Carnevali Davide, Conti Anastasia, Pellegrini Matteo, Dieci Giorgio
Department of Life Sciences, University of Parma, Parma, Italy.
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095 723, USA.
DNA Res. 2017 Feb 1;24(1):59-69. doi: 10.1093/dnares/dsw048.
With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution. While the majority of Pol III-transcribed MIR elements are cell-specific, we discovered a small set of ubiquitously transcribed MIRs mapping within Pol II-transcribed genes in antisense orientation that could influence the expression of the overlapping gene. We also identified novel Pol III-transcribed ncRNAs, deriving from transcription of annotated MIR fragments flanked by unique MIR-unrelated sequences, and confirmed the role of Pol III-specific internal promoter elements in MIR transcription. Besides demonstrating widespread transcription at these retrotranspositionally inactive elements in human cells, the ability to profile MIR expression at single-locus resolution will facilitate their study in different cell types and states including pathological alterations.
哺乳动物广泛散布重复序列（MIRs）是短散在核元件（SINEs）的一个亚组，拷贝数超过50万，占人类基因组的约2.5%，是RNA聚合酶（Pol）III转录机制最丰富的潜在靶标家族之一。由于MIR元件在约1.3亿年前就停止扩增，此前的研究主要集中在它们对基因组的影响上，而它们的表达问题尚未得到广泛探讨。我们将一个专门的生物信息学流程应用于7种人类细胞系的ENCODE RNA测序数据集，首次能够在单基因座分辨率下定义由Pol III驱动的MIR转录组。虽然大多数由Pol III转录的MIR元件具有细胞特异性，但我们发现一小部分普遍转录的MIRs以反义方向映射在由Pol II转录的基因内，可能会影响重叠基因的表达。我们还鉴定了源自带有独特的与MIR无关序列侧翼的注释MIR片段转录的新型Pol III转录的非编码RNA，并证实了Pol III特异性内部启动子元件在MIR转录中的作用。除了证明这些在人类细胞中逆转录不活跃的元件存在广泛转录外，在单基因座分辨率下分析MIR表达的能力将有助于在包括病理改变在内的不同细胞类型和状态下对它们进行研究。
