Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system

Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.
BMC Genomics (Impact Factor: 3.99). 02/2007; 8(1):352. DOI: 10.1186/1471-2164-8-352
Source: PubMed


Adjacent gene pairs in the yeast genome have a tendency to express concurrently. Sharing of regulatory elements within the intergenic region of those adjacent gene pairs was often considered the major mechanism responsible for such co-expression. However, it is still in debate to what extent that common transcription factors (TFs) contribute to the co-expression of adjacent genes. In order to resolve the evolutionary aspect of this issue, we investigated the conservation of adjacent pairs in five yeast species. By using the information for TF binding sites in promoter regions available from the MYBS database, the ratios of TF-sharing pairs among all the adjacent pairs in yeast genomes were analyzed. The levels of co-expression in different adjacent patterns were also compared.
Our analyses showed that the proportion of adjacent pairs conserved in five yeast species is relatively low compared to that in the mammalian lineage. The proportion was also low for adjacent gene pairs with shared TFs. Particularly, the statistical analysis suggested that co-expression of adjacent gene pairs was not noticeably associated with the sharing of TFs in these pairs. We further proposed a case of the PAC (polymerase A and C) and RRPE (rRNA processing element) motifs which co-regulate divergent/bidirectional pairs, and found that the shared TFs were not significantly relevant to co-expression of divergent promoters among adjacent genes.
Our findings suggested that the commonly shared cis-regulatory system does not solely contribute to the co-expression of adjacent gene pairs in yeast genome. Therefore we believe that during evolution yeasts have developed a sophisticated regulatory system that integrates both TF-based and non-TF based mechanisms(s) for concurrent regulation of neighboring genes in response to various environmental changes.

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Available from: Mei-Yeh J Lu, Oct 07, 2015
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    • "Evidence shows that physical proximity of gene localization in the genome is strongly associated with expression of genes (Chiaromonte et al., 2003). Genes localized close to each other generally show co-regulated expression (Fukuoka et al., 2004; Tsai et al., 2007). In the MOYO-S/MOYO-R strains of A. aegypti , genes that respond to dengue infection are expressed in highly modular manner and many of these expression modules are enriched with specific biochemical and signaling pathways (Behura et al., 2011). "
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    ABSTRACT: Dengue virus infection causes significant morbidity and mortality in humans world-wide. The Aedes aegypti mosquito is the major vector that spreads dengue virus to humans. Interaction between dengue viruses and A. aegypti is a multi-factorial phenomena that is determined by both virus and mosquito genotypes. Although, studies have suggested significant association of mosquito vectorial capacity with population variation of dengue virus, specifications of the vector factors that may influence vector-virus compatibility are very limited in the literature. Recently, we have shown that a large number of genes are differentially expressed between MOYO-S (susceptible) and MOYO-R (refractory) A. aegypti strains upon infection with dengue virus (JAM-1409 genotype). In the current study, we show that specific intrinsic features of A. aegypti genes are significantly associated with 'responsiveness' of mosquito genes to dengue infection. Binomial logistic regression analysis further reveals differential marginal effects of these features on gene responsiveness of mosquitoes to the viral infection. Thus, our result shows that intrinsic features of genes significantly affect differential expression of A. aegypti genes to dengue infection. The information will benefit further investigations on evolution of genes among natural populations of A. aegypti conferring differential susceptibility to dengue virus.
    Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 05/2012; 12(7):1413-8. DOI:10.1016/j.meegid.2012.04.027 · 3.02 Impact Factor
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    • "Although co-expressed divergent pairs are more likely to fall into the shared category under our method, some (1–15%) coexpressed divergent pairs belong to the not-shared category. According to our previous study, the proportions of adjacent genes that share similar expression patterns do not differ significantly, regardless of whether they are divergent, convergent, or tandem [16]. In that study, we also found that the divergent relationship was not appreciably favored by selection, and the co-expression of divergent gene pairs could not be attributed simply to a shared regulatory system. "
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    ABSTRACT: In budding yeast, approximately a quarter of adjacent genes are divergently transcribed (divergent gene pairs). Whether genes in a divergent pair share the same regulatory system is still unknown. By examining transcription factor (TF) knockout experiments, we found that most TF knockout only altered the expression of one gene in a divergent pair. This prompted us to conduct a comprehensive analysis in silico to estimate how many divergent pairs are regulated by common sets of TFs (cis-regulatory modules, CRMs) using TF binding sites and expression data. Analyses of ten expression datasets show that only a limited number of divergent gene pairs share CRMs in any single dataset. However, around half of divergent pairs do share a regulatory system in at least one dataset. Our analysis suggests that genes in a divergent pair tend to be co-regulated in at least one condition; however, in most conditions, they may not be co-regulated.
    Genomics 12/2010; 96(6):352-61. DOI:10.1016/j.ygeno.2010.08.008 · 2.28 Impact Factor
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    • "In fact, sharing regulatory elements encounters the same problem. Shared TFs were not significantly relevant to the coexpression of divergent pairs, although divergent pairs have a greater chance to share TFs [13]. We speculate that there might be some other mechanism that balances the effect of co-modification or sharing TFs on neighboring genes with different directions. "
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    ABSTRACT: Neighboring gene pairs in the genome of Saccharomyces cerevisiae have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important mechanism responsible for such coexpression. However, the extent of the contribution of histone modifications to the coexpression of neighboring genes is unclear. We investigated the similarity of histone modification between neighboring genes using autocorrelation analysis and composite profiles. Our analysis showed that neighboring genes had similar levels or changes of histone modifications, especially those transcribed in the same direction. The similarities, however, were restricted to 1 or 2 neighboring genes. Moreover, the expression of a gene was significantly correlated with histone modification of its neighboring gene(s), but this was limited to only 1 or 2 neighbors. Using a hidden Markov model (HMM), we found more than 2000 chromatin domains with similar acetylation changes as the cultures changed and a considerable number of these domains covered 2-4 genes. Gene pairs within domains exhibited a higher level of coexpression than random pairs and shared similar functions. The results of this study suggest that similar histone modifications occur within only a small local chromatin region in yeast. The modifications generally have an effect on coexpression with only 1 or 2 neighboring genes. Some blocking mechanism(s) might strictly restrain the distribution of histone modifications in yeast.
    BMC Genomics 10/2010; 11(1):550. DOI:10.1186/1471-2164-11-550 · 3.99 Impact Factor
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