Control of Gene expression Flashcards
Define promoter proximal element and enhancer
- Promoter proximal element: located within 200 bp upstream transcription start. Regulate transcription
- Enhancer: Contain multiple control elements within each which are 8-20 bps. Can be pretty much anywhere in the genome including within an intron
Describe a disease that arises from a mutation in a DNA control element, and how the mutation leads to the disease state (3)
- Thalassemias: mutations in splice sites of beta globin genes. Also occur in promoters, less severe bc under regulates protein rather than turning it off.
- Hemophilia B Leyden: Clotting disorder. Mutation in promoter region of factor 9, only create 1% needed. Also an overlapping promoter region activated by androgen receptor. After puberty make 60% factor 9.
- Fragile X syndrome: Transcription of FMR1 gene decreased due to an increase of CpG islands with replication. This causes methylation of the promoter regions.
Describe the role of transcriptional activators and repressors
Trans regulators of transcription of genes, either increase or decrease transcription
List the two classes of activators and repressors
- Sequence specific DNA binding proteins: recognize and bind to specific region of DNA directly
- Co-factors: recognize proteins that are bound to the DNA.
Describe the domains of a sequence specific DNA binding protein
Have modular discrete domains.
- DNA binding Domain: very specific
- Activation domain: less specific
If one took DNA domain and moved from one gene to another, that new protein would have the same DNA binding specificity or activation as previous protein (depending if transferred DNA binding or activation domain).
List the four major families of sequence specific DNA binding proteins and describe the means for categorizing the proteins into these families
1) Homeodomain: Helix turn helix structure, important in homeobox genes
2) Zinc finger: Bind zinc in structure (majority hormone receptors)
3) Basic leucine zipper: Every 7 AA has a hydrophobic AA. Forms dimerization of TF. Have basic domain that binds to DNA
4) Helix loop helix: Contain loop in middle of DNA binding domain. Also dimerize
Describe a particular human disorder that arises from a mutation in a sequence specific DNA
binding protein, explaining how the mutation leads to the disorder
- Craniosynostosis: Mutation in binding domain of Msx2 (homeodomain TF). Makes it so binds very tightly to DNA, causing hyperactive gene expression. Overdevelopment of bone plates in skull.
- Androgen insensitivity disorder: Mutation in zinc binding protein. Can’t recognize and bind to domain as efficiently, leading to low expression of genes normally activated by androgen receptor. (different severities)
Describe combinatorial control as a mechanism for controlling gene expression
Sequence specific DNA binding proteins that form dimers can bind to specific regions as either homo or heterodimers. This allows a small number of sequence specific DNA binding proteins to bind a large number of binding sites with a large variability of specificity.
Describe how chromatin structure affects transcriptional control and list the two classes of chromatin remodeling factors and briefly describe how they work
Two types of chromatin:
- Heterochromatin: condensed chromatin that doesn’t undergo transcription
- Euchromatin: rarefied chromatin that is available for transcription
Two Classes of chromatin remodeling proteins:
- ATP-dependent histone remodeling proteins: Use the energy from hydrolyzing DNA to break histone DNA interactions and move histone down DNA strand
- Histone modifying enzymes: HAT, HDAC
Define HATs and HDACs and describe how their activity influences transcription
HATs = histone acetyltransferases: add acetyl groups to N-termini of histones, neutralizing positive charge on lysine residues, leading to dissociation of DNA from chromatin, allowing for increased transcription. HATs are recruited to histones by transcription activators (CBP, p300). HDACs = histone deacetylases: decrease transcription by removing acetyl groups from N-termini of histones, making histone residues more positive and more closely binding DNA. HDACs are recruited to histones by transcription repressors.
Give an example of a disease in which histone acetylation is altered, and describe the defect that leads to altered histone acetylation
Rubinstein-Taybi syndrome: caused by haploinsufficiency of CBP, an important co-factor in many transcription factors. CBP has HAT activity, meaning that insufficiency leads to decreased transcription of multiple gene targets
Describe how activators/repressors modulate transcription via their interaction with general transcriptional machinery vs. with chromatin
Activators can activate the transcription of genes in multiple ways:
- If DNA is not condensed, activators can bind directly to DNA sequences and recruit general transcription machinery to transcription site.
- If DNA is condensed, activators will recruit HATs to histones, allowing for rarefaction of DNA, and binding of general transcription machinery.
Repressors can deactivate transcription by opposing activators:
- Repressors directly bind DNA sequences recognized by activators, essentially antagonizing activators and disallowing DNA transcription.
- Repressors can recruit HDACs to histones, causing condensation of DNA and disallow general transcription machinery to access DNA.
Discuss the basic principles of transcriptional regulation by trans factors.
- Transcriptional regulation allows for genes to be transcribed at different levels in different cell types at different times. Thus, it is an important mechanism behind normal physiological processes. Alterations of transcriptional regulation can lead to disease states.
- Transcriptional regulation relies on activator proteins being able to bind to DNA sequences. These sequences can be blocked by either repressor proteins or are tightly bound in chromatin.
Multiple ways specificity of transcriptional regulation achieved
- Modular nature of activator proteins allows for diversity of DNA sequences bound as well as diversity of transcription proteins recruited to transcription site.
- Different types of transcription factors exist that will only bind certain DNA sequences, providing specificity in TF binding.
- Certain transcription factors (e.g. nuclear hormone receptors) will only bind DNA after binding their ligand. Therefore, the ligand-binding nature of the TF lends specificity to the process.
For trans acting factors specifically, What 5 processes work to regulate trans acting factors
1) Conformation of TF binding a ligand (see nuclear hormone receptor explanation above)
2) Control of entrance to nucleus
3) Regulation of amount of TF in cell
4) Regulation of DNA binding
5) Phosphorylation of DNA-binding proteins alter their properties
