Departmet of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, A-1030, Austria.
Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, A-1030, Austria.
Nucleic Acids Res. 2022 Sep 23;50(17):9984-9999. doi: 10.1093/nar/gkac756.
Autogenous interactions between mRNAs and the proteins they encode are implicated in cellular feedback-loop regulation, but their extent and mechanistic foundation are unclear. It was recently hypothesized that such interactions may be common, reflecting the role of intrinsic nucleobase-amino acid affinities in shaping the genetic code's structure. Here we analyze a comprehensive set of CLIP-seq experiments involving multiple protocols and report on widespread autogenous interactions across different organisms. Specifically, 230 of 341 (67%) studied RNA-binding proteins (RBPs) interact with their own mRNAs, with a heavy enrichment among high-confidence hits and a preference for coding sequence binding. We account for different confounding variables, including physical (overexpression and proximity during translation), methodological (difference in CLIP protocols, peak callers and cell types) and statistical (treatment of null backgrounds). In particular, we demonstrate a high statistical significance of autogenous interactions by sampling null distributions of fixed-margin interaction matrices. Furthermore, we study the dependence of autogenous binding on the presence of RNA-binding motifs and structured domains in RBPs. Finally, we show that intrinsic nucleobase-amino acid affinities favor co-aligned binding between mRNA coding regions and the proteins they encode. Our results suggest a central role for autogenous interactions in RBP regulation and support the possibility of a fundamental connection between coding and binding.
mRNA 与其编码蛋白之间的自发相互作用与细胞内反馈环调节有关，但它们的程度和机制基础尚不清楚。最近有人假设，这种相互作用可能很常见，反映了内在的核碱基-氨基酸亲和力在塑造遗传密码结构中的作用。在这里，我们分析了一套涉及多种方案的全面 CLIP-seq 实验，并报告了在不同生物体中广泛存在的自发相互作用。具体来说，在 341 个研究的 RNA 结合蛋白 (RBP) 中有 230 个（67%）与自身的 mRNA 相互作用，其中高可信度的命中富集，并且对编码序列的结合有偏好。我们考虑了不同的混杂变量，包括物理因素（过表达和翻译过程中的接近程度）、方法学因素（CLIP 方案、峰调用者和细胞类型的差异）和统计学因素（对空背景的处理）。特别是，我们通过对固定边缘相互作用矩阵的空分布进行抽样，证明了自发相互作用具有很高的统计学意义。此外，我们研究了 RBP 中自发结合与 RNA 结合基序和结构域存在的依赖性。最后，我们表明，内在的核碱基-氨基酸亲和力有利于 mRNA 编码区与编码它们的蛋白质之间的共定位结合。我们的研究结果表明，自发相互作用在 RBP 调节中起着核心作用，并支持编码和结合之间存在基本联系的可能性。
