Table 4

Location of the target sequences relative to the NM using a higher DNA template concentration

AMPLICON

TOPOLOGICAL ZONES RELATIVE TO NM


C

D

P

VC

E

n


a

+

+

+

+

+

4

b

+

+

+

+

+/-

2

c

+

+

+

+

+/-

2

d

+

+

+

+

+

4

e

+

+

+

+

+/-

2

f

+

+

+

+

-

2

g

+

+

+

+/-

-

2

h

+

+

+

+

+

4

i

+

+

+

+

+

2

j

+

+

+

+

+/-

2

k

+

+

+

+

+

3

l

+

+

+

+

+/-

3


Location in control G0 hepatocytes of the fifteen target sequences from the 162 kbp genomic region studied within the topological zones relative to the NM using a higher DNA template concentration. Such topological zones were defined according to the kinetics of nucleoid-DNA digestion in samples from control G0 hepatocytes obtained from normal rat liver (Figure 2A). For these experiments the nuclear matrix-bound DNA template was increased six-fold (from 10 to 60 ng) and the DNA polymerase concentration was doubled (from 0.7 to 1.25 U) in order to facilitate the amplification of target sequences embedded within the NM. The amplicons were scored either as positive or negative as a function of endonuclease digestion time and for each topological zone relative to the NM, depending on whether or not they were detected by a digital image-analysis system (Kodak 1D Image Analysis Software 3.5) using the default settings. C, 0' digestion-time control. D, distal to the NM. P, proximal to the NM. VC, very close to the NM. E, embedded within the NM. All target sequences were mapped in repeated experiments with samples from separate animals (n indicated in the table). +/- indicates that one experiment was positive and the other experiment was negative.

Rivera-Mulia et al. BMC Cell Biology 2011 12:3   doi:10.1186/1471-2121-12-3

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