Regulation of Gene Expression Flashcards
DNA methylation:
- What is the role of cpG islands?
- hyper/hypomethylation does what?
- DNMT enzymes do what?
- Methylation of DNA occurs on cytosine residues adjacent to guanines (CpG dinucleotides) by DNA methyltransferase (DNMT) enzymes.
- clusters of regulatory CpG dinucleotides within promoter regions are referred to as CpG islands.
- The promoters of active genes are sparsely methylated, whereas silenced genes are associated with hypermethylation.
Is vimentin expressed in fibroblasts and epithelial cells? Why/why not?
Vimentin highly expressed in fibroblasts, but not in epithelial cells due to methylation
Disorders with methyl binding protein MeCP2
autism and Rett syndrome
HATs do?
Histone Acetyl Transferases (HATs) add acetyl groups onto histone tails.
Where are acetyl groups added? What charge does this area usually have? What effect does this have on affinities for DNA? Overall more or less transcription?
Acetyl groups are added to lysine residues on the histone tails that normally have a positive charge.
Adding the acetyl group reduces the attraction of the histone tail for DNA, resulting in in a more open configuration of the chromatin and easier access for transcription factors to bind to the DNA. MORE TRANSCRIPTION
How does acetylation help the transcription factor TFIID?
TFIID has two bromodomains that bind onto acetyl groups
Does methylate activate or silence DNA?
How can it affect acetylation?
What else might histone methylation do? Think transcription process…
- can be associated with gene activation or gene silencing
- Methylation of certain residues may block acetylation
- Histone methylation also plays a role in transcriptional elongation
What does acetylation do for H3K9? What about methylation?
acetylation with H3K9ac opens transcription. If methylated, HP1 is recruited, which causes further methylation down the line.
What do boundary elements do?
control spreading of heterochromatin, can silence things.
What do nucleosome remodeling engines do?
Nucleosome remodeling engines can shift the position of nucleosomes allowing access of transcription factors to gene promoter regions
Important note on promoters:
all promoters are different. They may contain some common elements, but they will be in a unique combination allowing for specific control of how efficiently an individual gene is transcribed at any particular time.
What 3 basic things do activators do?
Bind DNA
Interact with GTF
Recruit coactivators
basics of repressors
Bind DNA
Disrupt action of activators or GTFs
Recruit corepressors
definition of enhancers
- location
- cooperation
a DNA sequence associated with transcriptional activation that is position and orientation independent. Can be far away, upstream or downstream. show synergy
coactivators?
-3 ways they can help
proteins that do not bind DNA directly, but can bind to other proteins that are bound to the DNA.
• Bridging between gene specific activators and GTFs
• Scaffold for the formation of transcriptional complexes
• Histone acetylation (HAT) activity
Passive repression? 3 ways?
“Passive” repression occurs when a repressor interferes with the function of an activator. This can occur by
- preventing the activator from binding to the DNA
- by binding to the activation domain
- by preventing the activator from binding to the general transcriptional machinery.
co-repressors with HDACs?
corepressors can recruit these histone deacetylating transferases, which remove acetyl groups.
Translational control: Ferretin, Transferrin, and transferrin receptor
ferretin binds excess iron, and for storage in cells
transferrin is an iron transport protein in the blood
transferrin receptor binds transferrin and imports iron into cell
In iron starvation, what will happen with ferretin and transferrin receptor?
decrease in ferretin, and increase in transferrin receptor
In iron excess, what will happen to ferretin and transferrin receptor?
increase in ferretin, and decrease in transferrin receptor
When is the siRNA pathway used? What do they do?
The siRNA pathway is used as a defense against viral infection. Endogenous siRNAs silence transposons and maintain heterochromatin.
What processes and what are both siRNA and miRNA loaded in to?
Dicer processes both, and both loaded into RISC
Perfect binding to mRNA target, results in mRNA cleavage explains which one? siRNA or microRNA?
siRNA
Imperfectly binds to mRNA target and results in translational repression/mRNA degredation? siRNA or microRNA?
microRNA
siRNA and microRNA are generally what? what purpose?
non-coding RNA that negatively regulate gene expression
If iron is low, what does IRE-BP do?
Binds to IRE sequence on 5’UTR of ferretin mRNA, BLOCKING RIBOSOME from scanning, decreasing ferretin levels. IRE-BP binds to IRE sequence located on 3’UTR of transferrin receptor and acts as a shield from endonuclease activity. So, you get more transferrin receptor. Iron low= LESS FERRETIN AND MORE TRANSFERRIN RECEPTOR
do coactivators bind transcription factors or DNA?
Transcription factors, NOT DNA.
methylation in the open reading frame could still be an activated gene when/
If the promoter is acetylated.
methylation of H3K4 does what?
enhances transcription
