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