Gene Expression II&III Flashcards
How does chromatin structure affect transcriptional control?
Can affect the ability of transcription factors to bind DNA. (Remember that chromatin consists of DNA, histone proteins, RNA)
List the classes of chromatin remodeling factors and describe how they work
- DNA-dependent ATPases (SWI/SNF)- disrupt histone octamers and DNA.
- HATs and HDACs - Factors that reversibly modify histones through acetylation and deacetylation and acts as a code to recruit specific transcription factors.
Define HATs and describe how their activity influences transcription.
HATS are co-activators.
They acetylate N-termini of histones (lysine)
Trans-acting factors can switch from repressors to activators by recruiting HATs
Define HDACs and describe how their activity influences transcription.
HDACs are co-repressors.
They remove acetyl groups from histones.
Trans-acting factors can switch to repressors by recruiting HDACs
What are 2 diseases associated with histone acetylation (HAT’s and HDAC’s)
- Rubinstein-Taybi Syndrome
2. Leukemia
Rubinstein-Taybi Syndrome
Results from mutations in one copy of the CREB binding protein (CBP) gene. CBP is an essential transcriptional coactivator for different transcription factors and is a histone acetyltransferase. It is normally recruited to many genes to activate transcription, and thus haploinsufficiency can result in widespread transcriptional changes.
It is a rare genetic multisystem disorder (affects 1/125,000). Characterized by growth retardation, mental retardation, craniofacial dysmorphism, abnormally broad thumbs and great toes.
Leukemia
Generally the result of chromosomal translocations leading to gain of function fusion proteins- some of which involve fusions of transcriptional regulators with HATs or HDACs, altering the activity of the regulators .
- A hematopoietic malignancy.
Describe how activators/repressors modulate transcription via their interaction with general transcriptional machinery vs. with chromatin
- Interact with general transcription factors/RNA POLYMERASE II associated proteins to influence initiation of elongation of the primary transcript
- Interact with chromatin via HAT and HDAC recruitment to regulate accessibility of DNA to Pol II transcriptional apparatus
Discuss the basic principles of transcriptional regulation including how specificity is achieved and how protein-DNA interactions contribute to transcriptional control.
- Specificity depends on binding of transcriptional activators/repressors to DNA control elements.
- Regulation depends on DNA-protein and protein-protein interactions
- The interactions affect the conformation of DNA, modification of chromatin structure, formation of the transcription initiation complex.
- Control is combinatorial, allows for several thousand transcriptional activators/repressors to differentially alter the expression of genes in different cell types and in response to different stimuli.
Describe the mechanisms on how sequence specific DNA binding proteins are regulated
- Controlling protein conformation by binding a ligand
- Regulating entry into nucleus
- Regulating the amt of the transcription factor in the cell
- Regulating binding to DNA
- Phosphorylation of the DNA-binding protein can alter properties including protein degradation, recruitment of co-activators, and DNA binding
Describe how the activity of nuclear hormone receptors is controlled
The nuclear receptor family of Zinc finger transcription factors work by binding to steroid hormones. This binding can affect dimerization of receptor, recruitment of coactivators/repressors, and translocation into the nucleus.
How does tamoxifen act in breast cancer therapy.
It antagonizes estrogen by binding to ER and
preventing recruitment of HAT co-factors
Give an example of a sequence specific DNA binding protein regulated by nuclear entry and describe the mechanism by which its entry is controlled
NF-kB- NFkB is normally held in the cytoplasm by its binding to the inhibitor of NFB (IB), which masks the nuclear localization signal of NFB. In response to a variety of stimuli, IB can be phosphorylated, targeting it for degradation. NFB is then released and moves to the nucleus, where it turns on a number of target genes, including those involved in inflammation (see slide). the anti-inflammatory, aspirin, works in part by inhibiting the phosphorylation, and thus degradation of IkB. This prevents the translocation of NFB to the nucleus, thus inhibiting the transcription of genes involved in the inflammatory response.
Using Beta Catenin, describe how the amount of an activator/repressor can be regulated within the cell.
Beta catenin
• Absence of Wnt signaling: the cytoplasmic pool of beta-catenin is targeted for degradation through the ubiquitin-proteasome pathway via phosphorylation by glycogen synthase 3 (GSK3) in a complex with Axin and APC
• Presence of Wnt signaling: Axin-APC-GSK3 complex is destabilized
o Prevents phosphorylation of beta-catenin
o leads to Increase in the cytoplasmic pool of the beta-catenin protein
o This increase allows some cytoplasmic beta-catenin to move to the nucleus
o Interacts with the TCF family of transcription factors and promotes the expression of Wnt responsive genes
*Note importance of mutations in APC for colon cancer.
Describe a mechanism by which the DNA binding activity of a sequence specific DNA binding protein can be inhibited.
Id proteins- The Id family members negatively regulate DNA binding by heterodimerizing with other (helix-loop-helix) HLH proteins through their HLH domains, but preventing DNA binding due to their lack of a basic domain.
