The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes.
The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes.
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DOI：
10.1186/1471-2164-13-546
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发表时间：
2012-10-10
期刊：
影响因子：
4.4
通讯作者：
McAlear MA
中科院分区：
文献类型：
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作者：
Arnone JT;Robbins-Pianka A;Arace JR;Kass-Gergi S;McAlear MA
细胞的协调生长和发育需要细胞以适当的方式调节大量基因的表达，而细胞必须管理的最复杂和代谢要求最高的途径之一就是核糖体的生物发生。核糖体的生物合成依赖于数百种基因产物的活性，并且它受到广泛的调控，以响应不断变化的细胞条件。我们之前描述了参与酵母核糖体生物发生的基因的一个不寻常的性质；很大一部分基因以紧邻的基因对存在于染色体上。在某些物种中，基因配对的发生率可高达24%，并且在所有可能的串联、发散和收敛方向中都可以发现这种基因配对。除了与核糖体生物发生相关的基因外，我们还研究了酿酒酵母中的共同调控基因集，发现许多这些调控基因，包括那些参与DNA代谢、热休克和对细胞应激源的反应的基因，也显著丰富了相邻的基因对。我们发现，作为一个整体，相邻的基因对比未配对的基因更紧密地共同调控，并且在不同的真菌谱系中最广泛保守的特定基因配对关系与那些表现出最高转录水平的基因相关。最后，我们调查了核糖体相关基因在一组广泛差异的真核生物中的基因位置，并发现在酵母物种之外的相邻基因配对的水平很高。虽然长期以来人们都知道基因组组织和转录调控之间存在联系，但这项研究揭示了将基因从相关的、共同调节的途径组织到紧邻的基因对中的策略是广泛的、进化上保守的和功能上重要的。
Coordinated 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. We 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. While 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.
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影响因子：
9.8
作者：
Brickner DG;Cajigas I;Fondufe-Mittendorf Y;Ahmed S;Lee PC;Widom J;Brickner JH
通讯作者：
Brickner JH
影响因子：
30.8
作者：
GISH, W;STATES, DJ
通讯作者：
STATES, DJ
影响因子：
8
作者：
Chopra, Vivek S.
通讯作者：
Chopra, Vivek S.
影响因子：
2.6
作者：
Flagfeldt, Dongmei Bai;Siewers, Verena;Nielsen, Jens
通讯作者：
Nielsen, Jens
影响因子：
64.8
作者：
通讯作者：
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