05-11-2012, 12:38 PM
The Transcriptional Program of Sporulation in Budding Yeast
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Diploid cells of budding yeast produce haploid cells through the developmental
program of sporulation, which consists of meiosis and spore morphogenesis.
DNA microarrays containing nearly every yeast gene were used
to assay changes in gene expression during sporulation. At least seven
distinct temporal patterns of induction were observed. The transcription
factor Ndt80 appeared to be important for induction of a large group of
genes at the end of meiotic prophase. Consensus sequences known or
proposed to be responsible for temporal regulation could be identiÞed solely
from analysis of sequences of coordinately expressed genes. The temporal
expression pattern provided clues to potential functions of hundreds of
previously uncharacterized genes, some of which have vertebrate homologs
that may function during gametogenesis.
Sequential Induction of Genes During
Sporulation
Of the about 6200 protein-encoding genes in
the yeast genome, more than 1000 showed
significant changes in mRNA levels during
sporulation (20). About half of these genes
were induced during sporulation, and half
were repressed. To facilitate the visualization
and interpretation of the gene expression program
represented in this very large body of
data, we have used the method of Eisen et al.
(21, 22) to order genes on the basis of similarities
in their expression patterns and display
the results in a compact graphical format
(Fig. 4A).
The relatively small number of genes
(about 50) whose transcription has been studied
previously had defined four temporal
classes of sporulation-specific genes (1).
These classes were evident in this analysis
but were not sufficient to represent the diversity
of observed expression patterns. We
found it useful to distinguish seven temporal
patterns of induced transcription that reflect
sequential progression through this program,
even though well-defined boundaries between
temporal classes could not be determined.
(Increased synchrony and more frequent
time points might sharpen these boundaries
and reveal more classes.) For each of
these seven temporal patterns, a small, representative
set of genes was hand-picked and
used to define a model expression profile
(Fig. 4B). A variety of temporal expression
patterns were also observed for the genes
whose mRNA transcripts decreased during
sporulation.
Regulation of Middle Genes by Ndt80
We found that more than 150 genes were
induced between 2 and 5 hours after transfer
to sporulation medium, in a pattern like that
of the known targets of Ndt80. To further
characterize the role of Ndt80 in their induction,
we examined the consequences of expressing
Ndt80 ectopically in vegetative cells
(28) and of eliminating Ndt80 during sporulation
(17). Previous work had shown that
ectopic expression of Ndt80 in vegetative
cells induces several known middle genes
[SPS1, SPC42, CLB3, and CLB6, among others;
(4)]. Microarray analysis revealed that
more than 200 genes were induced at least
threefold when Ndt80 was expressed ectopically.
About 42% of these genes were expressed
in the middle induction pattern during
sporulation. In contrast, fewer than 20%
of the genes induced by ectopic expression of
Ndt80 exhibited the metabolic, early, earlymid,
mid-late, or late induction patterns during
sporulation.
Proposed Roles for Genes Induced
During Sporulation
How can we begin to understand what contribution
each of the induced genes makes to
the efficiency of sporulation or fitness of the
resulting spore? Because genes with related
functions tend to be expressed in similar patterns,
we can suggest possible roles for genes
of unknown function based on their temporal
association with genes of known function (a
“guilt-by-association” argument). These hypotheses
about gene function can then be
tested by making mutations in the genes in
question, and analyzing their effects.