BIO230 Midterm Review
1. Prokaryotic Transcriptional Regulation
2. Eukaryotic Transcriptional Regulation
Co-activator and Co-repressors does not directly bind to DNA
Eukaryotic transcriptional activation
o Eukaryotic Activator Protein: Modular Design (BD & AD)
Can bind directly
alters chromatin structure
Ways to alter chromatic structure
o Nucleosome sliding (ATP-dependent)
o Nucleosome removal (histone chaperones)
o Histone exchange (histone chaperones)
o Histone modifying enzyme
o Attract, Position and modifying:
General Transcription factor
RNA polymerase II
Eukaryotic transcriptional repression
o Interfering with activator function (block BD)
o Interfering with activator function (block AD, interaction with the general
o Altering chromatin structure
Recruitment of chromatin remodeling complexes
Recruitment of histone deacetylases
Recruitment of histone methyl transferase .
Epigenetic inheritance 3. Regulation of the Transcriptome
o RNA processing
RNA capping (additional of a modifies Guanine nucleotide to 5 end)
Cap bound by Cap-bounding complex
RNA splicing (removing introns of the RNA by splicosome)
Site of proper splicing bound by Exon Junction Complex ( serve as
a marker for properly splices RNA)
Different cells can splice an RNA differently: Alternative splicing
o Regulation of alternative splicing
Positive and negative control
Drosophila sex determination
Sex-lethal: splicing repressor
Transformer: splicing activator
Doublesex: regulated sex gene expression
RNA polymerase transfers protein complexes to RNA
o CstF (cleavage stimulation factor)
o CPSF (cleavage and polyadenylation specificity factor )
Poly-A polymerase(does not require template, not encode in the
genome) add 200A nucleotide, bound by Poly-A binding protein
Aid in RNA export and translation
Coupling of transcription and RNA processing
The C-terminal Domain of the RNA polymerase binds RNA
processing proteins and transfer them to RNA at appropriate time
Regulated by different phosphorylation on the polymerase allows
the binding of different complex at different time.
RNA nuclear export
o The cell must have: 3 mature markers added (Cap binding complex, exon junction
complex, poly-A-binding protein) those proteins travel with the mRNA to the
cytosol. And 1 immature marker removed: proteins involved in RNA splicing
(snRNPs) in order to export.
o Improperly processed mRNA will eventually be degraded in the nucleus by
o RNA transport from the nucleus can also be regulated: ex. human HIV
HIV: consist of 2 RNA molecules, and a reverse transcriptase (creates
double stranded DNA from RNA). The DNA is integrated in the host
To hijack the host cell, the HIV used the hosts polymerase to transcribe
RNA, export, and make new viral protein.
Challenge: need to export and overcome the check points. HIV transcribes
into 30 different mRNA, and some of them retain introns.
Have REV (mRNA with no introns, like a regular RNA) REV protein
binds to REV response elements in unsliced RNAs, interacts nuclear
export receptor and help it export, also allow HIV to divide. mRNA quality control
o Eukaryotic initiation factors (eIFs): quality control of RNA, recognizing poly-A
tail and 5 cap.
eIF4E: complete off with CBC and bound to 5 Cap.
eIF4G bound to poly-A bounding protein
o Once the eIFs are bound, it recruit small ribosomal complex which will initiate
translation at first AUG (exception: leaky scanning).
o Nonsense-mediated mRNA decay: function of EJC in translation regulation,
occurs as mRNA coming out the nucleus.
When the mRNA first exiting the nucleus, it is met by a ribosome, EJC are
displaced by the ribosome, the normal stop codon is reached when no EJC
remains (stop codon must occur last). PASS!
If the ribosome reach a premature stop codon (EJCs remains on mRNA
when ribosome reaches stop), Upf will trigger the mRNA degradation.
o Prokaryote mRNA quality control
o Ribosome stalls on broken mRNA and do not release, it recruit a special tmRNA
which carries an alanine to the A site (tRNA), and translated 10 more codons to
the nucleotide. This tag is recognized by proteases that degrade the entire protein.
o In prokaryotes, exonucleases rapidly degrade most mRNAs to adapt to the
changing environment rapidly.
o in eukaryotes, mRNA degradation is regulated by gradual shortening of poly-A-
tail, process carried by deadenylase (act as a timer of mRNA lifetime)
Once poly-A reaches a critical length 1) removal of 5 cap follow by a 5