Several cellular processes are regulated through coordinated mechanisms including those related to the expression of gene regulatory networks or transcriptional modules. The identification of these transcriptional modules is essential to understand how different genes are coordinately expressed in response to both positive or negative stimulus. In eukaryotic cells, due to the large number of genes, the identification of transcriptional modules is difficult. However, during the last years several studies have been performed to understand the coordinated expression of ribosomal protein genes (RPGs). Those genes form a gene regulatory network and contain in their promoter sequences one or more common cis DNA elements which can control and regulate their expression. Such is the case of the yeast Saccharomyces cerevisiae, where the conserved Rap1 sequence is the key element in the recruiting of the RNA polymerase II transcriptional machinery. This element binds the transcription factor Rap1. However, Rap1 sequence is absent in the yeast Schizosaccharomyces pombe, where this element was replaced by the HomolD-box sequence, which binds the transcription factor Rrn7. Interestingly, neither of both elements have been identified in metazoan RPGs promoters. However, analyses in Drosophila have shown the presence of the TCT element in the RPGs promoters, which may be recognized by the factor M1PB. The study of each of these elements and the transcription factors which are able to bind them, is essential to understand the coordination of the expression of RPGs, which are fundamental in ribosome biogenesis and in the cellular response to environmental cues.
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