Transcriptional Control of the Plant Cell Cycle 27
4
Approaches to Identify Transcription Networks
Advances in genome-wide technologies have recently and will continue to
provide novel opportunities for dissecting the mechanisms and identifying
the components of the cell cycle gene expression networks. The following sec-
tions will highlight current progress and identify key areas where advances
are required to address the challenging tasks ahead.
4.1
Expression Analysis
To better understand the regulation of plant genes expressed periodically
during the cell cycle, advances in several areas are needed: improved synchro-
nization methods, the analysis of gene expression in additional species, as
well as novel approaches to analyze cell cycle phase-specific expression.
Current synchronization methods are not optimal, because synchroniza-
tion methods based on inhibitor-mediated cell cycle arrest and release do
not constrain cell cycle progression from in-built cell cycle control points,
and are therefore likely to activate additional unrelated responses. This has
been clearly shown to be the case for Aphidicolin-based cell cycle synchro-
nization, which elicits replication stress responses. It is possible that using
nutrient withdrawal/supply will cause fewer such artifacts. Ultimately, it will
be necessary to compare results obtained with different synchronization
methods.
It would also be extremely useful to develop and characterize cell cycle
gene expression from additional plant systems with sequenced genomes. Ini-
tial developments have been made for rice and other cereal synchronization
systems, but these clearly still require improvements (Kaeppler et al. 1997;
Minami et al. 2000; Lendvai et al. 2002). The tobacco genome is currently be-
ing sequenced, facilitating progress with this excellent system for cell cycle
studies (Nagata et al. 1992). Recently, the genome sequence of the unicellular
green alga Ostreococcus was determined, revealing that this very simple eu-
karyote at the base of the green plant lineage has a simple complement of core
cell cycle regulators (Derelle et al. 2006). This system carries a lot of potential,
as its cell cycle is entrained by the circadian clock (Farinas et al. 2006), which
will provide unique opportunities.
Comprehensive analysis of periodically expressed genes has only been per-
formed in suspension cultured cells, which lack many of the developmental
pathways that control and interface with cell cycle regulation in intact plants.
New technologies, such as laser microdissection microscopy, are increasingly
being used to sample the transcript profile, proteome and even metabolites
from small numbers of well-defined cells within a tissue context (Nelson et al.
2006). When used with appropriate markers, this approach could be used to