Chapter 7
Regulation of Eukaryotic Gene Expression
7.1 Multilevel Eukaryotic Gene Regulation
1. The types of regulation in eukaryotes
2. Gene structure of eukaryotes
3. Features of Eukaryotic Genomes
4. Multi-level of gene expression and regulation
7.2
Gene Regulation at DNA Level
Chromatin Remodeling
1. Changes of DNA Topo structure
Formation of ssDNA
DNase I hypersensitive site
2. DNA Methylation
DNA Methylation
 CpG islands
----- are genomic regions that contain a high
frequency of CG dinucleotides.
----- CpG islands particularly occur at or near
the transcription start site of housekeeping genes.
TF
RNA pol
Active
transcription
Unmethylated CpG island
TF
CH3
CH3
RNA pol
CH3
Methylated CpG island
Repressed
transcription
 Housekeeping gene -A gene involved in basic
functions is required for the sustenance of the cell.
Housekeeping genes are constitutively expressed
 Luxury gene - are those coding for specialized
functions synthesized (usually) in large amounts in
particular cell types.
3. Histone modification
 methylation
 acetylation
TF
4. Changes of nucleosome
High Mobility Group (HMG) Protein

non-histone chromatin proteins

high mobility in PAGE

soluble in 2-5% TCA

small < 30 kDa

high content of charged amino acids: Asp, Glu
5. Other gene regulation at DNA Level
(1) Gene Deletion
(2) Gene Duplication
(3) DNA Rearrangement
(4) Gene Amplification
(5) Chemical Activator
(6) Environmental Activator
7.3 Transcriptional Regulation
1. Cis-acting element
(1) What is cis-acting element?
 Concept
Cis-acting elements - DNA sequences close
to a gene that are required for gene expression
 Features of cis-acting elements
(1)
Promoter
 Core promoter
 in eukaryote: TATA-box, Initiator (Inr)
 in prokaryote: -10 region, Inr
 Proximal elements of promoter
 in prokaryote: -35 region
 in eukaryote: CAAT-box, GC-box
UPE: upstream promoter element
UAS: upstream activating sequence
(2) Terminator
A DNA sequence just downstream of the coding
segment of a gene, which is recognized by RNA
polymerase as a signal to stop transcription.
(3) Enhancer
A regulatory DNA sequence that greatly
enhances the transcription of a gene.
(4) Silencer
A DNA sequence that helps to reduce
or shut off the expression of a nearby gene.
Animation
(5) Insulators
No transcription
2. What is trans-acting factor?
 Concept
trans-acting factors - usually they are
proteins, that bind to the cis-acting elements to
control gene expression.
These trans-acting factors can control gene
expression in several ways:
 may be expressed in a specific tissue
 may be expressed at specific time in development
 may be required for protein modification
 may be activated by ligand binding
(1) RNA polymerase
 prokaryotic RNA Pol
 eukaryotic RNA Pol
(2) Transcription factors
 Basal/general TFs
 Specific TFs
(3) Domains of trans-acting factors
 DNA binding domain DBD
DNA结合结构域
 transcription activating domain
转录活化结构域
a. HTH (helix-turn-helix)
α-helix (N-terminus)----specific
α-helix (C-terminus)----non-specific
b. homeodomain --60 aa long DNA binding protein motif
α-helix 1
α-helix 2
α-helix 3 ---- DNA major groove
helix turn helix motif: binds to DNA
c. Leu zipper
d. Zinc finger
GAL4
SP1
e. Helix-loop-helix
f. Bromodomain
g. Chromodomain
Ribbon diagram of the GCN5 bromodomain
from Saccharomyces cerevisiae
Transcription Activation Domains
 Acidic domains
 Glutamine-rich domains
 Proline-rich domains
7.4
Post-Transcriptional Regulation
1. Gene Regulation of mRNA Processing
exon shuffling
alternative gene splicing
2. Gene Regulation of mRNA Editing
3. mRNA Longevity
4. mRNA Transport Control
5. RNA Interference (RNAi)
 miRNA
 siRNA
The left petunia is wild-type; the right petunias contain
transgenes that induce suppression of both transgene and
endogenous gene expression, giving rise to the unpigmented
white areas of the flower.
RNA沉默(RNA silencing)是普遍存在于植物、动
物(RNAi)和真菌(quelling)等真核生物细胞中的一种抵
抗外源遗传因子(病毒、转座子或转基因)及调控基因
表达的防御机制，可特异而高效的降解靶mRNA，以
保持生物体自身基因组的完整和稳定。
7.5 Translational and Post-translational Regulation
1. Translation Control
Blocking mRNA Attachment to Ribosomes
2. Regulation of Protein Processing
Protein Modification
 Amino acid residus phosphorylated
 Ser/Thr type
 Tyr type
 Catalysis Features of Actions
 Reversible
 Integrated signals from different pathways effectively
 The same kind kinase or phosphatase is multible-substrates.
 modified different amino acids, different influences
3. Regulation of Protein Stability
7.6
Gene Regulation & Cancer
1. Features of Cancer Cells
2. Causes of Cancer:
 Viruses
 Tobacco smoke
 Food
 Radiation
 Chemicals
 Pollution
3. Proto-oncogene & Oncogene
 Proto-oncogene - is a normal gene that can
become an oncogene due to mutations or
increased expression.
 Oncogene - is a protein encoding gene, which when deregulated - participates in the onset and
development of cancer.
 Tumour suppressor gene - or antioncogene is a
gene that protects a cell from being cancer.
①
②
⑤
④
⑥
③
4. Proto-oncogene activation
5. p53 and cancer
 It can activate DNA repair proteins when DNA has
sustained damage.
 It can also hold the cell cycle at the G1/S regulation point
on DNA damage recognition
 It can initiate apoptosis, the programmed cell death, if
the DNA damage proves to be irreparable.
Summary
1. Genomic structure of eukaryotes
2. Regulation levels of eukaryotic gene expression.
3. Regulation at DNA level
4. Regulation at transcritional level
5. Transcriptional regulation
6. The mechanism of RNAi
7. Translational and post-translational regulation:
8. Protein phosphorylation and its mechanism