1. Eukaryotic Transcription

2. Eukaryotic Transcriptional
Transcription control is the most important mode of control in eukaryotes.
Three RNA polymerases:
RNA Polymerase I: synthesis of pre-rRNA, which is processed into 28S, 5.8S, and 18S rRNAs
RNA polymerase III: synthesis of tRNA, 18 S rRNA, and small, stable RNAs
RNA polymerase II: synthesis of mRNAs and four small nuclear RNAs that take part in RNA splicing

3. Eukaryotic Transcriptional
The main purpose is the execution of precise developmental decisions (irreversible).
Cis-acting control elements are located many kb away from the start site.
Promoter region is poorly characterized.

4. TATA box About 25-35 bp upstream of the start site +1 5’ TATAAA
mRNA start
-34 to
-26
Well-defined
transcription start

5. Initiator
Instead of a TATA box, some eukaryotic gene contain an alternative promoter element, called an initiator.
Initiator is highly degenerative. +1
5’ Y Y A N T/A Y Y Y
Y = pyrimidine (C or T)
N = any

6. CpG island
Genes coding for intermediary metabolism are transcribed at low rates, and do not contain a TATA box or initiator.
Most genes of this type contain a CG-rich stretch of nt within ~100 bp upstream of the start site region.
A transcription factor called SP1 recognizes these CG-rich region.
Gives multiple alternative mRNA start sites.
mRNA
~100 bp
CpG island
Multiple
5’-start sites

7. Enhancers Located several Kb away from the start site.
Usually ~ bp long, containing multiple 8- to 20-bp control elements.
Cell-type specific
Direction-less (invertible) +1
Enhancer
Enhancer

8. Promoter Proximal Elements
Occur within ~200 bp of the start site.
Contain up to ~20 bp.
Cell-type specific
Invertible +1
Promoter Proximal element

9. A hypothetic mammalian promoter region
Proximal
Element +1
Enhancer
Intron
Enhancer
TATA
Enhancer
-200
-30
-10~-50 Kb
+10~50 Kb
Exon

10. A hypothetic yeast promoter region+1
TATA
Enhancer
~-90

11. mRNA processing
Poly (A) site
Exon
Intron
Termination
Cap
transcription 5’
The 5’-Cap is added to Nascent RNAs (pre-RNAs) shortly after initiation
by RNA polymerase II.
Pre-mRNAs are associated with hnRNP (heterogeneous
ribonucleoprotein particles) proteins containing conserved
RNA-binding domains

12. Pre-mRNAs are cleaved at specific 3’ sites and rapidly polyadenylated
Poly (A) site
Exon
Intron
Termination
Cap 5’
Cap
endonuclease 5’
Poly(A) polymerase 5’ A
Pre-mRNAs are cleaved at specific 3’ sites and rapidly polyadenylated

13. Cleavage and polyadenylation
Poly(A) signal
Poly(A) site 5’
G/U rich
AAUAAA
Pre-mRNA 5’
AAAAAA
AAUAAA

14. Poly (A) site
Exon
Intron
Termination
Cap 5’
endonuclease 5’
Poly(A) polymerase 5’ A
RNA splicing 5’ A