A computational dissection in the evolution of cell growth

Gene regulation is a principle tool that all organisms utilize to control development, growth, and responses to environmental conditions. Understanding how organisms orchestrate the spatiotemporal regulation of gene expression remains a fundamental and unanswered biological question. Although poorly understood, the underpinnings of gene regulation are achieved, in part, by complex DNA-protein interactions that lead to changes in gene expression. These interactions are mediated by unique cis-regulatory elements (CREs) in DNA that recruit specific macromolecular complexes in trans to govern gene expression changes from transcription through to protein synthesis.;The cell achieves further regulatory control by embedding common CREs into multiple genes. An assemblage of genes all containing the same CRE is known as a gene regulatory network or regulon (GRN). GRNs are regulatory programs that function to conduct the concerted synthesis of gene products. Herein, the CREs and GRNs of cell growth, proliferation, and carcinogenesis are examined. Two GRNs principally controlled by the CREs corresponding to the proto-oncogenes Myc and E2F are discovered that regulate novel GRNs involved in ribosome biogenesis (RiBi) and DNA synthesis respectively.;The ribosome biogenesis (RiBi) genes encode a highly-conserved, eukaryotic set of nucleolar proteins involved in rRNA transcription, assembly, processing, and export from the nucleus. Here we present genome-wide analyzes supporting the hypothesis that a distinct core promoter-based mode of RiBi regulation co-evolved with the Myc:Max bHLH heterodimer complex in a stem-holozoan, the ancestor of both metazoa and choanoflagellata, the protozoan group most closely related to animals. These results indicate that a Myc GRN, which is activated in proliferating cells during normal development as well as during tumor progression, has primordial roots in the evolution of an inducible growth regime in a protozoan ancestor of animals.;Interestingly, this holozoan RiBi core promoter signature is absent in nematode genomes, which have not only secondarily lost Myc but also are marked by invariant cell lineages typically producing small body plans of 1000 somatic cells. Consideration of the divergent bHLH repertoires across holozoan genomes also suggests that both Mad and Mnt bHLH genes, additional members of the Myc/Max superfamily, are dispensable for this distinctive mode of RiBi regulation.;In addition to Myc, the RiBi regulon in Drosophila was further examined and a coordinating factor called DREF (DNA-replication related element factor) was identified. The presence of Myc and DREF within the core promoter uniquely defines genes within the RiBi regulon. A companion approach to decipher conserved targets of the E2F GRN revealed a novel regulon composed of genes associated with DNA synthesis functions that also are regulated by DREF. These results identified novel and conserved targets of E2F and provide evidence of cross-talk between RiBi and DNA synthesis mediated by DREF. Further, characterization of these DNA synthesis targets suggests that they may contribute to the oncogenicity of E2F as well.;Finally, a puzzling question in genomics centered on understanding how genomic complexity influences organismal complexity is examined. Several regulons identified in this work were analyzed in several genomes through a novel method to reveal a surprising correlation between genome size and the complexity of cis-regulatory information. This works supports a model whereby increased cis-regulatory information was a byproduct of increased genome size rather than active fixation to create novel complexity in higher organisms. In addition to providing novel insights into genomic complexity the methods developed here describe a novel strategy for identifying uncharacterized regulons within genomes.