gene regulation in eukaryotes Flashcards
Levels of genetic control: in decreasing efficiency hierarchy
Transcriptional control
RNA processing
mRNA degradation control
Translational control
Architecture of a typical eukaryotic gene
regulatory region: enhancers, prmotors (simple switches and complex microprocessors) transcribed region (corresponds to pre mRNA) coding region (translated) with in trans region
How does the TATA box function
TATA box functions as a premotor
Simplest DNA binding motif : helix turn helix motif
Two helicies held at a fixed angle
Carboxy terminal helix = recognition helix- fits into major groove
Aminoacid side chain recognises specific DNA binding sequence
These sorts of DNA binding proteins that pertain to transcription are called transcription factors
how do we measure DNA protein interactions?
Radio label DNA fragments
Incubate one set with cell extract. DNA binding proteins bind to regions. Then compare the mobility of the two samples as bound protein decreases DNA mobility.
what are the general properties of enhancers?
operate at distance from promoters
Can also be found downstream of genes
Can be in either orientation
DNA loops enable proteins bound to enhancer to directly effect transcription factors or RNA pol
DNA thus acts as a tether between the two proteins
what two ways do activation domains work?
Accelerate assembly of basal machinery for transcription
Enhance stability or activity of basal machinery
Acidic glutamate and proline rich domains
comment on Gene repressor proteins in eukaryotes
In eucaryotes not so well understood don’t generally act directly on DNA but suppress transcription.
give an example of and explain the utility of Promoter proximal pausing in gene regulation
Occurs in rapidly induced genes like heat shock genes:
Heat shock induces activation of the heat-shock transcription factor (HSTF) which binds to the promoter proximal region of hsb70
This then stimulates the paused polymerase to resume action and continue chain elongation
This mechanism enables for rapid response genes, no time is required to allow the assembly of transcription-initiation complexes
RNA synthesis is already primed
where does capping , cleavage and polyadenylation and splicing all happen
in the nucleus
how does regulation of mRNA stability occur?
Half life of mRNA vary from m-h
Many short lived mRNA contain sequence AUUUA in their 3’ UTR
This is thought to regulate removal of poly-A tail
what carries out splicing?
Carried out by large ribonucleotide complexes, the spliceosome
Their are optional intron exon areas that can be variably spliced
Nuclear packaging is very dense in eukaryotes and poorly modeled
Levels of compaction:
(1) nucleosomes (DNA wrapped around histone proteins)
(2) Further nucleosome packing
(3) higher order packing in heterochromatin
properties of inactive chromatin:
dephosphorylation of H1 histone
- deacetylation of core histones
- diminishment of histone variants
what is x chromosome inactivation?
One x chromosome is inactivated to prevent over expression of x
Is switched off in early embryos~ 1000 cells
As this is the case it means that half of the x chromosomes are suppressed differentially This prevents genetic disorders
This is part of how you get co-expression of genes
This process is regulated by one of the chromosomes producing a gene called XIST which functions as RNA coating the chromosome its produced by preventing transcription.
