KCNQOT1 ChIRP seq and perturbation epigentic profiles [Mouse eCLIP]

To study the molecular function of lncRNA KCNQOT1, we performed ChIRP-seq HEK293T cells, and we knocked it down in NIH3T3 and HEK293T cells, and created knockout of the repeat-rich and non-repeat regions of KCNQOT1 separately in HEK293T cells, then performed H3K9me3 ChIP-seq, DNA methylation MeDIP-seq and RNA-seq in the perturbed and control wild type cells. Overall design: HP1 alpha associated lncRNAs were analyzed by eCLIP-seq in NIH3T3 cells.

为研究长链非编码RNA（long non-coding RNA, lncRNA）KCNQOT1的分子功能，我们在HEK293T细胞中开展了RNA纯化染色质分离测序（ChIRP-seq）实验；分别在NIH3T3与HEK293T细胞中对该lncRNA进行基因敲低，并在HEK293T细胞中单独构建KCNQOT1富含重复序列区域与非重复序列区域的基因敲除模型；随后在扰动组与野生型对照组细胞中进行组蛋白H3赖氨酸9三甲基化染色质免疫沉淀测序（H3K9me3 ChIP-seq）、甲基化DNA免疫沉淀测序（MeDIP-seq）及RNA测序（RNA-seq）实验。整体实验设计：在NIH3T3细胞中通过增强型交联免疫沉淀测序（eCLIP-seq）分析与异染色质蛋白1α（HP1 alpha）结合的lncRNAs。