Large-scale expression analysis of natural antisense transcripts

描述（由申请人提供）：最近的研究已经鉴定了大量的天然反义转录物，其从充分注释的基因的基因组位点转录，但从相反的DNA链转录。目前还不清楚大多数反义转录物是功能性的还是仅仅是转录噪音。我们假设，如果反义转录本与某些生理功能相关，它们将在不同类型的组织中表现出不同的表达水平，并且模式将倾向于进化保守。通过调整商业高密度寡核苷酸微阵列，我们开发了一种具有成本效益的方法，可以监测哺乳动物基因组中所有外显子位点的反义表达。基于这种方法，我们将在人类、小鼠和大鼠的各种正常组织中进行反义表达的系统分析。结合相同样品中正义转录物的表达分析，这将在外显子水平上定义“双链”表达谱。这些数据将用于比较分析，以确定是否存在组织依赖性反义表达的保守模式。我们将比较反义转录物的正向排列对中表达模式的相关性与置换对中表达模式的相关性。我们还将确定高表达的正向反义转录物对是否具有较小的DNA序列差异，以及具有较小DNA序列差异的正向反义转录物对是否倾向于具有（1）它们在各种组织中的表达谱的较高相关性，（2）物种之间表达水平的较小变化，以及（3）表达宽度的较小变化，类似于在蛋白质编码基因中观察到的情况。这可以为反义转录的选择性纯化压力提供实质性证据，或者有利于“中性漂移”模型。综合数据集还将用于鉴定新的反义转录物和组织特异性反义转录物以供进一步研究。这种大规模的反义表达分析将严格评估反义转录是否是一个高度调控的过程。 公共卫生相关性：目前的建议代表了一种尝试，以获得全面的数据表达的某种类型的新基因，可以干扰普通的蛋白质编码基因。我们将研究它们在人、小鼠和大鼠的各种正常组织中的表达模式，以便深入了解其潜在的生理功能。

DESCRIPTION (provided by applicant): 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. PUBLIC HEALTH RELEVANCE: The present proposal represents an attempt to obtain comprehensive data on the expression of a certain type of novel genes that could interfere with ordinary protein- coding genes. We will study their expression patterns in various normal tissues of human, mouse and rat so that we could gain insight into their potential physiological function.