Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements.
Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements.
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RNA结合蛋白与重复衍生RNA序列的结合模式揭示了推定的功能性RNA元件。
DOI：
10.1093/nargab/lqab055
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发表时间：
2021-09
影响因子：
4.6
通讯作者：
Hamada M
中科院分区：
文献类型：
--
作者：
Onoguchi M;Zeng C;Matsumaru A;Hamada M
最近的研究表明，嵌入内含子或长链非编码RNA （lncRNAs）中的重复序列是RNA结合蛋白（rbp）的靶标，并参与RNA剪接或转录调控等生物过程。这些发现表明，重复来源的rna作为rbp和功能元件的支架是重要的。然而，重复序列衍生rna的整体功能序列尚不完全清楚。在这里，我们通过分析基于ENCODE eCLIP数据的rbp的结合模式来展示假定的功能重复衍生rna。我们将所有的eCLIP reads映射到重复序列，并观察到在K562和HepG2细胞中，平均有10.75%和7.04%的reads在重复序列中富集（至少是对照组的2倍）。利用这些数据，我们预测了长穿插元件1 （LINE1）序列的正义链和反义链上的功能性RNA元件。此外，我们在其他转座因子（TE）家族的片段上发现了几组新的rbp。其中一些片段显示出特异性和稳定的二级结构，并被发现插入基因或lncrna的内含子中。这些结果表明，重复序列衍生的RNA序列是内源性非编码RNA的功能RNA元件的有力候选。
Recent reports have revealed that repeat-derived sequences embedded in introns or long noncoding RNAs (lncRNAs) are targets of RNA-binding proteins (RBPs) and contribute to biological processes such as RNA splicing or transcriptional regulation. These findings suggest that repeat-derived RNAs are important as scaffolds of RBPs and functional elements. However, the overall functional sequences of the repeat-derived RNAs are not fully understood. Here, we show the putative functional repeat-derived RNAs by analyzing the binding patterns of RBPs based on ENCODE eCLIP data. We mapped all eCLIP reads to repeat sequences and observed that 10.75 % and 7.04 % of reads on average were enriched (at least 2-fold over control) in the repeats in K562 and HepG2 cells, respectively. Using these data, we predicted functional RNA elements on the sense and antisense strands of long interspersed element 1 (LINE1) sequences. Furthermore, we found several new sets of RBPs on fragments derived from other transposable element (TE) families. Some of these fragments show specific and stable secondary structures and are found to be inserted into the introns of genes or lncRNAs. These results suggest that the repeat-derived RNA sequences are strong candidates for the functional RNA elements of endogenous noncoding RNAs.