Los genes están organizados en redes complejas de expresión:

comportamientos complejos

importan el quién, el
cuándo, el cuánto y el
dónde

hay retroalimentación
positiva y negativa, y
múltiples puntos de
regulación

cada tipo celular

expresa un subconjunto
de genes
Las decisiones de desarrollo se toman regulando genes.

la expresión está bajo control

combinatorio

supondremos que el control es

sobre el inicio de la transcripción
Medidas de expresión: actividad enzimática o fluorescencia de proteínas
cantidad de enzima activa al momento de lisar las bacterias

cantidad de
proteína / célula
 Medidas de expresión: cantidad de RNA
microarreglos, PCR cuantitativo y transcriptomas

Para ver ocupación de sitios en el DNA:

inmunoprecipitación de cromatina y footprinting
 Asunto central: ocupación del promotor por la polimerasa
TetR

IdeR

FadR

los represores evitan la unión de la

polimerasa al promotor
PurR
 Los activadores facilitan la unión de la polimerasa al promotor.

CAP

p53

Además de activadores y represores, hay Zn finger

moléculas pequeñas que los regulan
mediante un mecanismo alostérico.
L zipper
 To compute the probability of promoterboth
Figure 19.8: Structures of activator
of the specific
occupancy, sites occupied.
we construct the This is represented m
cally as
ratio of all of thoseFrom
molecules. outcomes La that
top to bottom, the are favorable
acciónthe de
same un (that Dis,
activador
nonspecific polymerase
D epd on the DNA. This
ead site P A e–b (D epd + De ad
permits the
activators are CAP (pdb 1CGP), p53 NNS NNS
bound to the promoter) to the total set of
tumor suppressor (pdb 3KMD), zinc NNS !/(NNS −
outcomes
A(P, (Z
P)!N≈
− A; (N(P,
tot )A;
A+PNNS )),
introduced in Section−βεpdS
6.1
Ztot NS ) =NSZ(P, A; N NS ) + Z(P − 1, A; NNS )e
namely, finger DNA-binding domain (pdb 2GLI),
To compute the probability of promoter occupancy, w
and leucine zipper DNA-binding domain empty promoter RNAP
(pdb 1AN2). (Courtesy of D. Goodsell.)ratio
of all of those outcomes that are favorable S
(that
the same nonspecific
bound to the promoter) site on + the
Z(P,
to DNA.
A
the− 1;This
N
total permits
−βεad
NS set of outcomes
)e the appro(
pbound (P, A; NNS ) NNS !/(N NS − A − P)! ≈ (NNS )
A+P introduced in Section 6.1.2 (see
namely, activator
S Note
To compute the that, notationally,
probability the
S +εS +ε )of promoter meaning of Z(P,
occupancy, A;S N
S +ε weNS )con is
−βεpd −β(ε pa −β(εad +ε pa )
Z(P − 1, A; NNS )e + Z(P − 1, Aof
ratio 1;
allNof
− the partition ad
those function
NS )e
pd
outcomes +for
that 1, A − 1; NNS )emolecules and
are favorable (that is, .po
Z(P P− polymerase pd
A
= . (19.4) nonspecific
Ztot (P,bound molecules to be bound on the N
A; NNSp)bound
to the
(P,promoter)
A; NNS ) to the total set NS of
RNAP outcomessites
+ activator (Ztotan (P
by
namely,
the same nonspecific site −βε on Sthe DNA. This permits the approx S +
−β(εad
Z(P −
!/(NNS −Z(P, 1, A; N A+P pd N Z(P − 1,inASection
+ NS !
introduced −−βPε1; NpdNS
6.1.2
NNS A − P)! e−βAεad(see . p
)e) NS )e NS
810 Chapter 19 ORGANIZATION OF BIOLOGICAL A; N≈
NETWORKS NSNS
(N × e
We now propose to simplify this result by
= dividing both
NS ) = numerator
To compute the probability P!A!(NofNS − P − A)! occupancy,
Zpromoter
tot (P, A; N NS ) we const
and denominator by the numerator,presulting (P, A; in
N
ratio of all of
bound )
NS those outcomes that are favorable (that is, poly
number of arrangements weight of each state
bound to the promoter) S to the total set of outcomes
−βεpd S (Z
−β(εad +εpaA
S (P,
+εtot
“chap19.tex” — page 810[#12] WeZ(P
now− 1, A; N
propose + Z(P
to simplify − 1, A − 1; N pd
the this result
εpaNSby dividingforb
namely, )e
NS introduced )e
= We have also notation to account
1
probabilidad
pbound (P, A; NNS ) = and denominator
interaction , de
by
between Zocupación
the
the (P, A; NNSand
numerator,
(19.5)
polymerase
tot del promotor
) resulting in
activator. Like in Se
1 + [NNS /PF
(p. reg
244)
β#εpd
for the case of RNA polymerase, we introduce εad
(A)]e S
pbound (P, A; NNS )
characterize the binding energy of activator with its specifi
We now specific
propose totargets,
simplifyS this result byexpression
dividing
1 ad both
S +ε S +ε )n
Z(P − DNA respectively. Our involves
−βεpd −β(ε pa
1, A;
p N )e + Z(P
NS (P, A; NNS ) =− 1, A − 1; N NS )e pd

