Download Chapter 17 Transcriptional Regulation In Eukaryotes

Chapter 17
Transcriptional Regulation
In Eukaryotes
Introduction
-initiation of transcription is the most pervasively (왕성하게)
regulated step, i.e., before the assembly of RNA Pol II machinery
-Diverse (다양한) regulatory factors are involved
1)activators & repressors: DNA binding proteins and help or
hinder (방해하다) transcription initiation at specific genes
in response to appropriate (적절한) signal
2)promoters: region at the gene where transcriptional machinery
binds; regulatory binding sites  regulatory sequences (i.e.,
complete collection of regulator binding site)
3)enhancers: regulatory sequence function at a distance
4)insulator or boundary element: block activation of promoter
by activators bound at enhancer
-major differences from prokaryotes
1)nucleosome & their modifiers needed
2)more regulators and more extensive regulatory sequences
Introduction
-more extensive (광범위한) signal integration  more signals
are required to switch a given gene on at the right time
and place reflect more complex nature of transcription
regulation in eukaryotes
Figure 1
Activator have separate DNA-binding
and activating functions
-positive controller (e.g., Gal4 from Yeast)
-Gal4 activates GAL1 required for galactose
metabolism (Fig 3 for structure)
-two domains: DNA-binding & activating
Figure 2
X-Gal [5-bromo-4-chloro-3indolyl-β-D-galactopyranoside]
-complementary
Figure 3
experiment with Gal4
and bacterial LexA (bacterial repressor protein)
-experiment shows that activation is not mediated by
DNA binding alone
-two domains are separable, and even by separate
polypeptide
-used to detect protein-protein interaction
Figure 4. Domain swap experiment
Eukaryotic regulators use a range of DNA-binding
domains, but DNA recognition involves the same
principle as found in bacteria
-there is no fundamental difference in the ways of DNA binding proteins
-basic principles of DNA recognition in eukaryotes
1)proteins often bind as dimers (mostly heterodimer)
2)recognize specific DNA sequences using
α-helix inserted into major groove
3)heterodimers extend (확장하다) the range
of DNA-binding specificities
Homeodomain proteins
-a class of helix-turn-helix DNA-binding domain
-consist of three α-helixces: two resemble
helix-turn-helix, one is recognition helix
-found in all eukaryotes
-many of them bind as heterodimers
Figure 5
Eukaryotic regulators use a range of DNA-binding
domains, but DNA recognition involves the same
principle as found in bacteria
Zinc-containing DNA-binding domain
-incorporate zinc atom (s): e.g., zinc
finger protein (e.g., TFIIIA), zinc
cluster domain
-the Zn is coordinated by two His in
α-helix and two Cys in the β sheet
(sometimes by four Cys)  stabilize
its structure
- α-helix is the recognition helix
Figure 6
Eukaryotic regulators use a range of DNA-binding
domains, but DNA recognition involves the same
principle as found in bacteria
Leucine zipper motif
-two large α helices form both dimerization and
DNA-binding domain (pincer-like structure)
-each α helix inserts into major groove
-toward the top, two helices interact to form
a coiled-coil, wherein the two helices
are held together by hydrophobic
interactions between appropriately
spaced Leu
-form hetero- and homodimers
Figure 7
Eukaryotic regulators use a range of DNA-binding
domains, but DNA recognition involves the same
principle as found in bacteria
Helix-loop-helix proteins
-extended α-helical region from each of two
monomers inserts into the major groove
-dimerization surface is formed from two
helical regions 
one part is involved in DNA recognition,
and the other is a shorter α-helix
-two helices are separated by a flexible loop
-often called basic zipper and basic HLH
proteins because the region that
binds DNA contains basic amino
acid residues
Figure 8
Activators recruit the transcriptional machinery
to the gene
-generally activators stimulate transcription of gene by binding
to DNA with one surface and with another interacting with
RNA Pol and recruiting enzyme to that gene
-three ways of action
1)recruit polymerase directly or indirectly
2)recruit nucleosome modifiers
3)recruit other factors needed
after Pol has bound
-other components bind
cooperatively with the
machinery that are recruited
-which gene is activated depends
on which gene has the machinery
recruited to it
Figure 9
Activators also recruit nucleosome modifiers that help the
transcriptional machinery bind at the promoter or initiate
transcription
-two ways of nucleosome remodeling
1)chemical modification by histone acetyltransferase (HAT):
alters interaction between histone tail and nucleosome 
transcriptional machinery will have higher affinity to promoters
2)remodeler: increase mobility of nucleosome  free up
binding sites
for regulators
and machinery
-altogether,
“loosen” chromatin
Figure11
Action at a distance: loops and insulators
-how do enhancers affect (영향을 주다) transcription from
a distance, even tens or hundreds kb apart ?
-in prokaryotes, for example, IHF(integration host factor) 
induce DNA bending
-In Drosophila, Chip help DNA
form multiple mini-loops
-insulator: control action of
activator by inhibiting its
action when placed between
enhancer and promoter,
i.e., block communication
between the two,
also by inhibiting the spread
of chromatin modification 
transcriptional silencing
Figure 12
Appropriate regulation of some groups of genes
requires locus control region
-each gene has its own collection of regulatory sites needed to
switch that gene on at the right time during development and in
proper tissue
-a group of regulatory
elements called
locus control region
(LCR) is involved in
this orchestrated
control of gene
expression
(e.g., human globin
genes etc)
-combinatorial regulation
Figure13