Eukaryotic Gene Regulation I Flashcards
steps at which gene expression can be regulated
- transcriptional control
- RNA processing control
- RNA transport and localization
- translational control
- mRNA degradation control
- protein activity control
transcriptional control
which genes, when and how often a gene is transcribed
RNA processing control
control the splicing and processing of RNA transcripts
RNA transport and localization
control which mRNAs are transported out of the nucleus and where they go in the cytoplasm
translational control
select which mRNAs are translated
mRNA degradation control
selectively destabilize certain mRNAs in cytoplasm
protein activity control
selectively activate, deactivate, or locate specific protein molecules after they have been made
Why are transcriptional controls paramount?
limits the energetic and materials cost of aborting expression at any subsequent stages; fast and cheap
gene organization in prokaryotes
operons, poly-cistronic DNA for genes encoding proteins that function together, and no introns
gene organization in eukaryotes
no operons, monocistronic, each gene has separate promoter, introns
prokaryotic transcription
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
similarities in eukaryotic and prokaryotic transcriptional mechanisms
requirement for cis acting sequences, requirement for gene regulatory proteins (TFs), weak and reversible protein-protein interactions, DNA looping
cis-acting DNA elements
promoter, enhancers, silencers
regulatory sequences (enhancers/silencers) can be located _
upstream, downstream, or within gene
promoter
where RNA polymerase and other TFs bind to initiate transcription, located upstream of transcription start site
enhancers are bound by _
activators
silencers are bound by _
repressors
enhancers induce _
euchromatin formation
trans-acting proteins in eukaryotes
general TFs, site-specific regulatory proteins, remodeling machinery, and mediator
general transcription factors
RNA pol II requires 5 general TFs
site-specific regulatory proteins
recognize special DNA sequences and bind to DNA –> recruit factors to regulate rate of transcription (co-activators or co-repressors)
common structure of site-specific gene regulatory proteins
DNA binding domain and effector domain(s)
Foxa1 transcription activation
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)
activators recruit _
histone modification enzymes, chromatin remodeling proteins, co-activators, general TFs, RNA polymerase II
Foxa1 is an activator in _
breast cancer cells (ERE) and prostate cancer cells (ARE)
hallmark of transcriptional regulation in eukaryotes
combinatorial control with heterodimers –> can now recognize two different DNA sequences and alter DNA binding specificity
mediator is a _
co-activator because it does not bind directly to DNA
RNA polymerase II requires _
general transcription factors because it is incapable of recognizing promoter sequences by itself
general transcription factors require _
open chromatin in order to find the promoter
transcriptionally active chromatin is _
sensitive to DNase digestion due to being more open
transcriptionally active chromatin differences
deficient in H1 and core histones are modified by acetylation (DNA is still wrapped around nucleosomes)
DNase I hypersensitive site
completely nucleosome free
DNase I hypersensitive sites are found _
in promoters, enhancers, insulators, silencers, and locus control regions
how to alter chromatin structure
remodel nucleosomes (sliding), removing histones (hypersensitive sites), replacing histones, or modifying histones
histone chaperones
can remove histones or replace histones with variants
steps of gene activation
gene activator protein binds to chromatin –> chromatin remodeling –> covalent histone modification –> additional activator proteins –> assembly of pre-initiation complex –> transcription initiation
ways to repress transcription
- competitive DNA binding
- masking of an activating surface
- direct interaction with general TFs
- recruitment of chromatin remodeling complexes
- recruitment of histone deacetylases
- recruitment of methyl transferases
