Biology Reference
In-Depth Information
Using this relation, it is possible to convert mRNA decay half-lives mea-
sured by Wang
et al.
[32] into the corresponding transcript decay rate
constants.
(iii)
Since budding yeast cells are assumed to be at steady states at
t
0
with
respect to transcription and transcript decay (previously mentioned in
the first assumption), it would follow that
dn
S,i
/dt
=
dn
D,i
/dt
=
k
D,i
[
mRNA
i
]
0
=
0
.
693[
mRNA
i
]
0
t
2
,i
.
(12.4)
Thus Eq. (12.4) allows us to estimate the transcription rate,
dn
S,i
/dt
,at
t
0
from the [
mRNA
i
]
0
and
t
2
,i
values.
(iv)
The conversion factor, defined as
a
i
=(
dn
S,i
/dt
)
/TR
i
calculated at
t
0
is assumed to apply to all the other
TR
i
values measured at
t
1
,t
2
,t
3
,t
4
,
and
t
5
,where
TR
i
denoting the
TR
values associated with the
i
th
gene.
Since the
mRNA
i
decay measurements were made at 37
◦
Celsius (C)
[32], whereas the
TR
i
measurements were carried out at 28
◦
C [10], the
absolute rate values for
dn
S,i
/dt
calculated in (iii) were corrected for the
temperature difference by dividing
dn
S,i
/dt
by the factor 2
(v)
(9
/
10) =
1
.
9, which results from the assumption that the Q10 value (
i.e.
, the fac-
tor by which the rate increases due to a 10
◦
C increase in temperature)
was 2.
×
12.3.3.
Kinetic Analysis of the Changes in mRNA Levels
In the absence of any exchange of mRNA molecules between budding yeast cells
and their environment, it is possible to equate the rate of change of the
i
th
mRNA
molecules per cell,
dn
i
/dt
, with the balance between the rate of
mRNA
i
synthe-
sis,
dn
S,i
/dt
, and the rate of its degradation,
dn
D,i
/dt
given by
dn
i
/dt
=
dn
S,i
/dt
−
dn
D,i
/dt
(12.5)
In general, the rate of synthesis of the
i
th
mRNA,
dn
S,i
/dt
, would be a function
of many variables including the levels (or concentrations) of RNA polymerase II,
various transcription factors (encoded by the
j
th
gene, where
j
=
i
, except when
the
j
th
gene happens to code for a transcription factor that acts on the
j
th
gene
itself), and small molecules such as
ATP,ADP,AMP,Mg
++
,H
+
,etc. The
same would hold true for the rate of the degradation of the
i
th
mRNA,
dn
D,i
/dt
.
A system of ordinary differential equations describing the dynamics of mRNA
levels in a cell taking into account all the variables mentioned above has been
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