Molecular evolution in the yeast transcriptional regulation network

Abstract

We analyze the structure of the yeast transcriptional regulation network, as revealed by chromatin immunoprecipitation experiments, and characterize the molecular evolution of both its transcriptional regulators and their target (regulated) genes. We test the hypothesis that highly connected genes are more important to the function of gene networks. Three lines of evidence-the rate of molecular evolution of network genes, the rate at which network genes undergo gene duplication, and the effects of synthetic null mutation in network genes-provide no strong support for this hypothesis. In addition, we ask how network genes diverge in their transcriptional regulation after duplication. Both loss (subfunctionalization) and gain (neofunctionalization) of transcription factor binding play a role in this divergence, which is often rapid. On the one hand, gene duplicates experience a net loss in the number of transcription factors binding to them, indicating the importance of losing transcription factor binding sites after gene duplication. On the other hand, the number of transcription factors that bind to highly diverged duplicates is significantly greater than would be expected if loss of binding played the only role in the divergence of duplicate genes.

Recessive Loci Pps-1 and OM Differentially Regulate PISTILLATA-1 and APETALA3-1 Expression for Sepal and Petal Development in Papaver somniferum

“…Genes encoding products that function as key regulatory components, such as transcription factors, as well as those participating in large multi-protein complexes (e.g. MADS-domain proteins) [29], appear to be preferentially maintained owing to the requirement for a stoichiometric balance with other components in the pathway [39], [40]. Hence, it seems that the recessive Pps-1 locus might be influencing the expression of PapsAP3-1 and PapsPI-1 in sepals during development ( Figures 5 , 6 ).…”

Transcriptome profiling of individual larvae of two different developmental modes in the poecilogonous polychaeteStreblospio benedicti (Spionidae)

“…Even if S. benedicti exists as a sibling species complex, one can still argue for this least parsimonious conclusion from the standpoint that although the genomic background that expresses planktotrophic and lecithotrophic larval morphologies may not be exactly identical, these two genomes would still be nearly equivalent. The absolute molecular mechanism responsible for producing a direct or indirect larva in S. benedicti would likely arise through subtle variations within one developmental program (Peterson et al, 2000;Gilbert, 2001;Evangelisti and Wagner, 2004).…”

Complex networks and simple models in biology

“…Many important real networks, including the molecular networks, have degree distributions which decay much more slowly than exponentially (Alm & Arkin 2003;Evangelisti & Wagner 2004;Li et al 2004;Agrafioti et al 2005). In terms of the degree distribution classical random graphs are therefore unable to explain at least some aspects of real data.…”

“…Molecular networks, such as protein interaction (Uetz et al 2000;Maslov & Sneppen 2002;Agrafioti et al 2005), metabolic (Ma & Zeng 2003) and gene regulation networks (Ronen et al 2002;Evangelisti & Wagner 2004) aim to capture such sets of biological processes in a single and coherent framework. In reality, of course, these different networks are intricately connected and interwoven inside a cell; protein products will interact with each other, regulate the expression of genes as well as digesting nutrients and catalysing basic biochemical reactions in a cells metabolism.…”