1. Controlling Chromatin Structure
Why? It is related to gene expression and regulation

2. Model ? Transcription in vitro in vivo DNA TFs RNA polymerase
nucleosomes
Model ?
1-Equilibrium model: prokaryotes ( limited energy)
(evidence for semi-conservative. replication of the DNA molecule)
2-Discontinuous change-of-state: eukaryotes ( non-limited energy)
Dynamic, mutations and Cancer

3. DNA binding depends on protein concentration
Protein factors
What is (are) the limiting factor(s)?
Example: Transcription in bacteria
Equilibrium Vs
Non-Equilibrium
Stability Vs
Non-Stability

5. Chromatin can have alternative states
Inactive--DNA/histones
Active--DNA/RNApolymerase/TFs
Figure 30.2
RNA polymarase/TFs
NO TRANSCRIPTION
HISTONES
TRANSCRIPTION
“The addition of either TFs or nucleosomes may form stable structures
that can not be changed by modifying the equilibrium with free
components”
How is the chromatin structure regulated?

6. Chromatin Can Have Alternative States
Figure 30.2
Chromatin structure:
is stable
cannot be changed by altering the equilibrium of transcription factors and histones

7. Chromatin Remodeling Is an Active Process
Remodeling complex
(protein)
There are several chromatin remodeling complexes that use energy provided by hydrolysis of ATP (ENERGY)
Release of nucleosomes
Binding of TFs and RNA poly
Figure 30.3

8. Chromatin remodeling is an active process
Expose DNA Nucleosome
Sequence Spacing-out Release

9. Nucleosome Organization May Be Changed at the Promoter
Activator
Remodeling complexes are recruited to promoters by sequence-specific activators.
The factor may be released…. once the remodeling complex has bound.
Remodeling complexes are proteins that do not recognize specific DNA sequence.
All are ATPases complexes
Mechanisms--not well know--
--the ATP hydrolysis is used
to twist the DNA by creating a
mechanical forces--
Figure 30.6

10. The SWI/SNF, RSC, and NURF complexes all:
are very large
they share some common subunits
A remodeling complex does not itself have specificity for any particular target site.
It must be recruited by a component of the transcription apparatus.
CTD tail of the
RNA pol II
-coding regions-
What about non-
coding regions?
Figure 30.5

11. Mol Cell (2):

12. Histone modification is a key event
Silencing--gene -local effect
--heterochromatin-regional effect
How? Binding of additional proteins
Modifications--methylation (Met)
--acetylation (Ace)
--phosphorylation (Pho)
Effect? Reduce positive charge
Consequence? Ace--Active
Met-Inactive

13. Histone Modification Is a Key Event
Histones are modified by:
methylation
acetylation
phosphorylation
Figure 30.8

14. Histone Acetylation Occurs in Two Flavors
Histone acetylation occurs transiently at replication and during gene activation.
During DNA replication
Before
Histones are Acetylated before the
incorporation into the nucleosome.
Function--requires for the assembly/
structure of new nucleosomes
--recognizes new factors
(Enzymes: Histone Acetyltransferases-HAT)
Histones are Deacetylated after the incorporation into the nucleosome.
Function-- required for gene activaton (Enzymes: Histone Deacetylases-HDAC)
Figure 30.12

15. Histone acetylation is associated with activation of gene expression.
During gene activation
Histones are Acetylated after the
incorporation into the nucleosome.
Function--recognizes new factors
(Enzymes: Histone Acetyltransferases-HAT)
Figure 30.13

16. Acetylases Are Associated with Activators
Deacetylated chromatin may have a more condensed structure.
Transcription activators are associated with histone acetylase activities in large complexes.
Figure 30.14

17. Histone acetylases vary in their target specificity.
Acetylation could affect transcription in a quantitative or qualitative way.
HAT- Acetylase complex
P300 targets H4
PCAF targets H3

18. Deacetylases Are Associated with Repressors
Deacetylation is associated with repression of gene activity.
Deacetylases are present in complexes with repressor activity.
DHAC- Deacetylase complex
Rpd3 targets H4/H3
Figure 30.16

19. Constitutive
Facultative
Eurochromatin vs Heterochromatin

20. Methylation of Histones and DNA Is Connected
Methylation of both DNA and histones is a feature of inactive chromatin.
The two types of methylation event may be connected.
Histone methylation is associated with gene inactivation
-H3 Lys 9, Lys 4- and condensation of chromatin-
H4 Arg 3-
DNA methylation is associated with gene repression
CpG regions

21. Chromatin States Are Interconverted by Modification
Acetylation of histones is associated with gene activation.
Methylation of DNA and of histones is associated with heterochromatin.
Figure 30.17

22. Promoter Activation Involves an Ordered Series of Events
Key element
The remodeling complex may recruit the acetylating complex.
Acetylation of histones may be the event that maintains the complex in the activated state.
Promoter activation involves an ordered series of events
Activation
Figure 30.18

23. Glucose Regulation of β-pancreatic Cells
(Blood)
Sugars
Blood

25. Histone Phosphorylation Affects Chromatin Structure
At least two histones are targets for phosphorylation, possibly with opposing effects.
What kind of phosphorylation?
Serine Threonine Tyrosine
H1 Ser phosphorylation during mitosis by cd2 kinase
(control chromatin condensation)

26. Some Common Motifs Are Found in Proteins That Modify Chromatin
The chromo domain is found in several chromatin proteins that have either activating or repressing effects on gene expression (methylated sites).
The SET domain is part of the catalytic site of protein methyltransferases.
The bromo domain:
is found in a variety of proteins that interact with chromatin
is used to recognize acetylated sites on histones.

27. What is mechanism that control chromatin structure?
Genes Su(var) and E(var) (60 genes)
Su (suppressors) and E (enhancers) factors are enzymes that respond to environmental and metabolic signals.
HP1(Heterochromatin protein 1)
--structure:chromo domain
--bind metylated H3 lys position 9
SUV39H1 -SET domain- methyltransferase
Variegation
(Ace)