where we introduce the regulationand denominator

factor Freg
of
= terms
(A), of by
thethe
bound
which isnumerator,
formby resulting
given
general 1NS
Ztot (P, A; N
in
+) [NNS /PFreg (A)]eβ#εpd
.

NNS ! NS
−βPεpd NS
×e e−βAεad .
We nowad propose P!A!(NNS this
to simplify A)! by1dividing both num
− P −result
1 + (A/NNSwhere
)e−β#ε we bound (P, A;the
pintroduce
e−βε ap NNS regulation
)= factor Freg (A), ,
β#εpdwhich
Freg (A) = and denominator , by the numerator,(19.6)
1 + [Nresulting
/PFregin(A)]e
1 + (A/NNS )eAs weaddid earlier, we invoke a NS
−β#ε simplifying strategy tha
upon the fact that NNS ≫ A + P and hence there will be al
chance of RNA polymerase1and the NS
+factor
(A/N activator
)e e−βεapiseach
1 −β#εadfinding
where we introduce the
pbound (P,regulation
Freg
A; NNS= = F reg (A), which , , giv
S (A)
)
S NS NS 1 +
and where we have defined #εpd = ε − ε and #εad = ε − ε . The
pd pd ad ad
1 + NS
[N /PF
(A/Nreg −β#ε
(A)]e
NS )e
β#εpd
ad

details of the derivation are left to the problems at the end of the −β#ε −βε
El efecto del activador es mejorar la ocupación del promotor.

Δε da la diferencia entre unirse a NS y a S.

Si εap < 0, Freg > 1.

El efecto neto es similar al de añadir más polimerasas.
(B)
Freg = 2

P polimerasas + activador

F P polimerasas
expression
reg for cases in which the transcription factor of
present or not. This qualitative notion is made quantitativ
ducing the idea of the fold-change in activity, defined in the
setting as

pbound (A ̸= 0) 1 + (NNS /P)eβ"εpd

fold-change = = .
pbound (A = 0) 1 + [NNS /PFreg (A)]eβ"εpd

What this expression reveals is how much more expressio

in the presence of activators relative to the “basal” state in w
is no activation.
As before, an inherent assumption in this analysis is the
the relative change in what is measured (for example, pro
uct, mRNA concentration, or promoter occupancy) is eq
relative change in pbound . Figure 19.12 illustrates the fold
gene expression for the problem of simple activation wit
esto funciona
of parameters dictated bien
by in para promotoresfor
vitro experiments débiles
a value
conjunction with an educated guess for εap that results in ty
 Experimentos para estudiar activadores: quimeras

idéntico a lo ya tratado, nada más

cambiando Δεad y εpa

en este caso, polimerasa y activador son una sola molécula, con dos
energías de unión (pd y ad):
 polymerase.
La acción de un represor: hay un estado menos
The total partition function is given by
S
−βεpd
Ztot (P, R; NNS ) = Z(P, R; NNS ) + Z(P − 1, R; NNS )e
empty promoter RNAP on promoter
S
+ Z(P, R − 1; NNS )e−βεrd .
repressor on promoter

STATE RENORMALIZED WEIGHT

RNA repressor-
polymerase binding site repressor

promoter
1

Depd
P e– b Depd
NNS
ahora parece que hay menos polimerasas
Experimento de dilución para cuantificar represión
Cuantificación de fluorescencia/célula para ensayo de expresión
 Medición del cambio en expresión con fluorescencia

De estos experimentos se pueden extraer parámetros termodinámicos.

energía de unión de
una X con un D
 and activation simultaneously. In this case, we consider the five dis-
tinct outcomes shown in Figure 19.18 and captured through the total
Cuando hay represores y activadores
partition function

Ztot (P, A, R; NNS )

