Things happened during gene activation

Inactive chromatin

DNA binding proteins

Repressors Activators
Corepressors Coactivators
Scaffold Scaffold
Histone deacetylases Histone modifiers ex: acetyltransferases (HAT)
ATP-CRC ATP-dependent chromatin remodeling complexes
DNA methylases DNA demethylases?

DNase I hypersensitive sites

DNA demethylation
Histone hyperacetylation,
Active chromatin methylation…
Reduction of H1 content
Helix-turn-helix motif

Alberts et al. Molecular Biology of the Cell

Alberts et al. Molecular Biology of the Cell
 Figure 9-13, Homeodomain

60 amino acids
Identified from
Drosophila
(genes determine
the identity of
body structure)
Present in all
eukaryotes
Important in
development

Alberts et al. Molecular Biology of the Cell

Fig 9-14, Cys2/His2 Zinc finger

Alberts et al. Molecular Biology of the Cell

Fig 9-15, Cys2/His2 zinc finger binds DNA

TFIIIA (9
fingers)
SP1 (3)
/GC box
GATA
Gal4

Other than
DNA
binding

Alberts et al. Molecular Biology of the Cell

Genes & Signal, Ptashne and Gann, 2001, Cold
Spring Harbor Lab Press
Genes & Signal, Ptashne and Gann, 2001, Cold
Spring Harbor Lab Press
Cys2/Cys2 zinc
finger,
Steroid
receptors

3. Nonrepetitive
fingers
4. Ex:
glucocorticoid
receptor (2
fingers),
estrogen
receptor (2
fingers)
Gene VII
Gene VII
Gene VII
Group I
Ubiquiitous
E12/E47
Group II
Tissue-specific
MyoD
Myogenin
Myf-5
In myogenesis
Myc

Alberts et al. Molecular Biology of the Cell

bZiP protein

CREB/ATF
AP1-Fos/Jun

Alberts et al. Molecular Biology of the Cell

Fig 9-19,Heterodimerization of leucine zipper proteins

Alberts et al. Molecular Biology of the Cell

Alberts et al. Molecular
Biology of the Cell
Alberts et al. Molecular Biology of the Cell
Alberts et al. Molecular Biology of the Cell
Nature (2001) 409, 832
 Gene-specific transcriptional activation in eukaryotic chromatin

Inactive chromatin
Exchangeable subunits in
coactivator/corepressor complexes
Factor modifications: SUMO …
Repressors Activators (Tissue, Cell, developmental stage-specific)
Corepressors Coactivators
Scaffold Scaffold As a signal or code
Histone deacetylases Histone modifiers ex: acetyltransferases (HAT)
ATP-CRC ATP-dependent chromatin remodeling complexes
DNA methylases DNA demethylases?

DNase I hypersensitive sites

Change DNA demethylation
in Histone hyperacetylation, Reduction of
histone – TBP/RNAPII H1 content
DNA (Ubiquitous)
interacti
Incorporation of histone variants
on Active chromatin (H2A.Z and H3.3) and/or non-histone
chromosomal proteins (HMG proteins)
Malik and Roeder (2000) 25, 2
Malik and Roeder (2000) 25, 2
 Red: PC2 core
complex

Blue: loosely
associated

Yellow: not with PC2

but in intact
mediator

TIBS (2005) 30, 256

TIBS (2005) 30, 256
 Robert Tjian
錢澤南
University of California, Berkeley

Nature Reviews Mol Cell Biol (2004) 5, 403

 1.2 MDa
2 MDa

Human mediators

ature Reviews Mol Cell Biol (2004) 5, 403

Repressed C/EBPβ: ARC-L
Activated C/EBPβ: CRSP
 1.2 MDa
2 MDa

*Phosphorylate
activators and
target them
for
degradation
*only small complex
activates transcription
in vitro using chromatin
templates *ARC-L only
subunits are
negative
transcriptional
Human mediators regulators

ature Reviews Mol Cell Biol (2004) 5, 403

 Gene-specific transcriptional activation in eukaryotic chromatin

Inactive chromatin
Exchangeable subunits in
coactivator/corepressor complexes
Factor modifications: SUMO …
Repressors Activators (Tissue, Cell, developmental stage-specific)
Corepressors Coactivators
Scaffold Scaffold As a signal or code
Histone deacetylases Histone modifiers ex: acetyltransferases (HAT)
ATP-CRC ATP-dependent chromatin remodeling complexes
DNA methylases DNA demethylases?

