Carlevaro-Fita Joana, Rahim Anisa, Guigó Roderic, Vardy Leah A, Johnson Rory
Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain.
A*STAR Institute of Medical Biology, Singapore 138648, Singapore.
RNA. 2016 Jun;22(6):867-82. doi: 10.1261/rna.053561.115. Epub 2016 Apr 18.
Recent footprinting studies have made the surprising observation that long noncoding RNAs (lncRNAs) physically interact with ribosomes. However, these findings remain controversial, and the overall proportion of cytoplasmic lncRNAs involved is unknown. Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm. The majority of these (70%) have >50% of their cytoplasmic copies associated with polysomal fractions. These interactions are lost upon disruption of ribosomes by puromycin. Polysomal lncRNAs are distinguished by a number of 5' mRNA-like features, including capping and 5'UTR length. On the other hand, nonpolysomal "free cytoplasmic" lncRNAs have more conserved promoters and a wider range of expression across cell types. Exons of polysomal lncRNAs are depleted of endogenous retroviral insertions, suggesting a role for repetitive elements in lncRNA localization. Finally, we show that blocking of ribosomal elongation results in stabilization of many associated lncRNAs. Together these findings suggest that the ribosome is the default destination for the majority of cytoplasmic long noncoding RNAs and may play a role in their degradation.
最近的足迹研究有一个惊人的发现，即长链非编码RNA（lncRNA）能与核糖体发生物理相互作用。然而，这些发现仍存在争议，且涉及的细胞质lncRNA的总体比例尚不清楚。在这里，我们使用多聚核糖体分析结合掺入标准化微阵列分析，对人类细胞系中经过严格筛选的lncRNA的细胞质和核糖体相关群体进行了全面、绝对的估计。在细胞质中检测到54%的已表达lncRNA。其中大多数（70%）的细胞质拷贝有超过50%与多聚核糖体部分相关联。用嘌呤霉素破坏核糖体后，这些相互作用消失。多聚核糖体lncRNA具有许多5'端类似mRNA的特征，包括加帽和5'非翻译区长度。另一方面，非多聚核糖体的“游离细胞质”lncRNA具有更保守的启动子，并且在不同细胞类型中的表达范围更广。多聚核糖体lncRNA的外显子中内源性逆转录病毒插入较少，这表明重复元件在lncRNA定位中起作用。最后，我们表明核糖体延伸的阻断会导致许多相关lncRNA的稳定。这些发现共同表明，核糖体是大多数细胞质长链非编码RNA的默认归宿，并且可能在它们的降解中起作用。