A R e–b (Dead + Derd)
S
= Z(P, A, R; NNS ) + Z(P − 1, A, R; NNS )e
−βεpd NNS NNS
Dead Derd
empty promoter RNAP

−βεad S −β(εS +ε S +ε
pa )
+ Z(P,
Note that − 1, R; Nshows
the Acartoon NS )e a+ Z(P − 1, A representation
schematic − 1, R; NNS )e ad pd
of the dif-
ferent ways that activator
the region in the vicinity RNAP of the promoter can be
+ activator
occupied and what the statistical S weights are of each SsuchS state
+ Z(P, A, R − 1; NNS )e−βεrd + Z(P, A − 1, R − 1; NNS )e−β(εad +εrd ) .
of occupancy. We can compute the probability of RNA polymerase
binding by considering
repressor the ratio of favorable
activatoroutcomes
+ repressor to the total
partition function, resulting in (19.23)

pbound (P, A, R; NNS )

820 Chapter 19 ORGANIZATION OF BIOLOGICAL NETWORKS S S +ε S +ε )
−βεpd −β(εad pa
Z(P − 1, A, R; NNS )e + Z(P − 1, A − 1, R; NNS )e pd
= .
Ztot (P, A, R; NNS )
(19.24)
“chap19.tex” — page 820[#22] 5/10/20
As before, perhaps the simplest way to interpret this result is with
reference to the regulation factor, resulting in
1
pbound (P, A, R; NNS ) = S −ε NS )
, (19.25)
β(εpd
1 + [NNS /PFreg (A, R)]e pd

“chap19.tex” — page 821[#23]

La riqueza de escenarios aumenta, y la combinatoria también.
 El operón de lac

his definition based upon a measure of protein content (that is, the
product of the gene) with a definition based upon examining the prob-
ability that the promoter is occupied by RNA polymerase. The implicit
assumption here is that the protein content is linearly related to the
probability of promoter occupancy. More precisely, we define repres-
sion as the ratio of the probability of binding of RNA polymerase to
he relevant promoter in the absence of repressor to the probability
más de un sitio de unión para el represor, con distintas
of such binding in the presence of repressor, namely
afinidades
pbound (R = 0) Δεrd (kT)
repression = . (19.27)
pbound (R ̸= 0) -16.9
Concretely, this result depends on the number of repressors, R, and
their energy of binding to DNA. If we substitute for pbound using
-14.4
Equation 19.15, we find that the repression can be written as

-11.2
1 + (P/NNS )e−β"εpd + (R/NNS )e−β"εrd
repression(R) = . (19.28)
1 + (P/NNS )e−β"εpd

For the case of a weak promoter, this implies in turn that the
repression level can be written as

R −β"εrd
repression(R) = [fold-change(R)]−1 ≃ [Freg (R)]−1 = 1 + e .
NNS
Con la posibilidad de unirse a dos operadores, se hacen lazos.
 weights to all of the allowed states depicted in Figure 19.25. Using
exactly the same logic as in previous sections, the partition function
Represores y el costo de hacer lazos
can be written as
S
−βεpd
Ztot (P, R; NNS ) = Z(P, R; NNS ) + Z(P − 1, R; NNS )e
(0) (0) (0) (0)
P(0) , Omain and Oaux P(1) , Omain and Oaux

S
−βεpd S
−βεrda
+ Z(P − 1, R − 1; NNS )e e
(0) (1)
P(1) , Omain and Oaux

S S
+ Z(P, R − 1; NNS )e−βεrdm + Z(P, R − 1; NNS )e−βεrda
(1) (0) (0) (1)
P(0) , Omain and Oaux P(0) , Omain and Oaux

S S
+ Z(P, R − 2; NNS )e−βεrdm e−βεrda
(1) (1)
P(0) , Omain and Oaux
S S
+ Z(P, R − 1; NNS )e−βεrdm e−βεrda e−βFloop , (19.30
repressor/loop

“chap19.tex” — page 825[#27]

se obtiene ΔFloop para un experimento, y sirve para los demás
Todo junto, con inductores y con células

IPTG reduce la unión del represor al operador

importa in vivo el transporte a la célula (LacY):

hace al sistema más sensible
Cada arquitectura regulatoria tiene
su modelo.

Da el punto de contacto con los

datos experimentales y con las
variables de control.
 Puntos de control para la transcripción

para cada nivel se pueden armar modelos, y luego integrarlos

Transcripción en eucariotas: los nucleosomas

acceso de TBP
La intensidad de transcripción depende del número de elementos de unión.
de esto depende la forma del gradiente de la proteína codificada