CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India.
Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India.
Nucleic Acids Res. 2022 Jan 11;50(1):378-396. doi: 10.1093/nar/gkab1066.
MALAT1, an abundant lncRNA specifically localized to nuclear speckles, regulates alternative-splicing (AS). The molecular basis of its role in AS remains poorly understood. Here, we report three conserved, thermodynamically stable, parallel RNA-G-quadruplexes (rG4s) present in the 3' region of MALAT1 which regulates this function. Using rG4 domain-specific RNA-pull-down followed by mass-spectrometry, RNA-immuno-precipitation, and imaging, we demonstrate the rG4 dependent localization of Nucleolin (NCL) and Nucleophosmin (NPM) to nuclear speckles. Specific G-to-A mutations that abolish rG4 structures, result in the localization loss of both the proteins from speckles. Functionally, disruption of rG4 in MALAT1 phenocopies NCL knockdown resulting in altered pre-mRNA splicing of endogenous genes. These results reveal a central role of rG4s within the 3' region of MALAT1 orchestrating AS.
MALAT1 是一种丰富的长链非编码 RNA，特异性定位于核斑，调节选择性剪接（AS）。其在 AS 中的作用的分子基础仍知之甚少。在这里，我们报告了 MALAT1 3' 区域中存在的三个保守的、热力学稳定的平行 RNA-G-四链体（rG4），它们调节这一功能。使用 rG4 结构域特异性 RNA 下拉结合质谱分析、RNA 免疫沉淀和成像，我们证明了 rG4 依赖于核斑中核仁蛋白（NCL）和核磷蛋白（NPM）的定位。特异性的 G-A 突变会破坏 rG4 结构，导致这两种蛋白质从斑中的定位丢失。功能上，MALAT1 中 rG4 的破坏模拟了 NCL 敲低，导致内源性基因的前体 mRNA 剪接发生改变。这些结果揭示了 rG4 在 MALAT1 的 3' 区域内协调 AS 的核心作用。
