Quiz 5
translational level
-elongation factors -RNA interference
Cis acting elements
-promoter - very close to genes intiation site -enhancer -can lie far away from gene - can be reversed -augment or repress basal levels of transcription
transcriptional level
-transcription factors (environmental, physiological) - alternate splicing
gene expression can be regulated at four levels such that different cell types synthesize different sets of proteins
1. Differential gene transcription regulates which of the nuclear genes are transcribed into nuclear RNA 2. Selective nuclear RNA processing regulates which of the transcribed RNAs (or which parts of such a nuclear RNA) are able to enter into the cytoplasm and become messenger RNAs 3. Selective messenger RNA translation regulates which of the mRNAs in the cytoplasm are translated into proteins 4. Differential protein modification regulates which proteins are allowed to remain and or function in the cell.
Control of gene expression
1. transcriptional 2. Posttranscriptional 3. Translational 4. Posttranslational
modular
a gene can have several enhancer elements each of which may turn it on in different sets of cells
GFP
a very widely used system reporter that emits fluorescence after irradiation with UV
transactivation
activates or repress transcription often involved with proteins involved in binding RNA polymerase II; eg TFIIB TFIIE often involved with enzymes that modify histones
enhancers
are modular pax6 gene expressed in the eye pancreas nervous syetem
enhancers
are stretches of bases within dna about 50 to 150 base pairs in length; the activities of many promoters are greatly increased by _____________ which can exert their stimulatory actions over distances of several thousands base pairs
enhancers
are the major determinants of differential transcription in cell types and through developmental stages
core promter
basal level expression -binding site for TATA binding protein and associated factors
enhancers
become associated with particular transcription factors binds nucleosome regulatros and the mediator complex and engages with the promtoter to transcribe the gene in that particular type of cell
several transcription factors
can bind to an enhancer and it is the specific combination of transcription factors present that allows a gene to be active in a particular cell type that is the same transciption factor in conjunction with different combinations of factors will activate different promoters in different cells
Trans acting elements (not DNA)
can diffuse through
Trans acting elements (not dna)
can diffuse through the cytoplasm and act as a target DNA sites on any DNA molecule in cell (usually proteins)
Cis acting elements (DNA seqeunces)
can only influence expression of adjacent genes on same DNA molecule
Silencers
can prevent promoter use and inhibit gene transcription
enhancers
control the efficiency and rate of transcription from a specific promoter
Cis acting elements
cor prometer promoter proximal elements
Basal factors bind to the
core promoter -TBP - TATA box binding protein TAF - TBP associated factors RNA poly II binds to basal factors
RNA polymerase II
does not bind to every promoter in the genomoe at the same time
Trans acting elements
elements that originate from another DNA strand eg regulatory proteins
cis acting elements (same or same side)
elements that reside on the same DNA strand eg DNA sequences
combinatorial
enhancers are ______ various dna sequences regulate temporal and apatial gene expression these can be mixed and matched
remodeling chromatin
enhancers generally activate transcription by _________________ to expose the promoter or by facilitating the binding of RNA polymerase to the protmer by stabilizing TAFS possible looping of DNA brings transcription factors together
reporter genes
fuse enhancer regulatory elements for a atarget gene to a gene that will produce a detectable protein
neural restrictive silencer element (NRSE)
has been found in several mous genes whose expression is limited to the nervous system: those encoding synapsin I sodium channel type II brain derived neurotrophic factor, Ng-CAM and L1is
basal transcription factors
in response to injuctions from activators these factors position RNA polymerase at the start of transcription and intiate the transcription process
NRSE
is a transcription factor called neural restrictive silencer factor appears to be expressed in every cell that is not a mature neuron
RNA polymerase II
is recruited to and stabilized on the promoters by DNA sequences called enhancers that singal where and when a promoter can be used and how much gene produc to make
transcription
is regulated by the interaction of transcription factors bound to enhancers and the transcription initation complex assembled at the promoter
promoter region
located immediatly upstream of the transcription start site and serves as a binding site for the RNA polymerase II complex
transcription
most gene _______________ requires an enhancer
