El papel de la curvatura de DNA en la regulacin

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El papel de la curvatura de DNA en la regulación
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Clues and consequences of DNA bending in
transcription

• Nature of DNA bending. Bendability vs curved DNA
• Clues of DNA bending
• Inducer/ inhibitor of protein-DNA interactions
• Catalyst of protein-protein interactions
• DNA chaperones
• Consequences of DNA bending
• Channeling signals through promoter architecture
• Helping response-amplification signals
• Avoiding transcriptional promiscuity
• DNA bending A new signal-transduction mechanism?

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Curved DNA
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Bendability

• Bendability the ability of specific short
  sequences to assume preferentially conformations
  that accommodate the deformation associated with
  protein-induced bending.

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Bendability vs curved DNA

• Curved DNA is deformed even in the absence of
  external forces, thereby resulting in a very
  rigid structure.
• Bendable DNA allows a mixture of many different
  conformational states, the equilibrium of which
  can be displaced toward one specific form by
  external forces such as proteins interacting with
  them.

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Protein-mediated DNA bending

• Neutralization of charges in the DNA backbone
• Setting up extended protein-DNA contacts
• Intercalation of protein side chains in the minor
  groove

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Bend DNA is important for DNA-protein interactions

• CAP Correlation between bendability of CAP site
  and the affinity of the protein (Gartenberg and
  Crothers, 1988)
• Bacterial s70-RNA polymerase induces a strong
  bend in the promoter upon binding (Pérez-Martín
  and Espinosa, 1994)
• TBP and holo-TFIID bend DNA (Starr et al., 1995)

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Clues of DNA bending in transcription

• Inducer/ inhibitor of protein-DNA interactions
• Catalyst of protein-protein interactions
• DNA chaperones

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DNA bending as an inducer or inhibitor of
DNA-protein interactions

• Structural synergy
• Pre-curved CAP DNA binding sites
• HMG1 and the human progesterone receptor
• Structural inhibition
• Out of phase RepA-induced bends

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Structural synergy at the CAP-binding sites (Kahn
and Crothers, 1992)
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Structural synergy between HMG1 and PR (Oñate et
al., 1994)
HMG1
PR
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Structural inhibition (Pérez-Martín and Espinosa,
1991)
RNApol RepA
RNApol
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Clues of DNA bending in transcription

• Inducer/ inhibitor of protein-DNA interactions
• Catalyst of protein-protein interactions
• DNA chaperones

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DNA bending as a catalyst of protein-protein
interactions

• Short distances
• bendability XylR enhancer
• extra factors LEF-1 enhancer

• Long distances
• IHF
• histones

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XylR enhancer (Pérez-Martín and de Lorenzo, 1996)
30 bp
ATP
Bendable DNA
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LEF-1 enhancer in TCRa (Giese et al., 1992)
ATF/CREB
LEF-1
Ets-1
PEBP2a
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DNA bending as a catalyst of protein-protein
interactions

• Short distances
• bendability XylR enhancer
• extra factors LEF-1 enhancer

• Long distances
• IHF
• histones

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IHF at Pu promoter (Pérez-Martín and de Lorenzo,
1996)
gt200 bp
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Nucleosome positioning at the Drosophila hsp26
promoter (Thomas and Elgin, 1988)
-100
-200
-300
-400
TATA box
HSTF-box
GAGA-box
GAGA-box
HSTF-box
RNApolII
nucleosome
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Clues of DNA bending in transcription

• Inducer/ inhibitor of protein-DNA interactions
• Catalyst of protein-protein interactions
• DNA chaperones

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DNA chaperones (Travers, 1994)

• DNA chaperones are DNA-bending proteins that
  stabilize an otherwise loose structure in a
  particular conformation which sustains the
  assembly of additional proteins into a
  higher-order complex, being displaced away from
  the DNA in the final assembly.

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DNA chaperones HMG1 and PR (Oñate et al., 1994)
HMG1
PR
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DNA chaperones HU at Ps promoter (Pérez-Martín
and de Lorenzo, 1995)
s54-RNAP
HU
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Consequences of DNA bending in transcription

• Channeling signals through promoter architecture
• Helping response-amplification signals
• Avoiding transcriptional promiscuity

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Channeling signals through promoter architecture

• Co-activation
• CAP and MalT
• nucleosome in Xenopus vitellogenin B1 promoter
• Anti-repression
• CAP in ParaBAD
• Anti-induction
• YY1 in c-fos promoter
• IHF in nac promoter

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Co-activation MalT and CAP at PmalE-PmalK in
E.coli (Richet et al., 1991)
PmalE
RNApol
MalT
CAP
RNApol
PmalK
cAMP
Maltose
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Co-activation Xenopus vitellogenin B1 promoter
(Schild et al., 1993)
Cell-type
Hormone
NF1
HNF3
RNApolII
Oestrogen receptor
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Anti-repression AraC and CAP at ParaBAD in
E.coli (Lobell and Schleif, 1991)
AraC
RNApol
RNApol
RNApol
cAMP
Arabinose
CAP
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Anti-induction YY1 at the c- fos promoter
(Natesan and Gilman, 1993)
cAMP
YY1
RNApolII
CREBP
Cell status
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Anti-induction Nac at the nac promoter from K.
aerogenes (Feng et al., 1995)
Nitrogen status
Nac levels
NtrC
Nac
HU
Pnac
RNApol
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Consequences of DNA bending in transcription

• Channeling signals through promoter architecture
• Helping response-amplification signals
• Avoiding transcriptional promiscuity

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DNA bending in response-amplification mechanisms
LYSIS
LYSOGENY

• Stimulation of lysis/lisogeny of phage Mu by DNA
  bending (Goosen, van de Putte, 1995)

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Consequences of DNA bending in transcription

• Channeling signals through promoter architecture
• Helping response-amplification signals
• Avoiding transcriptional promiscuity

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DNA bending and transcriptional promiscuity

• Mechanisms to suppress non-specific activation at
  enhancers restrictors

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Restrictor a new role of IHF in Pu promoter
(Pérez-Martín and de Lorenzo, 1995)
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Clues and consequences of DNA bending in
transcription

• DNA bending A new signal-transduction mechanism?

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Characteristics of signal-transduction mechanisms

• Integration of signals
• Amplification of signals
• Specificity of signals

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Integration of signals
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Characteristics of signal-transduction mechanisms

• Integration of signals
• Amplification of signals
• Specificity of signals

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Amplification of signals
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Characteristics of signal-transduction mechanisms

• Integration of signals
• Amplification of signals
• Specificity of signals

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Specificity of signals(Scaffolding)
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Designing promoters a la carte
Specificity
Amplification
Integration