Origem evolutiva de unidades regulatórias de eucariotos: quem surgiu primeiro, reguladores ou regulados?

Abstract

High-throughput functional analysis of genes, RNAs and proteins demands new computational strategies in order to extract relevant regulatory information. In prokaryotes, genes related to the same biological functions are usually located in operons. In eukaryotes, however, the transcriptional process is organized in a different way, as each gene is independently transcribed. Despite these differences, functional units controlled by transcription factors are present in eukaryotes, which are called regulons, and consist of a set of genes whose activation or repression are under the control of the same transcription factor. The regulatory relations of a regulon can emerge along the development of an organism, in a certain tissue, or even during the evolution process. Describing the formation of regulons may contribute to the understanding of how they act in the extant organisms, such as transcriptional control in cancer. In this research we investigated the evolutionary patterns of eukaryotic regulatory units in order to address the following question: who came first, regulators or regulated targets? Three hypotheses were tested: i) transcription factors and its targets appeared independently; ii) transcription factors came prior to their targets; iii) transcription factors came after their targets. We reconstructed regulons from gene expression data and developed a method to estimate the evolutionary distance between regulators and targets, inferring the point of emergence in a given species tree. A total of 307 regulatory units were evaluated, of which 76 (24.7%) had regulators rooted along with their targets, 137 (44.3%) had regulators rooted before their targets, and 94 (30.6%) had regulators rooted after their targets. These results suggest evolutionary scenarios that are consistent with the three hypotheses stated in this study. We then assessed the significance of these observations and found that the overall distribution of the inferred evolutionary roots of the regulators precedes the evolutionary roots of the targets (p-value = 1e-6, Wilcoxon-Mann-Whitney test). In addition, the identification of different evolutionary scenarios offers the opportunity to explain functional aspects found in the inferred regulons for breast cancer. Using a metric that estimates the functional similarity between regulons, regulatory units were clustered according to a regulatory network, and onto this regulatory network we mapped the evolutionary roots. Four important patterns were observed: (I) in general, regulons rooted at near evolutionary distances cluster to each other in the regulatory network; (ii) most of the regulons are rooted at the LCA of unicellular organisms; (iii) regulons associated with the development of breast cancer are more recent; (iv) most of the regulons related with positive/negative estrogen tumors are rooted at the LCA of metazoans. These results are consistent with one of the main aspects of cancer, in which tissue disarrangement is only possible in organisms able to form tissues.