Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
PLoS One. 2013 Oct 3;8(10):e76194. doi: 10.1371/journal.pone.0076194. eCollection 2013.
Recent findings have revealed the complexity of the transcriptional landscape in mammalian cells. One recently described class of novel transcripts are the Cytoplasmic Intron-sequence Retaining Transcripts (CIRTs), hypothesized to confer post-transcriptional regulatory function. For instance, the neuronal CIRT KCNMA1i16 contributes to the firing properties of hippocampal neurons. Intronic sub-sequence retention within IL1-β mRNA in anucleate platelets has been implicated in activity-dependent splicing and translation. In a recent study, we showed CIRTs harbor functional SINE ID elements which are hypothesized to mediate dendritic localization in neurons. Based on these studies and others, we hypothesized that CIRTs may be present in a broad set of transcripts and comprise novel signals for post-transcriptional regulation. We carried out a transcriptome-wide survey of CIRTs by sequencing micro-dissected subcellular RNA fractions. We sequenced two batches of 150-300 individually dissected dendrites from primary cultures of hippocampal neurons in rat and three batches from mouse hippocampal neurons. After statistical processing to minimize artifacts, we found a broad prevalence of CIRTs in the neurons in both species (44-60% of the expressed transcripts). The sequence patterns, including stereotypical length, biased inclusion of specific introns, and intron-intron junctions, suggested CIRT-specific nuclear processing. Our analysis also suggested that these cytoplasmic intron-sequence retaining transcripts may serve as a primary transcript for ncRNAs. Our results show that retaining intronic sequences is not isolated to a few loci but may be a genome-wide phenomenon for embedding functional signals within certain mRNA. The results hypothesize a novel source of cis-sequences for post-transcriptional regulation. Our results hypothesize two potentially novel splicing pathways: one, within the nucleus for CIRT biogenesis; and another, within the cytoplasm for removing CIRT sequences before translation. We also speculate that release of CIRT sequences prior to translation may form RNA-based signals within the cell potentially comprising a novel class of signaling pathways.
最近的研究结果揭示了哺乳动物细胞中转录景观的复杂性。最近描述的一类新型转录本是细胞质内含子序列保留转录本（CIRTs），据推测它们具有转录后调控功能。例如，神经元 CIRT KCNMA1i16 有助于海马神经元的发射特性。无核血小板中 IL1-β mRNA 内的内含子亚序列保留被牵连到活性依赖性剪接和翻译中。在最近的一项研究中，我们表明 CIRTs 含有功能 SINE ID 元件，据推测这些元件介导神经元中的树突定位。基于这些研究和其他研究，我们假设 CIRTs 可能存在于广泛的转录本中，并构成转录后调控的新型信号。我们通过对微切割亚细胞 RNA 分数进行测序，对 CIRTs 进行了全转录组调查。我们对来自大鼠海马神经元原代培养物的 150-300 个单独切割树突进行了两批测序，对来自小鼠海马神经元的 3 批进行了测序。在进行了最小化人为因素的统计处理后，我们发现两种物种中的神经元中 CIRTs 的广泛存在（44-60%的表达转录本）。序列模式，包括典型长度、特定内含子的偏向性包含和内含子-内含子连接，提示 CIRT 特异性核处理。我们的分析还表明，这些细胞质内含子序列保留转录本可能作为 ncRNA 的初级转录本。我们的结果表明，保留内含子序列不仅局限于少数基因座，而且可能是在某些 mRNA 中嵌入功能信号的全基因组现象。结果假设了一种新的顺式序列来源用于转录后调控。我们的结果假设了两种潜在的新剪接途径：一种是在核内进行 CIRT 生物发生；另一种是在细胞质中进行翻译前去除 CIRT 序列。我们还推测，在翻译前释放 CIRT 序列可能会在细胞内形成基于 RNA 的信号，可能构成一类新的信号通路。
