The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes

BMC Genomics

Research Article

James T Arnone¹  Jeffrey R Arace¹  Michael A McAlear¹  Sara Kass-Gergi¹  Adam Robbins-Pianka² 

[1] Department of Molecular Biology and Biochemistry, Wesleyan University, 06459, Middletown, CT, USA;Department of Molecular Biology and Biochemistry, Wesleyan University, 06459, Middletown, CT, USA;Department of Computer Science, University of Colorado Boulder, 80309-0430, Boulder, CO, USA;

关键词: Gene Pair;    Regulon;    Ribosome Biogenesis;    Adjacent Gene;    Adjacent Pair;   

DOI  :  10.1186/1471-2164-13-546

 received in 2012-02-27, accepted in 2012-10-03,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundCoordinated cell growth and development requires that cells regulate the expression of large sets of genes in an appropriate manner, and one of the most complex and metabolically demanding pathways that cells must manage is that of ribosome biogenesis. Ribosome biosynthesis depends upon the activity of hundreds of gene products, and it is subject to extensive regulation in response to changing cellular conditions. We previously described an unusual property of the genes that are involved in ribosome biogenesis in yeast; a significant fraction of the genes exist on the chromosomes as immediately adjacent gene pairs. The incidence of gene pairing can be as high as 24% in some species, and the gene pairs are found in all of the possible tandem, divergent, and convergent orientations.ResultsWe investigated co-regulated gene sets in S. cerevisiae beyond those related to ribosome biogenesis, and found that a number of these regulons, including those involved in DNA metabolism, heat shock, and the response to cellular stressors were also significantly enriched for adjacent gene pairs. We found that as a whole, adjacent gene pairs were more tightly co-regulated than unpaired genes, and that the specific gene pairing relationships that were most widely conserved across divergent fungal lineages were correlated with those genes that exhibited the highest levels of transcription. Finally, we investigated the gene positions of ribosome related genes across a widely divergent set of eukaryotes, and found a significant level of adjacent gene pairing well beyond yeast species.ConclusionWhile it has long been understood that there are connections between genomic organization and transcriptional regulation, this study reveals that the strategy of organizing genes from related, co-regulated pathways into pairs of immediately adjacent genes is widespread, evolutionarily conserved, and functionally significant.

【 授权许可】

Unknown   
© Arnone et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.