NMR Division, RIKEN SPring-8 Center (RSC), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Nucleic Acids Res. 2020 Sep 18;48(16):9346-9360. doi: 10.1093/nar/gkaa598.
Long non-coding RNAs (lncRNAs) are attracting widespread attention for their emerging regulatory, transcriptional, epigenetic, structural and various other functions. Comprehensive transcriptome analysis has revealed that retrotransposon elements (REs) are transcribed and enriched in lncRNA sequences. However, the functions of lncRNAs and the molecular roles of the embedded REs are largely unknown. The secondary and tertiary structures of lncRNAs and their embedded REs are likely to have essential functional roles, but experimental determination and reliable computational prediction of large RNA structures have been extremely challenging. We report here the nuclear magnetic resonance (NMR)-based secondary structure determination of the 167-nt inverted short interspersed nuclear element (SINE) B2, which is embedded in antisense Uchl1 lncRNA and upregulates the translation of sense Uchl1 mRNAs. By using NMR 'fingerprints' as a sensitive probe in the domain survey, we successfully divided the full-length inverted SINE B2 into minimal units made of two discrete structured domains and one dynamic domain without altering their original structures after careful boundary adjustments. This approach allowed us to identify a structured domain in nucleotides 31-119 of the inverted SINE B2. This approach will be applicable to determining the structures of other regulatory lncRNAs.
长非编码 RNA（lncRNA）因其新兴的调控、转录、表观遗传、结构和各种其他功能而受到广泛关注。全面的转录组分析表明，逆转座元件（RE）被转录并富集在 lncRNA 序列中。然而，lncRNA 的功能和嵌入的 RE 的分子作用在很大程度上是未知的。lncRNA 和其嵌入的 RE 的二级和三级结构可能具有重要的功能作用，但对大 RNA 结构的实验测定和可靠的计算预测一直极具挑战性。我们在这里报告了基于核磁共振（NMR）的 167nt 反向短散布核元件（SINE）B2 的二级结构测定，该元件嵌入在反义 Uchl1 lncRNA 中，并上调了正义 Uchl1 mRNA 的翻译。通过使用 NMR“指纹”作为在结构域调查中的敏感探针，我们成功地将全长反向 SINE B2 分成了两个离散的结构域和一个动态域的最小单元，在仔细调整边界后，这些结构域没有改变它们的原始结构。这种方法使我们能够识别出反向 SINE B2 的核苷酸 31-119 中的一个结构域。该方法将适用于确定其他调节性 lncRNA 的结构。
