使用 RNA 纯化染色质免疫沉淀技术（ChIRP）进行全基因组范围的长非编码 RNA 占据研究。

Study of Genome-Wide Occupancy of Long Non-Coding RNAs Using Chromatin Isolation by RNA Purification (ChIRP).

机构信息

Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France.

出版信息

Methods Mol Biol. 2021;2300:107-117. doi: 10.1007/978-1-0716-1386-3_11.

Abstract

Long noncoding RNAs (lncRNAs) have recently emerged as masters of gene expression regulation by exerting their functions in all cell compartments through a wide repertoire of mechanisms. A high portion of lncRNAs are robustly enriched in the chromatin fraction suggesting a broad regulatory role in the nuclear compartment. Despite the advances in this field, the interaction between lncRNAs and the chromatin is still poorly understood. This led to the emergence of numerous hybridization capture assays such as the Chromatin Isolation by RNA Purification (ChIRP) which revealed at high resolution the genomic binding sites of several nuclear lncRNAs. In this chapter, we describe the ChIRP protocol that was successfully applied to the lncRNA ANRIL. We also provide a user-friendly bioinformatic pipeline for ChIRP-seq data analysis.

摘要

长链非编码 RNA（lncRNA）通过广泛的机制在所有细胞区室中发挥作用，最近成为基因表达调控的大师。大量 lncRNA 强烈富集在染色质部分，这表明它们在核区室中有广泛的调节作用。尽管在这一领域取得了进展，但 lncRNA 与染色质之间的相互作用仍知之甚少。这导致了许多杂交捕获检测方法的出现，如 RNA 纯化的染色质分离（ChIRP），该方法以高分辨率揭示了几种核 lncRNA 的基因组结合位点。在本章中，我们描述了成功应用于 lncRNA ANRIL 的 ChIRP 方案。我们还提供了一个用户友好的 ChIRP-seq 数据分析生物信息学管道。