Intergenic and genic sequence lengths have opposite relationships with respect to gene expression.
Intergenic and genic sequence lengths have opposite relationships with respect to gene expression.
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DOI：
10.1371/journal.pone.0003670
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发表时间：
2008
期刊：
影响因子：
3.7
通讯作者：
Benfey PN
中科院分区：
文献类型：
--
作者：
Colinas J;Schmidler SC;Bohrer G;Iordanov B;Benfey PN
真核生物基因组主要由非编码DNA组成，其作用仍然知之甚少。对几种生物的研究表明，基因的基因间序列和基因序列的长度与其相应的mRNA转录本的表达之间存在相关性。一些研究发现基因间序列长度与组织间表达多样性之间存在正相关关系，并得出结论，受更大调控的基因需要更多的基因间序列调控信息。其他报告发现表达水平和基因长度之间存在负相关关系，解释为高表达基因存在选择压力以保持较小。然而，基因序列长度和表达多样性之间的相关性，相反，观察到的基因间序列，也有报道，迄今为止，没有可测试的解释，这一观察。为了阐明这些不同的，有时相互矛盾的结果，我们进行了一个彻底的研究序列长度和基因表达之间的关系，使用细胞类型（组织）特定的微阵列数据在拟南芥。我们测量了组织间的中值基因表达（表达水平）、组织间的表达变异性（表达模式均匀性）和重复间的表达变异性（表达噪音）。我们发现，基因间（上游和下游）和基因（编码和非编码）序列的表达，无论是组织变异性，中位数，或表达噪音一般相反的关系。为了解释这些结果，我们提出了一个模型，在该模型中，基因间序列和基因序列的长度有相反的影响的能力的转录区域的基因的表观遗传调控的差异表达。这些发现可能有助于阐明非编码序列对基因表达的作用和影响。
Eukaryotic genomes are mostly composed of noncoding DNA whose role is still poorly understood. Studies in several organisms have shown correlations between the length of the intergenic and genic sequences of a gene and the expression of its corresponding mRNA transcript. Some studies have found a positive relationship between intergenic sequence length and expression diversity between tissues, and concluded that genes under greater regulatory control require more regulatory information in their intergenic sequences. Other reports found a negative relationship between expression level and gene length and the interpretation was that there is selection pressure for highly expressed genes to remain small. However, a correlation between gene sequence length and expression diversity, opposite to that observed for intergenic sequences, has also been reported, and to date there is no testable explanation for this observation. To shed light on these varied and sometimes conflicting results, we performed a thorough study of the relationships between sequence length and gene expression using cell-type (tissue) specific microarray data in Arabidopsis thaliana. We measured median gene expression across tissues (expression level), expression variability between tissues (expression pattern uniformity), and expression variability between replicates (expression noise). We found that intergenic (upstream and downstream) and genic (coding and noncoding) sequences have generally opposite relationships with respect to expression, whether it is tissue variability, median, or expression noise. To explain these results we propose a model, in which the lengths of the intergenic and genic sequences have opposite effects on the ability of the transcribed region of the gene to be epigenetically regulated for differential expression. These findings could shed light on the role and influence of noncoding sequences on gene expression.
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