Poised PABP–RNA hubs implement signal-dependent mRNA decay in development

• Published in: Nature structural & molecular biology Vol. 31; no. 9; pp. 1439 - 1447
• Main Authors: Modic, Miha, Kuret, Klara, Steinhauser, Sebastian, Faraway, Rupert, van Genderen, Emiel, Ruiz de Los Mozos, Igor, Novljan, Jona, Vičič, Žiga, Lee, Flora C. Y., ten Berge, Derk, Luscombe, Nicholas M., Ule, Jernej
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.09.2024; Nature Publishing Group
• Subjects: 3' Untranslated regions; 3' Untranslated Regions - genetics; 631/136/2444; 631/337/1645/2020; 631/337/458/1733; 631/553; Animals; Biochemistry; Biological Microscopy; Biomedical and Life Sciences; Cell fate; Convergence; Decay; Deep learning; Embryos; Extracellular signal-regulated kinase; Gene expression; Gene Expression Regulation, Developmental; Hubs; Humans; Implantation; Kinases; Life Sciences; MAP kinase; Membrane Biology; Mice; mRNA turnover; Nucleotide sequence; Phosphorylation; Pluripotency; Poly(A)-binding protein; Poly(A)-Binding Proteins - genetics; Poly(A)-Binding Proteins - metabolism; Polyadenine; Protein Structure; Proteins; Ribonucleic acid; RNA; RNA Stability; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Signal Transduction; Transcriptomes
• ISSN: 1545-9993; 1545-9985; 1545-9985
• DOI: 10.1038/s41594-024-01363-x

Signaling pathways drive cell fate transitions largely by changing gene expression. However, the mechanisms for rapid and selective transcriptome rewiring in response to signaling cues remain elusive. Here we use deep learning to deconvolve both the sequence determinants and the trans -acting regulators that trigger extracellular signal-regulated kinase (ERK)–mitogen-activated protein kinase kinase (MEK)-induced decay of the naive pluripotency mRNAs. Timing of decay is coupled to embryo implantation through ERK–MEK phosphorylation of LIN28A, which repositions pLIN28A to the highly A+U-rich 3′ untranslated region (3′UTR) termini of naive pluripotency mRNAs. Interestingly, these A+U-rich 3′UTR termini serve as poly(A)-binding protein (PABP)-binding hubs, poised for signal-induced convergence with LIN28A. The multivalency of AUU motifs determines the efficacy of pLIN28A–PABP convergence, which enhances PABP 3′UTR binding, decreases the protection of poly(A) tails and activates mRNA decay to enable progression toward primed pluripotency. Thus, the signal-induced convergence of LIN28A with PABP–RNA hubs drives the rapid selection of naive mRNAs for decay, enabling the transcriptome remodeling that ensures swift developmental progression. Here the authors show that, upon embryo implantation, signaling triggers a large-scale rearrangement of protein–RNA interactions. Phosphorylated LIN28A reassembles onto the 3′ untranslated region termini of pluripotency-associated mRNAs, where it converges with the binding of poly(A)-binding protein and drives selective mRNA decay.