22 P. Doerner
lators such as A- and B-type cyclins, B- and C-type CDK genes, as well of
many genes associated with DNA replication (e.g. ribonucleotide reductase,
histones). This experiment showed for the first time that transcriptional reg-
ulation is a widespread, important and integrated aspect of overall cell cycle
control in plants, just as has been observed in other eukaryotic model sys-
tems. However, this experiment suffered from the unavailability of a tobacco
genome sequence, ambiguities in gene identification due to the amphidiploid
nature of tobacco and, despite the tedium of individual handling of each tran-
script, many remaining unidentified transcripts.
2.2
Analysis of Cell Cycle Regulated Gene Expression in Arabidopsis Cells
Taking advantage of the full suite of genomics tools available for Arabidopsis,
Menges and colleagues (2002) developed and validated two cell culture sys-
tems derived from a long established Arabidopsis cell culture line. These were
used in experiments in which cells were synchronized by Aphidicolin treat-
ments, by withdrawal and provision of sucrose to either freshly subcultured
cells or cells in the mid-exponential phase of the culture cycle (Menges et al.
2003, 2005).
Using rigorous statistics to validate their results, Menges and colleagues
confirm that the transcripts of the vast majority of canonical cell cycle reg-
ulators are expressed in the cell culture system and fluctuate in the course
of the cell division cycle. The transcripts whose levels periodically changed
with sinusoidal kinetics were defined as “cell cycle regulated”. By contrast,
those genes whose abundance changed greater than threefold, and that were
expressed over background levels for at least three time points over the entire
time course but not with sinusoidal kinetics were classified as “cell cycle asso-
ciated”. In the absence of detailed understanding of the cognate transcription
factors involved in cell cycle regulated gene expression in Arabidopsis, the
significance of this distinction is currently not readily apparent.
With the ATH1 gene chip,∼1100 genes were found to be cell cycle reg-
ulated or cell cycle associated, and were regulated in cells synchronized by
either Aphidicolin or by sucrose withdrawal and supply, corresponding to
∼ 7 % of all genes detected in the cell culture sample. A substantially higher
proportion of all genes expressed in cell cultures showed a similar magni-
tude of change in cells synchronized by sucrose starvation ( 31 %). In the latter
time course, a large number of genes are presumably responding to changes
in metabolism and not to cell cycle phase per se.
Overall, two major waves of periodic transcript accumulation could be
identified: the first was observed at late G1 and into S-phase, the second at
late G2 and into M-phase (Menges et al. 2002, 2003, 2005). In contrast to bud-
ding yeast, where a clear peak is also associated with exit from the cell cycle at
the M/G1 transition, this is not unequivocally clear in the synchronized Ara-