Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, 115 27, Athens, Greece.
BMC Genomics. 2011 Oct 17;12:511. doi: 10.1186/1471-2164-12-511.
The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest.
We present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of isochores' base composition on their expression activity. Our analyses also cover the relations between the genes' expression activity and their localization in the isochore families.
This study is the first where next-generation sequencing data are used to associate the effects of both genomic and genic compositional properties to their corresponding expression activity. Our findings confirm previous results, and further support the existence of a relationship between isochores and gene expression. This relationship corroborates that isochores are primarily a product of evolutionary adaptation rather than a simple by-product of neutral evolutionary processes.
全基因组测序和转录组技术的应用，增加了对各种组织、条件和物种表达谱的研究。在这项研究中，我们使用三种不同组织（脑、肝和肌肉）的 RNA-seq 数据，研究碱基组成如何影响哺乳动物基因表达，这是一个具有重要实际和进化意义的问题。
我们展示了三种不同组织的小鼠同型区（碱基组成相当均匀的 DNA 片段）的转录组图谱，以及同型区碱基组成对其表达活性的影响。我们的分析还涵盖了基因表达活性与其在同型区家族中的定位之间的关系。
这是首次使用下一代测序数据将基因组和基因组成特性的影响与相应的表达活性联系起来的研究。我们的发现证实了之前的结果，并进一步支持了同型区和基因表达之间存在关系。这种关系证实了同型区主要是进化适应的产物，而不是中性进化过程的简单副产品。
