MicroRNAs and Robustness in Biological Regulatory Networks. A Generic Approach with Applications at Different Levels: Physiologic, Metabolic, and Genetic - Systems Biology of Metabolic and Signaling Networks - page 76

G13 and G14
frozen to 0
until G20=1

G9 G10 G19

G1 G2 G13 G14

no block
update

G8 G3 G15

G7 G4 G16

G6 G5 G18 G17

G20 G20=0 miRNA

G12 G11

Fig. 4.10 Influence of the chromatin clock on the genetic network dynamics: the down-tree leaf
G20 expresses or not a chromatin clock's enzyme, which authorizes or prevents the expression of
the updating block G13-G14

In Table 4.1 , the variable W equal to the observed number of subsequences of
length 5 common to specified sets of RNA sequences and to the reference sequence
AL is calculated for RNA sequences of the database R fam (Griffiths-Jones
et al. 2005 ). is the expected mean of the random variable equal to the

number of subsequences of length 5 common to the sets of RNA sequences and to a
random ring of length 22. The quantity

< W R >

σ R denotes the standard deviation of < W R > .

In each case, the value of the ratio S exceeds 1, with a significance less

than 10 3 for the tRNA conserved domains, which justifies the use of AL as
reference sequence, especially for miRNAs and tRNAs. We will introduce in the
following the notion of genetic threshold Boolean random regulatory network
(getBren) with n genes, which is a set N of n random automata as defined in
(Hopfield 1982 ; Hartwell et al. 1999 ; Weaver et al. 1999 ; Kauffman 1969 ; Thomas
1973 ; Demongeot et al. 2003 ) and in the present Mathematical Annex.

¼ W / < W R >

4.4.2 MicroRNAs and Chromatin Clock

The genes coding for enzymes involved in the chromatin clock as histone
acetyltransferases, endonucleases, exonucleases, helicases, replicases,
polymerases, etc., called clock genes, can be inhibited by many microRNAs
preventing some blocks of genes to be co-expressed (cf. Fig. 4.10 ), e.g.,
RNA-dependent Helicase P68 and Endonuclease CCR4 are inhibited by the same
miR-20, Helicase-DNA-binding protein KIAA1416 by miR181b, Exoribonuclease
2 and DNA Polymerase by the same miR-93. The influence of microRNAs on

chromatin clock is partly ambiguous: Table 4.2 shows that (1) several steps like

θ