Coordinated regulation by lncRNAs results in tight lncRNA–target couplings [ChIRP-Seq]. Coordinated regulation by lncRNAs results in tight lncRNA–target couplings [ChIRP-Seq]

The determination of long non-coding RNA (lncRNA) function is a major challenge in RNA biology with applications to basic, translational, and medical research. Our efforts to improve the accuracy of lncRNA-target inference identified lncRNAs that coordinately regulate both the transcriptional and post-transcriptional processing of their targets. Namely, these lncRNAs may regulate the transcription of their target and chaperone the resulting message until its translation, leading to tightly coupled lncRNA and target abundance. Our analysis suggested that hundreds of cancer genes are coordinately and tightly regulated by lncRNAs and that this unexplored regulatory paradigm may propagate the effects of non-coding alterations to effectively dysregulate gene expression programs. As a proof-of-principle we studied the regulation of DICER1—a cancer gene that controls microRNA biogenesis—by the lncRNA ZFAS1, showing that ZFAS1 activates DICER1 transcription and blocks its post-transcriptional repression to phenomimic and regulate DICER1 and its target microRNAs. Overall design: To identify ZFAS1-bound DNA regions (RNA-DNA interactions), we performed Chromatin Isolation by RNA Purification followed by DNA sequencing (ChIRP-Seq) in two cell lines, ECC-1 and NCI-H460. For each cell line, we generated two datasets: an input control and a ZFAS1 pulldown. We then identified DNA regions enriched in the ZFAS1 pulldown relative to the input control. These enriched regions were processed and output as standard narrowPeak format files.

长链非编码RNA（long non-coding RNA，lncRNA）的功能解析是RNA生物学领域的重大挑战，其研究成果可应用于基础研究、转化研究与医学研究。我们为提升lncRNA靶标推断的准确性开展相关研究，最终发现了一类可协同调控靶标转录与转录后加工过程的lncRNA。具体而言，这类lncRNA可调控靶标基因的转录，并作为分子伴侣辅助其转录生成的mRNA直至翻译阶段，从而实现lncRNA与其靶标丰度的紧密耦联。我们的分析显示，数百个癌症基因均受lncRNA的协同精准调控，且这一尚未被探索的调控范式可传递非编码序列变异的效应，进而有效紊乱基因表达程序。作为原理验证，我们针对长链非编码RNA ZFAS1调控DICER1的过程展开研究——DICER1是一个调控微RNA（microRNA，miRNA）生物生成的癌症基因——结果证实ZFAS1可激活DICER1的转录，并阻断其转录后抑制过程，从而模拟并调控DICER1及其靶标微RNA的相关表型。实验整体设计：为鉴定ZFAS1结合的DNA区域（RNA-DNA相互作用），我们在ECC-1与NCI-H460两种细胞系中开展了RNA纯化染色质分离测序（Chromatin Isolation by RNA Purification followed by DNA sequencing，ChIRP-Seq）实验。针对每种细胞系，我们均设置两组数据集：输入对照组与ZFAS1下拉富集组。随后我们鉴定出相较于输入对照组，在ZFAS1下拉富集组中显著富集的DNA区域，并将这些富集区域处理为标准narrowPeak格式文件输出。