Regulation of Transcription in Eukaryotes Flashcards
How do Pol I and Pol II regulate transcription
By modulating activity across all their target genes in response to growth and stress levels
How is transcription by Pol II further regulated
On a gene-specific basis
What determines when a gene is expressed
Environmental or developmental signals
What determines where genes are expressed
Tissue-specific needs (e.g. heme biosynthesis in liver, WUSCHEL in the meristem)
What does extent of expression mean
The level of gene activation (e.g. low tyrosinase = red hair, high KNOX1 = lobed leaves)
What binds first to initiate Pol II transcription
TBP (TATA-binding protein), which binds the TATA box (~-35 position)
What does TBP recruit
TFIID, followed by GTFs: TFIIA, TFIIB, TFIIF, TFIIE, TFIIH
How is transcription started by Pol II
GTFs phosphorylate the CTD of Pol II, enabling RNA synthesis
In what direction does Pol II read and write
Reads 3’→5’ on template strand, writes RNA 5’→3’
What strand does the resulting RNA from Pol-II activity resemble
The coding strand
What post-transcriptional modifications occur in the nucleus
Addition of a 5’ cap, poly-A tail, and splicing
Where does translation occur
In the cytoplasm
Is gene regulation mainly transcriptional in eukaryotes
Yes. Activation is key since basal state is off due to chromatin
What % of genes are TFs
5–10% of eukaryotic genomes
What are the key domains of TFs
DNA Binding Domain (DBD)
Activation or repression domain
Often also: dimerisation/signal sensing domains
How are DBDs classified (4)
Basic: bZIP, bHLH
Zinc-coordinating: Zinc fingers
Helix-turn-helix: Homeodomain, forkhead
Minor groove: MADS box, HD-ZIP
Why do many TFs function as dimers
Increases binding specificity
Stabilises DNA interaction
Adds regulation flexibility
What are TADs
Disordered regions that recruit co-activators like Mediator and chromatin modifiers
Are TADs predictable by sequence
No, they lack conserved motifs - must be found empirically
How do repression domains work
Recruit co-repressors
Compete for DNA binding
Form inactive heterodimers
Occlude TADs
How can TF activity be regulated
Phosphorylation
Ligand or protein binding
Nuclear translocation
Protein stability changes
External cues (light, pH, etc.)
How is GAL4 in yeast regulated
GAL80 represses GAL4 → Galactose binds GAL3 → GAL3 binds GAL80 → GAL4 activated
How is NFκB in animals regulated
NFκB held in cytoplasm by IκB → stress activates IκB kinase → NFκB freed → nuclear translocation
What happens in Notch signalling
Notch binds ligand → cleaved → NICD enters nucleus and forms dimer → gene expression activated
How are genes coordinated by TFs
TFs are themselves gene products
A single TF can regulate many genes
TFs can initiate entire developmental programs
