Large-scale expression analysis of natural antisense transcripts

摘要 最近的研究已经发现了大量的天然反义转录本，它们是 从注释良好的基因的基因组位置转录而来，但来自相反的DNA 思特斯。目前还不清楚大多数反义转录本是有功能的还是 只是转录噪音。我们假设如果反义转录本与 某些生理功能，它们会表现出不同程度的不同表达 组织的类型和图案在进化上往往是保守的。通过适应 商业高密度寡核苷酸微阵列，我们开发了一种性价比高的 一种可以监测哺乳动物所有外显子基因反义表达的方法 基因组。基于这种方法，我们将对反义基因进行系统的剖析 在人、小鼠和大鼠的各种正常组织中表达。加上表达式 对同一样本中的正义转录本进行分析，这将定义为“双链” 外显子水平的表达谱。这些数据将用于比较分析 确定是否存在组织依赖性反义表达的保守模式。 我们将比较同源对中表达模式的相关性 反义转录本与相关的表达模式的排列对。 我们还将确定高表达的一对同源反义 转录本的DNA序列差异较小，以及是否存在同源对 DNA序列差异较小的反义转录本往往具有更高的(1) 它们在不同组织中表达谱的相关性，(2)较小的变化 物种间的表达水平，以及(3)表达广度的变化较小， 与已观察到的蛋白质编码基因相似。这可能会提供 反义转录或转录存在选择性纯化压力的确凿证据 支持“中性漂移”模式。综合数据集还将用于识别 新的反义转录本和组织特异性反义转录本 调查。如此大规模的反义表达分析将进行批判性评估 反义转录是否是一个高度调控的过程。

Summary Recent studies have identified a large number of natural antisense transcripts that are transcribed from the genomic loci of well annotated genes, but from the opposite DNA strands. It is still unclear whether the majority of antisense transcripts are functional or merely transcriptional noise. We hypothesized that if antisense transcripts are related to certain physiological functions, they will exhibit variable levels of expression in different types of tissues and the pattern would tend to be evolutionarily conserved. By adapting commercial high-density oligonucleotide microarrays, we developed a cost-efficient approach that can monitor antisense expression across all exonic loci in mammalian genomes. Based on this approach, we will perform systematic profiling of antisense expression in various normal tissues in human, mouse and rat. Coupled with expression analysis of sense transcripts in the same samples, this will define a "double stranded" expression profile at the exon level. The data will be used for comparative analyses to determine if there are conserved patterns of tissue-dependent antisense expression. We will compare the correlations of expression patterns in orthologous pairs of antisense transcripts with the correlation of the expression pattern of permutated pairs. We will also determine whether highly expressed pairs of orthologous antisense transcripts have smaller DNA sequence divergence and whether orthologous pairs of antisense transcripts with smaller DNA sequence divergence tend to have (1) higher correlation in their expression profiles across various tissues, (2) smaller changes in expression level between species, and (3) smaller change in breadth of expression, similar to what have been observed in protein-coding genes. This could either provide substantial evidence for a selective purifying pressure on antisense transcription or favor a "neutral drift" model. The comprehensive datasets will also be used to identify novel antisense transcripts and tissue-specific antisense transcripts for further investigation. Such large-scale analysis of antisense expression will critically evaluate whether antisense transcription is a highly regulated process.