Additional material for Interlinked nonlinear sub-networks underlie the formation of
cellular patterns in Arabidopsis epidermis: a spatial model of coupled gene regulatory
networks.
Mariana Benítez, Carlos Espinosa-Soto1, Pablo Padilla-Longoria and Elena R. AlvarezBuylla1
Logical rules constitute the precise description of the network topology and of the
function with which the nodes’ values are calculated in every time-step:
gn(t+1)=Fn(gn1(t),gn2(t),..., gnk(t)).
Values of the regulators are on the left side of the tables, while the regulated node or
nodes are on the right side. X indicates that, given the entrances of the rest of the table,
the node can take any value. Y and Z are temporal variables that integrate the values of
two groups of nodes (WER/GL1, GL3, EGL3, TTG1 and TRY, CPC, ETC, respectively)
and are then used to estimate the expression value of other nodes. The definition of Y and
Z facilitates the presentation and implementation of the logical rules, but does not affect
the synchronic updating schema or the interactions among elements of the network.
1
eabuylla@gmail.com
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1. Logical rules for updating the discrete gene regulatory network model for the leaf
epidermis.
GL1
0
X
X
1
2
2
Inputs
Output
GL3
EGL3 TTG1
Y
X
X
GL3+EGL3=0
GL3+EGL3<3
2
2
2
X
1
2
ELSE
Inputs
CPC
TRY
0
0
2
1
Inputs
Y
Z
0
0
Y<Z
1
2
1
2
0
0
1
1,2
GL1
1
1
2
2
2
2
X
X
0
1,2
1,2
1,2
ETC
CPC+ETC<2
2
0
CPC+ETC>0
2
X
ELSE
0
0
0
2
2
2
1
Output
Z
0
0
2
2
1
Outputs
GL3 EGL3 GL2 TTG1 ETC CPC
0
0
1
1
1
1
0
0
1
1
1
1
0
0
1
2
1
2
Input Output
GL2 TRY
0
1
2
0
1
2
2
1
1
1
1
1
1
0
0
1
2
1
2
0
0
1
2
1
2
2. Logical rules for updating the discrete gene regulatory network model for the root
epidermis.
Inputs
Output
GL3
EGL3 TTG1
Y
WER
0
X
X
1,2
2
2
X
X
GL3+EGL3<3
0
0
2
2
1
2
2
0,1
ELSE
Inputs
TRY
CPC
0
X
2
Inputs
Y
Z
0
0
0
1
1
1
2
2
2
0
1
2
0
1
2
0
1
2
ETC
0,1
2
X
ELSE
0
X
X
0
0
0
2
2
2
1
Output
Z
0
2
2
1
Outputs
CPC WER TTG1
GL3 EGL3
1
2
2
0
1
1
0
0
2
X
0
1
X
1
1
1
2
2
0
1
1
0
0
2
0
0
0
1
0
0
2
2
1
1
0
0
1
0
0
2
2
1
Input Output
GL2 TRY
0
1
2
0
1
2
3
1
1
1
1
1
1
1
1
1
GL2 ETC
0
0
0
1
0
0
2
2
1
0
0
0
1
0
0
1
1
1
TABLE S1. Reported and simulated phenotypes corresponding to single and double loss
of function (italics low case), as well as to overexpression (+) lines for the leaf metaGRN. All simulations were carried out with the same parameter values (DCPC= 0.05,
DTRR= 0.05, DTTG= 0.03).
Cell type patterns in the leaf epidermis of Arabidopsis thaliana
Genotype
Reported phenotype
Simulated phenotype
Wild type
Trichomes spaced out with
no clusters
More trichomes than in wt,
no clusters
High cluster probability
No phenotype
Enhancement of the cpc
phenotype
High number of trichomes
and clusters
High cluster probability
(try-like phenotype)
No trichomes
No trichomes
More trichomes than in wt
Wt phenotype
ttg phenotype
No trichomes
Many more trichomes than
in wt, but still with few
pavemente cells
Trichomes spaced out with
no clusters
~5% more tricomes than in
wt, no clusters
High cluster probability
No phenotype
Enhancement of the cpc
phenotype with few clusters
High number of trichomes
and clusters
High cluster probability
(try-like phenotype)
No trichomes
No trichomes
More trichomes than in wt
Wt phenotype
ttg phenotype
No trichomes
Only trichomes and no
pavement cells
cpc
try
etc
cpc etc
cpc etc try
cpc try
ttg
bhlh
bHLH (+)
ttg bHLH (+)
ttg GL1(+)
gl1
GL1 (+) bHLH (+)
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TABLE S2. Reported and simulated phenotypes corresponding to single and double loss
of function (italics low case), as well as to overexpression (+) lines for the root metaGRN. All simulations were carried out with the same parameter values (DCPC= 0.01,
DGL3= 0.01, DEGL3= 0.01).
Cell type patterns in the root epidermis of Arabidopsis thaliana
Genotype
Wild type
scm
wer
bhlh
cpc
try
cpc etc
CPC (+)
WER (+)
Reported phenotype
Simulated phenotype
Alternated bands of hair and Alternated bands of hair and
no-hair cells
no-hair cells
Hairs and no-hair cells
Hairs and no-hair cells
without banded pattern.
without banded pattern.
Many ectopic hairs
Only hair cells
Remarkable increase in the Remarkable increase in the
number of hair cells
number of hair cells
Ectopic atrichoblasts
Ectopic atrichoblasts
Ectopic atrichoblasts
Ectopic atrichoblasts
Enhanced cpc phenotype
Enhanced cpc phenotype
Ectopic hair cells
Ectopic hair cells
Wt phenotype
Wt-like phenotype with
some ectopic cells
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