Eukaryotic Gene Regulation I

Question 1

steps at which gene expression can be regulated

Answer 1

1. transcriptional control
2. RNA processing control
3. RNA transport and localization
4. translational control
5. mRNA degradation control
6. protein activity control

Question 2

transcriptional control

Answer 2

which genes, when and how often a gene is transcribed

Question 3

RNA processing control

Answer 3

control the splicing and processing of RNA transcripts

Question 4

RNA transport and localization

Answer 4

control which mRNAs are transported out of the nucleus and where they go in the cytoplasm

Question 5

translational control

Answer 5

select which mRNAs are translated

Question 6

mRNA degradation control

Answer 6

selectively destabilize certain mRNAs in cytoplasm

Question 7

protein activity control

Answer 7

selectively activate, deactivate, or locate specific protein molecules after they have been made

Question 8

Why are transcriptional controls paramount?

Answer 8

limits the energetic and materials cost of aborting expression at any subsequent stages; fast and cheap

Question 9

gene organization in prokaryotes

Answer 9

operons, poly-cistronic DNA for genes encoding proteins that function together, and no introns

Question 10

gene organization in eukaryotes

Answer 10

no operons, monocistronic, each gene has separate promoter, introns

Question 11

prokaryotic transcription

Answer 11

no histone proteins (no chromatin) so RNA polymerase always has some access to DNA, can have attenuation since transcription and translation are coupled, RNA pol only needs one general TF

Question 12

similarities in eukaryotic and prokaryotic transcriptional mechanisms

Answer 12

requirement for cis acting sequences, requirement for gene regulatory proteins (TFs), weak and reversible protein-protein interactions, DNA looping

Question 13

cis-acting DNA elements

Answer 13

promoter, enhancers, silencers

Question 14

regulatory sequences (enhancers/silencers) can be located _

Answer 14

upstream, downstream, or within gene

Question 15

promoter

Answer 15

where RNA polymerase and other TFs bind to initiate transcription, located upstream of transcription start site

Question 16

enhancers are bound by _

Answer 16

activators

Question 17

silencers are bound by _

Answer 17

repressors

Question 18

enhancers induce _

Answer 18

euchromatin formation

Question 19

trans-acting proteins in eukaryotes

Answer 19

general TFs, site-specific regulatory proteins, remodeling machinery, and mediator

Question 20

general transcription factors

Answer 20

RNA pol II requires 5 general TFs

Question 21

site-specific regulatory proteins

Answer 21

recognize special DNA sequences and bind to DNA –> recruit factors to regulate rate of transcription (co-activators or co-repressors)

Question 22

common structure of site-specific gene regulatory proteins

Answer 22

DNA binding domain and effector domain(s)

Question 23

Foxa1 transcription activation

Answer 23

Foxa1 can bind closed chromatin because it resembles H1 –> will replace H1 and induce formation of euchromatin –> once bound, will recruit chromatin remodeling machinery and histone modification enzymes –> DNA now accessible to additional regulatory proteins (ex. androgen receptor)

Question 24

activators recruit _

Answer 24

histone modification enzymes, chromatin remodeling proteins, co-activators, general TFs, RNA polymerase II

Question 25

Foxa1 is an activator in _

Answer 25

breast cancer cells (ERE) and prostate cancer cells (ARE)

Question 26

hallmark of transcriptional regulation in eukaryotes

Answer 26

combinatorial control with heterodimers –> can now recognize two different DNA sequences and alter DNA binding specificity

Question 27

mediator is a _

Answer 27

co-activator because it does not bind directly to DNA

Question 28

RNA polymerase II requires _

Answer 28

general transcription factors because it is incapable of recognizing promoter sequences by itself

Question 29

general transcription factors require _

Answer 29

open chromatin in order to find the promoter

Question 30

transcriptionally active chromatin is _

Answer 30

sensitive to DNase digestion due to being more open

Question 31

transcriptionally active chromatin differences

Answer 31

deficient in H1 and core histones are modified by acetylation (DNA is still wrapped around nucleosomes)

Question 32

DNase I hypersensitive site

Answer 32

completely nucleosome free

Question 33

DNase I hypersensitive sites are found _

Answer 33

in promoters, enhancers, insulators, silencers, and locus control regions

Question 34

how to alter chromatin structure

Answer 34

remodel nucleosomes (sliding), removing histones (hypersensitive sites), replacing histones, or modifying histones

Question 35

histone chaperones

Answer 35

can remove histones or replace histones with variants

Question 36

steps of gene activation

Answer 36

gene activator protein binds to chromatin –> chromatin remodeling –> covalent histone modification –> additional activator proteins –> assembly of pre-initiation complex –> transcription initiation

Question 37

ways to repress transcription

Answer 37

1. competitive DNA binding
2. masking of an activating surface
3. direct interaction with general TFs
4. recruitment of chromatin remodeling complexes
5. recruitment of histone deacetylases
6. recruitment of methyl transferases