DNase I hypersensitive sites

Change DNA demethylation
in Histone hyperacetylation, Reduction of
histone – TBP/RNAPII H1 content
DNA (Ubiquitous)
interacti
Incorporation of histone variants
on Active chromatin (H2A.Z and H3.3) and/or non-histone
chromosomal proteins (HMG proteins)
Workman, Annu. Rev. Biochem. (1998) 67, 545
 Family of ATP-dependent Chromatin
Remodeling Complex

Binds Binds
acetylated methylated
lysines lysines

Oncogene (2001) 20, 3076

Curr Opin Genet Dev (2003) 13, 136
Family of ATP-dependent Chromatin
Remodeling Complex

Recognizing histone tails

Oncogene
(2001) 20,
3076
 ISWI is homologous to brahma
ISWI: imitation switch
SANT-like domains in the C-terminal
MCB ISWI: homozygous lethal
Acf1 Not localized to RNAPII: suggesting
(2000) functions other than transcription
20, 1899 Histone fold proteins

Acf1, a bromodomain and PHD finger protein

Was originally found as a nucleosome assembly
factor
 Family of ATP-dependent Chromatin
Remodeling Complex

Binds methylated lysines

Oncogene
(2001) 20,
3076
 Nucleosome
remodeling and
deacetylation

H4 interacting protein

ATPase activity
increases deacetylase
activity

MCB (2000) 20, 1899

 How ATP-dependent complexes
Assist in transcriptional regulation?
Stimulation of GAL4 Derivative
Binding to Nucleosomal DNA by
the Yeast SWI/SNF Complex

Jacques Cote, Janet Quinn, Jerry L. Workman,

Craig L. Peterson

Science (1994) 265, 53

Move Nucleosomes?
 Enzyme site

Sea urchin 5SRNA gene

32
P

GAL4 binding sites

Nature (1999) 400: 784
 Tom Owen-Hughes
Jerry Workman
Jacques Cote

Patric Grant
2003 Penn State Workman Lab Reunion
Science (2004) 303, 343
 Current Models

Curr Opin Genet Dev (2004) 14, 165

Current Models

Tom Owen-
Hughes
Curr Opin
Genet Dev
(2004) 14,
165
Beyond transcription?
Cell (2001) 106, 523
Nature (2002) 418, 994
 Gene-specific transcriptional activation in eukaryotic chromatin

Inactive chromatin
Exchangeable subunits in
coactivator/corepressor complexes
Factor modifications: SUMO …
Repressors Activators (Tissue, Cell, developmental stage-specific)
Corepressors Coactivators
Scaffold Scaffold As a signal or code
Histone deacetylases Histone modifiers ex: acetyltransferases (HAT)
ATP-CRC ATP-dependent chromatin remodeling complexes
DNA methylases DNA demethylases?

DNase I hypersensitive sites

Change DNA demethylation
in Histone hyperacetylation, Reduction of
histone – TBP/RNAPII H1 content
DNA (Ubiquitous)
interacti
Incorporation of histone variants
on Active chromatin (H2A.Z and H3.3) and/or non-histone
chromosomal proteins (HMG proteins)
Santos-Rosa and Caldas, Euro J. Cancer (20
 Histone Modifiers

Histone acetylation: Histone acetyltransferase (HAT)

Lys Histone deacetylase (HDAC)

Histone methylation: Histone methyltransferase (HMT)

Lys, Arg Histone demethylase

Histone phosphorylation:Histone kinase

Ser, Thr Histone phosphatase

Histone ubiquitination: Ubiquitin ligase

Lys

Histone sumoylation:
Lys
 Histone Modifiers

Histone acetylation: Histone acetyltransferase (HAT)

Lys Histone deacetylase (HDAC)

Histone methylation: Histone methyltransferase (HMT)

1994/1995
Lys, Arg Histone demethylaseBreakthrough

Histone phosphorylation:Histone kinase

Ser, Thr Histone phosphatase

Histone ubiquitination: Ubiquitin ligase

Lys

Histone sumoylation:
Lys
 Histone Modifiers

Histone acetylation: Histone acetyltransferase (HAT)

Lys Histone deacetylase (HDAC)

Histone methylation: Histone methyltransferase (HMT)

Lys, Arg Histone demethylase

Histone phosphorylation:Histone kinase 2004/2005

Breakthrough
Ser, Thr Histone phosphatase

Histone ubiquitination: Ubiquitin ligase

Lys

Histone sumoylation:
Lys
The ubiquitin pathway wins 2004 Nobel
Science 2004, 306, 400

Kiss of Death
 Histone Modifiers

Histone acetylation: Histone acetyltransferase (HAT)

Lys Histone deacetylase (HDAC)

Histone methylation: Histone methyltransferase (HMT)

Lys, Arg Histone demethylase

Histone phosphorylation:Histone kinase

Ser, Thr Histone phosphatase

Histone ubiquitination: Ubiquitin ligase

Lys

Histone sumoylation:
Lys