Lecture 3 gene expression

two types of eukaryotic transcription factors

general and gene specific

how many base pairs upstream from the promoter is the TATA box found in eukaryotes?

-30bp

how many base pairs upstream from the promoter are the Cat box and GC box found in eukaryotic cells?

-75bp

what kind of RNA do Pol I, Pol II and Pol III produce in eukaryotic cells? (list with numbers)

1. rRNA

2. mRNA

3. tRNA and 5S rRNA (small RNAs)

what is the most important subunit of the TFIID transcription factor?

TATA box binding protein (TBP)

the DNA binding domain of TBP consists of a β-sheet which forms a structure of what shape?

saddle shaped

binding of the TBD subunit of TFIID induces dramatic … in the region of DNA it binds and causesa large … in the DNA helix 

distortion, kink

the kink caused by the TBP … the DNA and allows access of the RNA Pol II

unwinds

order in which the general TFs bind to the promoter in eukaryotic cells

DABF, Pol II, EHJ

upon assembly of the RNA Pol II preinitiation complex, the largest subunit of RNA Pol II becomes heavily …

phosphorylated

which TF (a kinase) phosphorylates RNA Pol II

TFIIH

phosphorylation of the largest subunit of RNA Pol II causes the enzyme to … from the TFs

uncouple

examples of gene specific TFs

myc, max, fos, jun, nfkb and nfat

the DNA binding domains of gene specific TFs in eukaryotes interact with which groove of DNA?

major

what are the four common structural features of the DNA binding domains in gene specific TFs

1. the zinc finger motif

2. the helix loop helix (HLH) motif

3. the leucine zipper motif

4. the high mobility group (HMG) motif

all the motifs of gene specific TFs present a solution to the problem of allowing … of specific DNA sequences by the TFs

recognition

what kind of interactions occur between the motif (often an alpha helix segment) of a gene specific TF and the major groove of DNA?

noncovalent

what is the name of the proteins associated with gene specific TFs in chromatin looping?

mediators

where are mediators (mediator proteins) bound to?

activators (gene specific TFs)

where do activator proteins usually bind to?

enhancers

which TFs are usually directly involved in and essential for the formation of chromatin loops?

gene specific TFs

which TFs are usually indirectly involved in chromatin loop formation, but are essential in the assembly of the pre-initiation complex?

general TFs

is the TATA box located “in” the promoter?

yes

which protein enables DNA to bend to bring regulatory regions closer together?

DNA bending protein

3 possible ways of modifying histones

1. methylation

2. phosphorylation

3. acetylation

if a histone’s positive charge is neutralized does this increase or decrease its affinity for DNA?

decrease

does lowering of a histone’s affinity for DNA make that region more or less accessible?

more

which enzymes acetylate the c-terminal tails of histones?

histone acetyltransferases (HATs)

which enzyme deacetylate the c-terminal tails of histones?

histone deacetylases (HDACs)

does acetylation lead to more open or closed chromatin state?

open chromatin state

are hyperacetylated genes more active or inactive?

active

some histone modifications can also recruit proteins (such as Polycomb proteins) which stay associated with the DNA in that region and permanently repress expression of that gene. this can even be inherited by a daughter cell. what is this type of gene expression control called?

epigenetic control

what is the name of the DNA binding proteins which regulate gene expression as well as accessibility of the stretch of DNA harboring a specific gene?

transcriptional regulators

which coplexes can move nucleosomes (histone octamers) off promoters?

swi/snf complexes

swi/snf complexes facilitate the … (3 words)

initiation of transcription

full name of the SWI/SNF complex

switch/sniff complex

do swi/snf complexes require ATP?

yes

the SWI/SNF complex is thought to bulldoze … off …

histones, promoters

what are CG rich regions in DNA called?

CpG islands

what is formed when cytosine residues are methylated?

5 methylcytosine

almost all of methylated cytosine residues are found in … within … sequences

CG dinucleotides, symmetrical

CpG islands are often located close to … regions

gene regulatory

does methylation enhance or silence gene expression?

silence

enzymes which remove methyl groups from DNA

demethylases

during the first few division of the zygote is the DNA methylated or demethylated compared to the inherited DNA?

demethylated

when the embryo is implanting is DNA de novo methylated or demethylated?

methylated

which enzyme ensures that the CG sequences which are methylated are maintained that way?

maintenance methylase

what happens to mice during gestation which have been engineered to lack the enzyme responsible for de novo methylation during embryo implantation?

they die

methylation is unlikely to be the initial event that inactivates genes, rather it may serve to maintain a gene in an inactive state. this is important please copy

methylation is unlikely to be the initial event that inactivates genes, rather it may serve to maintain a gene in an inactive state

two ways in which methylation inhibits transcription

1. by interfering with the recognition of DNA binding sites by TFs

2. by attracting transcriptional repressors

which enzyme adds the poly A tail to the 3’ end of pre-mRNA?

poly A polymerase

function of the H1 proteins?

help with chromatin condensation and stability

consensus of the euk -30bp TATA box

TATAAAA

the A’s in the euk TATA box consensus are often replaced by T’s to form what consensus

TATATAT

what is the consensus of the -75bp Cat box in euk cells?

CCAAT

what is the consensus of the -75bp GC box in euk cells?

GGGCGG

as a general rule, promoters recognised by the RNAP II typically contain the … box and at least one …

TATA, other upstream element

name for the huge number of possible patterns of histone modifications

histone code