific due to the action of two different enhancers
what does LCR stand for?
locus control region
what does LCR do?
it is a highly specialized enhancer that regulates transcription of multiple genes packaged into complexes of closely related genes
how many sequences does the LCR regulating the beta-globin complex contain & what are they?
4
HS1, HS2, HS3, HS4
what do the four distinct sequences regulating beta globin work together to do?
produce the correct expression of each type of beta-globin gene throughout development
how does the LCR function
by recruiting the chromatin-modifying, coactivator, & transcription complexes
what do HS1 & HS2 do?
they bind regulatory proteins that direct formation of small DNA loops & recruitment of additional factors
muations in the sigma- & beta-globin genes produce hereditary anemias called what
thalassemia
can some thalassemia patients have no discernible muations?
yes, some may have no discernible mutations in the protein-coding part of the globin genes, nor in their promoters
what are some thalassemia cases due to?
deletions that alterd the LCR region, causing abnormal expression of the globin genes
what is UAS
yeat upstream activator sequences
in the yeast Saccharomyces cerevisiae, transcription of genes in what pathway are carefully refulated by enhancer-like sequences
galactose utilization pathway
what happens in the UAS when galactose is the only sugar available?
wild-type yeast induce transcription of four enzyme-producing genes
GAL1, GAL2, GAL7, GAL 10
what are the four enzyme producing genes in UAS & what do they do?
GAL1, GAL2, GAL7, GAL10
they import and break down galactose
do each of the GAL genes have their own promote and similar enhancer like sequencesr?
yes
what are the GAL genes bound by?
Gal4
what is Gal4 encodes by?
GAL4 gene
is Gal4 sometime are always present in cells?
always
it is continuously present in cells
what is the enhancer like element
upstream activator sequence
UAS of UASg
what happens to Gal4 in the absence of Galactose
Gal4 is bound & inactivated by Gal80
what is Gal4 like?
an enhancer like sequence
things about UASG (how many, how many bp, binding site for what)
UASg element contains two 17 bp repeat sequences that are binding sites for Gal4
what does Gal4 function as?
a homodimer
what happens when Gal80 is bound to Gal4 (when galactose is absent)
the Gal4 DNA-binding domain is unable to bind to UASG
what binds to Gal80 when galactose is present?
galactose & Gal3 bind to Gal80
what is Gal3 encoded by?
the GAL3 gene
what happens when galactose is present
-galactose & Gal3 bind to Gal80
-Gal80 releases Gal4- freeing the DNA-binding domain of Gal4 to recognize & bind to the UASG sites
-the transcriptional activation domain of Gal4 homodimer then activates transcription of GAL genes
what activates transcription of the GAL genes
transcriptional activation of the Gal4 homodimer when it binds to UASG sites
what leads to formation of a mediator
when Gal4 binds UASG
what is a mediator
a multiprotein complex
an enhaceosome that induces formation of a DNA loop, contacting the general transcription apparatus at the GAL gene promoters
what allows the transcription factors to bind?
physical changes in the DNA
what does physical distortion of the DNA allow?
it allows UASG promoter to bring this sequence into contact with the promoter & RNA pol II to initiate transcription
-UASG is NOT a proximal promoter; it is further upstream
do eukaryotic repressors & bacteria repressors inhibit transcription through the same mechanisms?
no- eukaryotic repressors do it differently
what is one mechanism of binding repressor proteins?
through silencer sequences that directly prevent enhancer-mediated transcription
what do silencer sequences do
they directly prevent enhancer-mediated transcription
are silencer sequences cis or trans acting?
they are cis-acting
what genes utilize silencer sequences?
GAL genes
what binds the silencer sequences upstream of the GAL genes?
protein Mig1 is produced in the presence of glucose & binds the silencer sequence
is Mig1 produced in the presence or absence of glucose?
in the presence
where are the silencer sequences of GAL genes located?
located between the UASG sequences & the promoters
what protein does Mig1 attract?
Tup1 & the two together form a repressor complex that prevents UASG from initiating transcription
what prevents UASG from initiating transcription?
when Mig1 attracts Tup1 & they form a repressor complex
what are insulator sequences?
they are cis-acting sequences located between enhancers & the promoters of genes that need to be protected from the action of the enhancers
what do insulators ensure?
there is only the target gene is regulated by the enhancer
what may insulators allow?
DNA loops that contain the enhancers & their intended target promoters while excluding non-target genes
what do DNA loops exclude?
non-target genes
Some insulator sequences function by containing the spread of ________________.
heterochromatin
what is constitutive heterochromatin
when regions of the genome are always heterochromatic
facultative heterochromatin
regions that switch between euchromatin & heterochromatin often based on tissue type or cellular needs during certain times
when does positron effect variegation occur?
(PEV) occurs when the euchromatin is placed (by mutation) neat heterochromtain, which can then spread converting some of the euchromatin or heterochromatin, this can silence genes
when euchromatin is converted into heterochromatin, when can occur to genes?
it can silence them
