Whole transcriptome profiling of rat pineal glands and retinas collected throughout a 24-hour cycle

The rat pineal transcriptome is highly dynamic, with many hundreds of transcripts changing more than two-fold on a 24-hr basis, as revealed earlier using Affymetrix GeneChip analysis. The retina is evolutionally related to the pineal gland so these two tissues share many gene expression patterns. This study more completely characterizes the temporally dynamic transcriptomes of these tissues using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, and coding transcripts not represented on the Affymetrix chips. We also identified transcripts that were selectively expressed in the pineal gland relative to other tissues by comparing pineal samples to a sample of pooled non-pineal tissues.此前通过Affymetrix基因芯片（Affymetrix GeneChip）分析已证实，大鼠松果体转录组（transcriptome）具有高度动态性，数百个转录本的表达水平在24小时周期内的变化幅度超过两倍。视网膜在进化起源上与松果体（pineal gland）密切相关，因此这两种组织共享大量基因表达模式。本研究采用RNA-Seq技术，对这两种组织的时序动态转录组进行了更为全面的表征，以捕获可变剪接（alternative splicing）、新外显子（exon）、未注释mRNA、非编码RNA（non-coding RNA）以及Affymetrix基因芯片未覆盖的编码转录本相关信息。此外，本研究通过将松果体样本与混合的非松果体组织样本进行比对，鉴定出了在松果体中相较于其他组织呈现选择性表达的转录本。