Many biological processes are regulated at the level of transcription. Effector genes with specific roles in biological processes are activated and shut down by transcriptional activators and repressors. The strategy of using such transcription factors to amplify a signal to many target genes is conserved in evolution, and many examples for such regulation are known from yeast to human.
In many cases, specific interactions between transcription factors influence the fate of the process as a whole (some examples are the action of several transcription factors in the Notch signaling pathway, [1
], and the activity of the YY1 transcription factor, [2
]). Thus, in order to understand a biological process, it is vital to understand the interplay between the transcription factors that govern the process. Very often, transcription networks are very complex, and it becomes difficult to understand the interaction between the transcription factors. To simplify the picture, model organisms with simpler transcription networks are used, of which budding yeast Saccharomyces cerevisiae
is most useful.
In budding yeast, meiosis has been extensively used as a model for complex developmental processes. The transcriptional control of meiosis in budding yeast is of special interest, since it is composed of several transcriptional waves, controlled by different transcription factors, and has therefore been studied extensively [3
In yeast, meiosis initiates in diploid cells upon exposure to medium lacking a fermentable carbon source and nitrogen. Typically, meiosis is completed in the formation of a rigid ascus that contains four spores (meiotic products), surrounded by a spore wall.
Budding yeast meiosis was shown to consist of three distinct phases, each characterized by a different set of transcripts [4
]. Upon meiosis induction, early phase genes are activated within minutes. The promoter regions of many of these early genes contain a common binding site (termed URS1), which is closely associated with the transcription factor Ime1 [6
]. Originally, Ime1 was thought to work together with Ume6 in early meiosis; however, recent work has shown that Ume6 is sent to degradation at this stage and thus cannot participate in early meiotic regulation [9
]. Early phase of meiosis extends to the pachytene checkpoint, when homologous chromosomes are aligned after having recombined with each other.
Middle and late genes are transcribed during the meiotic divisions and transcription continues through the formation of the rigid ascus wall [4
]. Analysis of promoters of middle meiotic genes revealed that they share several elements, which might be binding sites for transcription factors [10
]. Later, the transcriptional activator of many middle meiotic genes, Ndt80, was discovered, and its binding site was identified [11
Several genome-wide expression studies have been performed on meiotic yeast cultures [12
]. These studies have both confirmed and extended classical studies of yeast meiosis. Many more genes were grouped into the previously defined temporal categories, confirming the identity and mode of action of meiosis transcriptional regulators.
Middle meiosis is tightly regulated. Once a cell has passed the pachytene checkpoint and entered middle meiosis it is committed to the meiotic process [15
]. Moreover, at this stage the temporal variability between cells is reduced to a minimum and all cells that have started meiosis proceed in a synchronized manner [17
]. It has been suggested that this tight regulation and the transient expression of the middle phase transcripts is achieved through the interplay between the transcriptional activator Ndt80 and the repressor Sum1 [18
]. Ndt80 was shown to be essential for entry into meiotic divisions, and in its absence cells arrest at the pachytene stage [19
]. Ndt80 is induced in early meiosis by the Ime1 transcriptional activator [20
] and its activation is facilitated by phosphorylation by Ime2 (a meiosis specific kinase) [21
]. Ndt80 binds and activates promoters of genes containing the MSE (middle sporulation element) sequence [12
]. Sum1 is a repressor that is associated with the Hst1 histone deacetylase and represses the transcription of many middle phase genes during vegetative growth [23
] and during early meiosis phase [20
]. Sum1 protein levels fluctuate during meiosis, decreasing prior to entry into meiosis I and increasing after meiosis II [24
]. The expression of several Sum1 target genes (such as SMK1
and probably also NDT80
) is deregulated in sum1Δ
cells, and their expression levels remain high both in early and late meiosis phases [24
]. However, no meiotic phenotype has been observed in this sum1Δ
deleted strain. Sum1 binds a DNA binding site which resembles, and partly overlaps, the binding site of Ndt80 [23
]. In vitro experiments have suggested that both transcription factors compete for binding on target promoters [18
]. Taken together, it has been suggested that the tight transcriptional regulation during middle meiosis is achieved through competition between Ndt80 and Sum1.
Although this model is possible, it has not been shown to operate in vivo. Additionally, it is not known which genes are regulated by both factors, and to what extent Sum1 is active and necessary in late meiosis.
Here we use chromatin immunoprecipitation coupled with hybridization to genomic DNA microarrays (ChIP-on-chip), together with expression profiling, to determine the complete set of targets of Ndt80 and Sum1 in middle/late meiosis. These data, together with genetic experiments, challenge the generality of the competition model and suggest that Sum1's role in late meiosis may be achieved, in a great part, through its down-regulation of NDT80. Our data also help to decipher the transcriptional network during middle/late meiosis. We show that a feed-forward loop governs this network and we analyze the network structure in different transcriptional scenarios. The study may thus be used as a model study for more complex transcriptional networks.