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RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs
Mobile DNA ( IF 4.9 ) Pub Date : 2021-02-09 , DOI: 10.1186/s13100-021-00233-3
Erica M Briggs 1 , Wilson McKerrow 1, 2 , Paolo Mita 1, 2 , Jef D Boeke 1, 2 , Susan K Logan 1, 3 , David Fenyö 1, 2
Affiliation  

Long INterspersed Element-1 (LINE-1) is an autonomous retroelement able to “copy-and-paste” itself into new loci of the host genome through a process called retrotransposition. The LINE-1 bicistronic mRNA codes for two proteins, ORF1p, a nucleic acid chaperone, and ORF2p, a protein with endonuclease and reverse transcriptase activity. Both proteins bind LINE-1 mRNA in cis and are necessary for retrotransposition. While LINE-1 transcription is usually repressed in most healthy somatic cells through a plethora of mechanisms, ORF1p expression has been observed in nearly 50% of tumors, and new LINE-1 insertions have been documented in a similar fraction of tumors, including prostate cancer. Here, we utilized RNA ImmunoPrecipitation (RIP) and the L1EM analysis software to identify ORF1p bound RNA in prostate cancer cells. We identified LINE-1 loci that were expressed in parental androgen sensitive and androgen independent clonal derivatives. In all androgen independent cells, we found higher levels of LINE-1 RNA, as well as unique expression patterns of LINE-1 loci. Interestingly, we observed that ORF1p bound many non-LINE-1 mRNA in all prostate cancer cell lines evaluated, and polyA RNA, and RNA localized in p-bodies were especially enriched. Furthermore, the expression levels of RNAs identified in our ORF1p RIP correlated with RNAs expressed in LINE-1 positive tumors from The Cancer Genome Atlas (TCGA). Our results show a significant remodeling of LINE-1 loci expression in androgen independent cell lines when compared to parental androgen dependent cells. Additionally, we found that ORF1p bound a significant amount of non-LINE-1 mRNA, and that the enriched ORF1p bound mRNAs are also amplified in LINE-1 expressing TCGA prostate tumors, indicating the biological relevance of our findings to prostate cancer.

中文翻译:

RIP-seq 揭示了 LINE-1 ORF1p 与 p-body 富集 mRNA 的关联

Long INinterpersed Element-1 (LINE-1) 是一种自主的逆转录元件,能够通过称为逆转录转座的过程将自身“复制并粘贴”到宿主基因组的新基因座中。LINE-1 双顺反子 mRNA 编码两种蛋白质:ORF1p(一种核酸伴侣)和 ORF2p(一种具有核酸内切酶和逆转录酶活性的蛋白质)。两种蛋白质都以顺式方式结合 LINE-1 mRNA,并且是逆转录转座所必需的。虽然 LINE-1 转录通常通过多种机制在大多数健康体细胞中受到抑制,但在近 50% 的肿瘤中观察到了 ORF1p 表达,并且在包括前列腺癌在内的类似部分的肿瘤中也发现了新的 LINE-1 插入. 在这里,我们利用 RNA 免疫沉淀 (RIP) 和 L1EM 分析软件来识别前列腺癌细胞中的 ORF1p 结合 RNA。我们确定了在亲本雄激素敏感和雄激素非依赖性克隆衍生物中表达的 LINE-1 基因座。在所有雄激素非依赖性细胞中,我们发现了更高水平的 LINE-1 RNA,以及 LINE-1 基因座的独特表达模式。有趣的是,我们观察到 ORF1p 在所有评估的前列腺癌细胞系中结合了许多非 LINE-1 mRNA,并且 polyA RNA 和定位于 p 体中的 RNA 特别富集。此外,在我们的 ORF1p RIP 中鉴定的 RNA 的表达水平与癌症基因组图谱 (TCGA) 的 LINE-1 阳性肿瘤中表达的 RNA 相关。我们的结果显示,与亲代雄激素依赖性细胞相比,雄激素非依赖性细胞系中 LINE-1 基因座表达的显着重塑。此外,我们发现 ORF1p 结合了大量的非 LINE-1 mRNA,
更新日期:2021-02-09
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