homomers
multimeric proteins composed of identical subunits
heteromers
multimeric proteins composed of nonidentical subunits
enhancer sequences
on the DNA are the same in every cell type what differs is the combination of transcription factor proteins that the enhancers experience
histone acetylation
opening/ access to dna
transcriptional repressor
prevents transcription of a gene by interfering with RNA polymerase activity on a pormoter
transcriptional repressor
prevents transcription of a gene by interfering with RNA polymerase activity on a promoter
Cis actig regulatory elements
promoter region enhancer region insulators
protein protein interaction domain
promotes dimerization allows it to be modulated by TAFs or other transcription factors
enhancer region
promotes transcription by recruiting histone modifying enzymes that opn the crhomatin structre making the sequence more accessible. sometimes acts in trans
dna binding
recognizes particular DNA sequnece
transcriptional activators
recruits the RNA polymerase complex to the transcription start site by binding to either sequences in the promoter or distant cis acting elements to increase transcription
transcriptional activators
recruits the rna polymerase complex to the transcription start site by binding to either sequences in the promter or distant cis-acting elements to increase transcription
Selective messenger RNA translation
regulates which of the mRNAs in the cytoplasm are translated into proteins
Differential gene transcription
regulates which of the nuclear genes are transcribed into nuclear RNA
Selective nuclear RNA processing
regulates which of the transcribed RNAs (or which parts of such a nuclear RNA) are able to enter into the cytoplasm and become messenger RNAs
Differential protein modification
regulates which proteins are allowed to remain and or function in the cell
insulators
sequences that have the ability to proctect genes from inappropriate singlas emanating from their surrounding genome
negative enhancers
silencers can b viewed as ________ and they can silence gene expression spatially (in particular cell types) or temporally (at particalr times) in the mouse for instance there is a DNA sequence that prvenets a promter activeation in any tissue except neurons
CTCF
some insulator DNA regions have been found to bind to a zinc gfinger trancsription factor called _________________ which functions to alter the three dimensional conformiation of chromatin and thereby separate (or insulate) enhancer elements from the promoter
insulators
the boundaries of gene expression appear to be set by DNA sequences called __________________ limit the range in which an enhancer can activate gene exprsesion they thereby _____________ a promoter from being activated by another gene's enhancers
multiple signals
there can be ________________ for a given gene and each enhancer can be bound by more than one transcription factor (Though not at the same time)
coactivators
these adapter molecules intergrate signals from activators and perhaps repressors
activators
these proteins bind to genes at sites known as enhancers and speed the rate of transcription
repressors
these proteins bind to selected sets of genes at sites known as silencers and thus slow transcription
activators
these regulatory proteins bind to DNA at distant sites known as enhancers. When DNA fold so that the enhancer is brought into proximity with the intiation complex, the activator proteins interact with the complex to increase the rate of transcription
general factors
these transcription factors postion RNA polymerase at the start of a protein coding sequence and then release the polymerase to intiate transcription
coactivators
these transcription factors transmit signals from activator proteins to the general factors
transcription factors
trans acting regulatory elements (proteins) also called activator proteins and suppressor proteins bind to promoter enhancer and silencer DNA in specific ways interact with other proteins to actiavte and increase transcription
cascades
transcription factors operate in ____________ one stimulates the production of several others
bound to an enhancer
transcription factorts are able to enahance or supress the ability of RNA polymerase II to initaate transcrition
TAFs
trasncriptional initation complex stabilized by TAFs - minimal complex of TBP and ATAF fails to activate transcription - addition of the p110 TAF and the p150 TAf allows stabilization of the TBP by both NTF and Sp1
promoter proximal elements
true level of expression - binding site for transcription factors
transcription factors
two structural domains mediate these functions -dna binding domain - transcription activator domain
NRSE
when deleted from particular neural genes these genes are expressed in non neural cells thus neural specific genes are actively repressed in non neural cells
Lac z
widely used reporter system the enzyme hydrolyzes the coloreless substrate x gal to give a blue precpitate