Gene repression and activation Flashcards
deletion analysis for identifying activators and repressors
- identifies activators and repressors by getting rid of different parts of the DNA and analyzing if there is an increase or decrease in activity
- increase = repressor was deleted
- decrease = activator was deleted
What is a motif
- a frequently found (conserved) sequence in proteins with a similar function
common motifs: zinc fingers and leu zipper - interactions of 2 separate peptides form a functional enhancer
Combinatorial binding of DNA-binding proteins
- if you have 3 monomers that can form dimers you have 6 combinations of these proteins
- recognize 6 binding sites
- adding an inhibitor for one of the three proteins increases the possibility of combinations
what is the function of lipid hormone receptors in gene expression
- they act as transcription activators
- upon binding to the hormone-receptor complex it moves to the nucleus - now a TF and binds to HRE in target genes to regulate expression
- share homology at structural level with activators
TF activities regulated by cell-surface receptors and transduction cascades
- lipid insoluble peptide hormone reaches the membrane receptor and initiates a signal transduction
- eventually a TF is activated by phosphorylation
what is the role of the ligand binding domain in the glucocorticoid receptor/transcription activator
- when the ligand binding domain is intact, b-galactosidase goes to the nucleus
- the ligand binding domain is needed to activate all the machinery required to move into the nucleus
Regulation of entry and leaving of RNA pol at pause sites
- nucleosomes block pol II from starting to bind promoters
- activators associate with DNA and modify nucleosomes
- Pol II is loaded via GTFs
- NELF and DSIF cause the pause
- PTEFb comes along and NELF comes off via phosphorylation
- DSIF stays on but can’t function alone
how do activators/repressors affect gene expression with their co-activators/co-repressors
- they modulate chromatin structure or interact with GTFs
- activator/co-activators stimulate the assembly of preinitiation complexes and move nucleosomes away from promoters
- repressors work through the build up of chromatin
what is the histone code
a variety of post-translational modifications on histone tails (N-terminus). 4 types…
1. phosphorylation
2. methylation
3. acetylation
4. ubiquitination
what is position-dependent repression of genes
- silencers are large heterochromatin blocks that repress genes close to or within them
- independent of various promoters
position-dependent repression: mating type loci in yeast
- HML and HMR are genes that are constantly repressed by 3 proteins
1. Rap1 - binds next to the repressed loci and recruits Sir
2. Sir - proteins that spread over the locus
3. Sir2 - a histone deacetylase: removes acetyl groups on the histones at HML and HMR - the deacetylted histones bind tighter to DNA, form heterochromatin and prevent association of activators to promoters
Positional repression at telomeres
- the subtelomeric region is the area between the telomere and the silencer
- Rap1 and Sir proteins bind to telomeres
- many telomeres are covered with condensed hypoacetylated nucleosomes
Hypoacetylation vs hyperacetylation of nucleosomes
Hypo-acetylation: maintains repression at telomeres
- encourages tight interactions between DNA and histones, prevents TATA from being exposed
Hyper-acetylation: abolishes repression at telomeres
- relaxes interactions with surrounding domain, exposes TATA
How is repression maintained in mating type loci
- Rap1 is the repressor , the telomere is the silencer
- Rap1 binds to the telomere
- Sir proteins are co-repressors (recruited by Rap1)
- Sir2 is a histone-deacetylase (actual enzyme)
- The SIr2/3/4 complex binds to Rap1 and spreads away from the telomere
What is promotor-dependent repression and activation
- position independent
- works via histone acetylation/deacetylation
- repressors and activators bind and recruit co-repressors and co-activators which do not spread
