Pessina Patrizia, Nevo Mika, Shi Junchao, Kodali Srikanth, Casas Eduard, Cui Yingzhi, Richards Alicia L, Park Emily J, Chen Xi, Levin-Ferreyra Florencia, Stevenson Erica, Krogan Nevan J, Swaney Danielle L, Ying Qilong, Chen Qi, Brumbaugh Justin, Di Stefano Bruno
Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
bioRxiv. 2025 May 10:2025.05.08.652299. doi: 10.1101/2025.05.08.652299.
Recent studies have emphasized the significance of biomolecular condensates in modulating gene expression through RNA processing and translational control. However, the functional roles of RNA condensates in cell fate specification remains poorly understood. Here, we profiled the coding and non-coding transcriptome within intact biomolecular condensates, specifically P-bodies, in diverse developmental contexts, spanning multiple vertebrate species. Our analyses revealed the conserved, cell type-specific sequestration of untranslated RNAs encoding key cell fate regulators. Notably, P-body contents did not directly reflect active gene expression profiles for a given cell type, but rather were enriched for translationally repressed transcripts characteristic of the preceding developmental stage. Mechanistically, microRNAs (miRNAs) direct the selective sequestration of RNAs into P-bodies in a context-dependent manner, and perturbing AGO2 or alternative polyadenylation profoundly reshapes P-body RNA content. Building on these mechanistic insights, we demonstrate that modulating P-body assembly or miRNA activity dramatically enhances both activation of a totipotency transcriptional program in naïve pluripotent stem cells as well as the programming of primed human embryonic cells towards the germ cell lineage. Collectively, our findings establish a direct link between biomolecular condensates and cell fate decisions across vertebrate species and provide a novel framework for harnessing condensate biology to expand clinically relevant cell populations.
最近的研究强调了生物分子凝聚物在通过RNA加工和翻译控制来调节基因表达方面的重要性。然而，RNA凝聚物在细胞命运决定中的功能作用仍知之甚少。在这里，我们分析了完整生物分子凝聚物（特别是P小体）在多种脊椎动物物种不同发育背景下的编码和非编码转录组。我们的分析揭示了编码关键细胞命运调节因子的未翻译RNA的保守、细胞类型特异性隔离。值得注意的是，P小体的成分并不直接反映给定细胞类型的活性基因表达谱，而是富含前一发育阶段特征性的翻译抑制转录本。从机制上讲，微小RNA（miRNA）以依赖于上下文的方式指导RNA选择性隔离到P小体中，并且干扰AGO2或可变聚腺苷酸化会深刻重塑P小体RNA含量。基于这些机制见解，我们证明调节P小体组装或miRNA活性可显著增强幼稚多能干细胞中全能转录程序的激活以及将人原始胚胎细胞重编程为生殖细胞谱系的过程。总的来说，我们的研究结果在脊椎动物物种中建立了生物分子凝聚物与细胞命运决定之间的直接联系，并为利用凝聚物生物学来扩大临床相关细胞群体提供了一个新框架。
