MTA1 interacts with primary RNAs to regulate expression and AS by protein dependent manner [RNA]. Homo sapiens

MTA1 is known as its metastatic and invasive function in cancers and the core member of NuRD complex. But the mechanism of regulating gene expression by MTA1 is limited. Besides the interaction with chromosome, MTA1 may play important role at the transcriptional level. We performed co- immunoprecipitation (co-IP) on HCT116 cells and found numerous RNA binding proteins (RBPs), which functions as spliceosome and RNA transport. We then validated that MTA1 interacts with RBPs by RNA dependent manner. By performing the CLIP-seq of MTA1, ten thousands of peaks and thousands of genes were emerged. More detailed analysis and high level of intronic peaks reveal MTA1 prefers to bind pre-mRNAs and regulate the alternative splicing progression by binding the splice site. High overlapping between MTA1 binding and MTA1 regulated genes highlights the direct regulation of RNAs by MTA1 coupling with RBPs. LTK is one of the obvious examples regulated by MTA1. Together, these findings uncover a novel mechanism of MTA1 regulation in transcriptional level as RBPs, and suggest MTA1 regulates pre-mRNA splicing with other RBPs. Overall design: RNA-seq experiments performed on siMTA1 and WT samples from HCT116 cells. Each was performed with three replicates.

MTA1在癌症中以其转移侵袭功能为人所知，同时是NuRD复合物（NuRD complex）的核心成员。但目前关于MTA1调控基因表达的分子机制研究仍较为有限。除了与染色体的相互作用外，MTA1或许在转录层面发挥重要调控功能。我们在HCT116细胞中开展了免疫共沉淀（co-immunoprecipitation，co-IP）实验，鉴定得到大量功能涉及剪接体组装与RNA转运的RNA结合蛋白（RNA binding proteins，RBPs）。随后我们验证了MTA1与RBPs的相互作用依赖于RNA分子。通过开展MTA1的紫外交联免疫沉淀测序（cross-linking immunoprecipitation sequencing，CLIP-seq）实验，我们获得了数以万计的结合峰与数千个靶基因。进一步的详细分析以及内含子区域富集的结合峰提示，MTA1倾向于结合前体mRNA（pre-mRNA），并通过结合剪接位点调控可变剪接进程。MTA1结合靶基因与MTA1调控靶基因之间存在高度重叠，这表明MTA1可通过与RBPs协同作用直接调控RNA分子。LTK便是MTA1调控的典型靶基因之一。综上，本研究揭示了MTA1作为RNA结合蛋白在转录层面发挥调控功能的全新机制，并表明MTA1可与其他RBPs协同调控前体mRNA的剪接过程。实验整体设计：在HCT116细胞的siMTA1敲低组与野生型（wild type，WT）样本中开展RNA测序（RNA sequencing，RNA-seq）实验，每组均设置3次生物学重复。