Biology Reference
In-Depth Information
The study of cell cycle regulated gene expression in yeasts has been
ongoing since the early 1980s, when it was discovered that the transcript levels of
the budding yeast histone genes fluctuated dramatically through the cell cycle
(Hereford
, 1981, 1982). Since then many cell cycle regulated genes in both
budding and fission yeasts have been identified by traditional methods, and in
many cases the transcriptional control mechanisms characterized (B¨hler,
2005a; Breeden, 1996; Futcher, 2000, 2002; McInerny, 2004; Tyers, 2004).
Furthermore, the advent of global analyses of transcript levels by microarrays
and the binding of cell cycle transcription factors throughout the genome by
ChIP-on-chip technologies has consolidated the field (Banerjee and Zhang,
2003; Cho
et al.
et al.
, 1998; Iyer
et al.
, 2001; Kato
et al.
, 2004; Oliva
et al.
, 2005;
Peng
, 1998). Such studies have
also permitted complex hierarchies and networks to be proposed, suggesting how
cell cycle regulated transcription fits into general cycle controls, and how each
wave of gene expression may control, and be controlled by, those before and after
(de Lichtenberg
et al.
, 2005; Rustici
et al.
, 2004; Spellman
et al.
et al.
, 2005; Horak
et al.
, 2002; Jensen
et al.
, 2006; Lee
et al.
,
2002; Simon
, 2001) (Fig. 2.3).
This accumulated knowledge means that the field is now at a mature
stage, with a reasonably comprehensive picture of the process in both model
yeast species (B¨hler, 2005a; Breeden, 2003; McInerny, 2004; Toone
et al.
, 1997;
Tyers, 2004; Wittenberg and Reed, 2005). These paradigms are of wide interest,
as related mechanisms operate in all eukaryotes, including humans, where
deregulated cell cycle gene expression is a signature of many diseases.
In this review, I first describe in detail the various waves of gene
expression in the two yeast species, budding and fission yeasts, and the different
transcriptional control mechanisms that regulate them. Particular emphasis will
be made on those genes and mechanisms that are conserved between the two
species, as in many cases these have orthologs in higher eukaryotes. Having
described the basic architecture of cell cycle regulated gene expression, the
mechanisms by which these various waves are integrated to each other and to
more general cell cycle controls will be described.
et al.
B. Gene expression
In the context of cell cycle gene expression, we will be focussing on genes whose
transcription is controlled by RNA polymerase II. These include most genes
whose transcription produces messenger RNAs (mRNAs), which when translat-
ed produce polypeptides or proteins with functions within the cell. The molecu-
lar mechanisms by which these genes are controlled during transcription have
been well studied (Fig. 2.1). Upstream of the start methionine of the open
reading frames of genes, lie DNA regions described as promoters. Within these
promoter regions are found short, conserved DNA sequence motifs, to which
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