Understanding the targeting and spreading patterns of long non-coding RNAs (lncRNAs) on chromatin requires a technique that can detect both high-intensity binding sites and reveal genome-wide changes in spreading patterns with high precision and confidence. Here we determine lncRNA localization using biotinylated locked nucleic acid (LNA)-containing oligonucleotides with toehold architecture capable of hybridizing to target RNA through strand-exchange reaction. During hybridization, a protecting strand competitively displaces contaminating species, leading to highly specific RNA capture of individual RNAs. Analysis of Drosophila roX2 lncRNA using this approach revealed that heat shock, unlike the unfolded protein response, leads to reduced spreading of roX2 on the X chromosome, but surprisingly also to relocalization to sites on autosomes. Our results demonstrate that this improved hybridization capture approach can reveal previously uncharacterized changes in the targeting and spreading of lncRNAs on chromatin.

了解染色质上长非编码 RNA (lncRNA) 的靶向和扩散模式需要一种能够检测高强度结合位点并以高精度和可信度揭示扩散模式的全基因组变化的技术。在这里，我们使用含有生物素化锁定核酸 (LNA) 的寡核苷酸确定 lncRNA 定位，该寡核苷酸具有能够通过链交换反应与靶 RNA 杂交的立足点结构。在杂交过程中，保护链竞争性地取代污染物种，导致单个 RNA 的高度特异性 RNA 捕获。果蝇分析使用这种方法的 roX2 lncRNA 表明，与未折叠的蛋白质反应不同，热休克会导致 roX2 在 X 染色体上的扩散减少，但令人惊讶的是，它还会重新定位到常染色体上的位点。我们的研究结果表明，这种改进的杂交捕获方法可以揭示 lncRNA 在染色质上靶向和扩散的先前未表征的变化。