Condensates with mediator and rna pol ii to initiate

condensates with mediator and RNA Pol II to initiate transcription
o Chromosomes enter droplet containing all the elements required for transcription
 Explains how you can have transcriptional bursts on two different chromosomes at
the same time
lect. 23 – RNA Processing I
RNA Pol II CTD
- CTD is full of repeats: YSPTSPS (x52 in humans)
- C-terminal domain = highly disordered
- TFIIH protein kinase is responsible for the phosphorylation of the 2
nd
S (Ser5) in the CTD
repeats
- Another protein kinase is responsible for phosphorylation of 1
st
S (Ser2)
Phosphorylation of the C-terminal domain (CTD) of RNA Pol II large subunit
- Transcriptional initiation:
o Pol II is on the promoter
o DNA helicase opens the transcription complex
o TFIIH phosphorylates the CTD on ser5 so that RNA Pol II can leave the promoter
o RNA Pol II switches to elongation phase and leaves the promoter  begins
elongation and extends the chain
- Pol II stops at the first nucleosome after the promoter:
o Pausing is important as a quality check before starting full elongation
o Need to protect the mRNA product from digestion  protect 5’ end of mRNA by
the addition of a 7-methyl-guanylate cap
1. TFIIH protein kinase phosphorylates ser5 in CTD  RNA Pol II switches to elongation
phase and leaves the promoter
2. RNA Pol II pauses soon after leaving the promoter
3. Ser5-phosphorylation recruits the capping enzyme

4. Capping enzyme caps the 5’ end of the mRNA product with a 7’ methyl-guanylate cap
through a 5’-5’ triphosphate linkage , 1 st and 2 nd base are also methylated
a. Protects the pre-mRNA
b. Facilitates nuclear transport
c. Allows recognition by translation factors
5. P-TEFb protein kinase phosphorylates ser2 in CTD  full elongation and finishing
transcription
a. Recruits in new factors for RNA processing in CTD
b. Releases negative elongators
 2 phosphorylation events occur and are mediated by 2 protein kinases
Proteins bind to RNAs
- Proteins protect or mediate effects on RNA
- Interactions mediated by specific domains
- RNA + Protein = ribonucleoprotein complex (RNP)
o RRM domain: impart the ability to interact with RNAs
o KH domains, RGG repeats  interaction of protein & RNA
Pre-mRNA  mRNA: splicing
- Eukaryotic genes have big introns
- Introns get spliced out of the pre-mRNA transcript and only exons are present in the
mature mRNA
- Introns have evolved regulatory elements  often in DNA that encodes introns
- Exons code for proteins or are in 5’ & 3’ UTRs
Introns
- Discovered due to the difference in mRNA size and gene size & visualized by
hybridization experiments
- Branch-point adenosine is near the pyrimidine-rich region & is 100% conserved
- Intron borders are highly conserved
o 3’ splice site = AG

o 5’ splice site = GU
o Branch point = A
- Conserved splice sites of introns are recognized by small nuclear RNAs (snRNAs) in the
spliceosome
Spliceosome functionality: snRNAs
- Spliceosome is responsible for splicing out introns
o Consists of 5 snRNPs (small nuclear ribonucleoprotein particles)
o snRNPs consist of an snRNA (U1, U2, U3, U4, U5 or U6) + 6-10 proteins
-