Charles E. Vejnar, Mario Abdel Messih, Carter M. Takacs, Valeria Yartseva, Panos Oikonomou et al.
Posttranscriptional regulation plays a crucial role in shaping gene expression. During the maternal-to-zygotic transition (MZT), thousands of maternal transcripts are regulated. However, how different cis-elements and trans-factors are integrated to determine mRNA stability remains poorly understood. Here, we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. By using a massively parallel reporter assay, we identified cis-regulatory sequences in the 3′ UTR, including U-rich motifs that are associated with increased mRNA stability. In contrast, miR-430 target sequences, UAUUUAUU AU-rich elements (ARE), CCUC, and CUGC elements emerged as destabilizing motifs, with miR-430 and AREs causing mRNA deadenylation upon genome activation. We identified trans-factors by profiling RNA–protein interactions and found that poly(U)-binding proteins are preferentially associated with 3′ UTR sequences and stabilizing motifs. We show that this activity is antagonized by C-rich motifs and correlated with protein binding. Finally, we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.
Charles E. Vejnar, Mario Abdel Messih, Carter M. Takacs, Valeria Yartseva, Panos Oikonomou, Romain Christiano, Marlon Stoeckius, Stephanie Lau, Miler T. Lee, Jean-Denis Beaudoin, Damir Musaev, Hiba Darwich-Codore, Tobias C. Walther, Saeed Tavazoie, Daniel Cifuentes, Antonio J. Giraldez. Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. 2019-06-21. https://doi.org/10.1101/gr.245159.118
An RNA-element selection assay (RESA) was performed by injecting an in-vitro-transcribed, high-density reporter library containing endogenous 3′-UTR fragments into one-cell-stage wild-type zebrafish embryos. This package represents the public WT total-RNA targeted-library profile as overlapping sequence windows with the 2-to-6 hpf stability score used as input to the authors' random-forest model.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 10 files (ZIP)RESA_random_forest_prediction.RRESA_random_forest_README.mdRESA_random_forest_training.RRESA_targeted_WT_total_WindowSequences.tsvsource_notes.txtSRP090954_SRA_runinfo_previously_published_RESA.csvSRP189389_SRA_runinfo.csvSupplemental_Methods.pdfSupplemental_Table_S1_sequencing_summary.xlsxSupplemental_Table_S6_iCLIP_top_kmers.csv