Biology Reference
In-Depth Information
dependent, but other factors are involved in maintenance of
the PLT gradient
[24,25]
. The relationships between auxin
accumulation and transcription factor action are not so
much complicated in the sense of having many compo-
nents, but are complex in the sense of being connected in
a way that does not intuitively reveal the properties of the
network. Here, formal descriptions and computer simula-
tions of the relationships between components will be
necessary to understand the developmental logic of root
initiation and stem cell programming.
development as a simple addition of modular gene regu-
latory networks. Rather, 'modules' only appear as such
after crude analysis, and they may collapse into larger
networks upon closer inspection. This posits a considerable
challenge for next-generation computational models that
summarize regulatory interactions and loops in the context
of an entire organ.
Integrated Analysis of Shoot Development
Plant shoots contain tip regions that are sites of continuous
cell division, growth and pattern formation. In the slowly
dividing center of shoots, stem cells reside within a 'central
zone' (CZ) (
Figure 20.1
). The underlying 'rib meristem'
(RZ) zone contains transiting cells that dynamically form
a spatially stable organizing center required to maintain the
overlying stem cells. Organs such as leaves initiate when
stem cell daughters emanating from the CZ reach the
peripheral zone (PZ) (
Figure 20.1
)
[34,35]
. Roots branch
by creating new stem cells through dedifferentiation of
cells from one internal cell layer well outside the growth
zones. Shoot branching and differentiation events, on the
contrary, are scattered over the growing apex as new organs
repeatedly form in close proximity to the stem cell region.
These organs in turn develop new stem cell regions,
creating nested patterns of differentiating organs and stem
cell groups. While performing this iterative developmental
act shoots can undergo major phase changes, dramatically
illustrated in the switch from vegetative development,
characterized by the production of leaves, to the formation
of flowers, which is brought about by extensive modulation
of developmental programs.
Mutual Support for Root Hair Patterning
Epidermal cell patterns are highly accessible, and the ease
by which mutants in such patterns can be selected have
made them favorites for the genetic dissection of pattern-
forming mechanisms in animals and plants alike. The
Arabidopsis root epidermis is one of the examples where
molecular genetic analyses have yielded a wealth of
components involved in the binary decision of whether or
not to make hairs
[26,27]
. The primary role of root hairs,
which protrude from the base of certain epidermal cells, is
to expand the absorptive surface of the root. Genetic
screens for roots with increased or decreased numbers of
hairs resulted in the identification of two variants of tran-
scription factor complexes in hair cells and hairless cells. In
hairless cells, the active WEREWOLF (WER) complex
promotes transcription of downstream targets that suppress
the hair fate
[28]
. In hair cells, this complex is prevented
from forming and replaced by a CAPRICE (CPC) complex
through a combination of signaling from subepidermal cell
layers through the SCRAMBLED (SCM) receptor kinase
and by the lateral cell-to-cell movement of inhibitory
transcription factors such as CPC originating from the
hairless cells
[29,30]
. Several working models had been
proposed for the way in which this regulatory network leads
to correct pattern formation, relying on conventional
notions of local activation and lateral inhibition, but formal
analysis of the components indicated that a novel mecha-
nism, where neighboring cells support the alternative cell
type, best fitted all results
[31]
. This work indicates once
more that complex networks are rarely amenable to intui-
tive explanations but need downstream analysis for deeper
understanding. Interestingly, a study on regulators of SHR
and SCR activity which function in the ground tissue to
restrict the range of SHR action
[32]
, revealed that these
have a cell-autonomous role in the ground tissue for the
production of signals that guide root hair patterning
[33]
.
This work indicates that movement of SHR from stele to
ground tissue is connected to a biasing system that
impinges on epidermal patterning. This illustrates how
interconnected the gene regulatory networks involved in
root development are. One of the lessons to be learned is
that
Gene Activity in Space and Time
The mix of patterning and differentiation zones in the
growth regions of shoots has not precluded the use of
dissection methods similar to those described for root
transcriptome mapping. Expression profiles corresponding
to developmental zones have been collected by enzy-
matically digesting the cells walls of the shoot apex fol-
lowed by FACS using markers for CZ, RZ and PZ in
a mutant background with a highly enriched shoot apical
meristem tissue fraction (
Figure 20.2
)
[36]
. As observed
in root samples, this approach significantly increased the
sensitivity with which rare transcripts could be detected,
and yielded about 1000 genes that were unique to cell
population-specific data. In addition, mining and valida-
tion of differentially expressed genes revealed novel
markers for the stem cell niche, and indicated an
enrichment in DNA repair as well as DNA- and histone-
modifying enzymes, in line with important roles for
epigenetic control and control of genome stability in stem
cells. The study also revealed novel expression patterns in
it may not be possible to reconstruct organ
