run_metadata: 51615
This data as json
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| 51615 | SRR8788626 | SRX5578497 | SRS4540274 | SRP189512 | PRJNA529241 | Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse | PRJNA529241 | Other | Post transcriptional 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 is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with 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 three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study. | Developmental timecourse WT 4c R0 B1 | Developmental timecourse WT 4c R0 B1 AGN000666 | strain:TU/AB|age:1.0|dev stage:4 cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000585|replicate ref:AGN000666|replicate order:1|BioSampleModel:Model organism or animal | Developmental timecourse WT 4c R0 B1 | AGR000861 | AGR000861 | RNA | RNA-Seq | TRANSCRIPTOMIC | unspecified | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP189512 | AGR000861_R2.fastq.gz AGR000861_R1.fastq.gz | fastq fastq | 2888554344.0 | 19003647.0 | AGR000861 R1.fastq.gz | 0:76 1:76 | A:673571075;C:760569181;G:775244536;T:678822696;N:346856 | 76 | 76 | 673571075 | 760569181 | 775244536 | 678822696 | 346856 | SRX5578497 | SRS4540274 | SRA866166 | Yale_Giraldez|Genetics | Yale_Giraldez_Group | 2 | 0.75836 | 0.8073 | 0.07453 | 0.07791 | 0.76566 | 0.76745 | 0.48548 | 0.48444 | 76 | 76 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | unknown | unknown | bulk | unknown | unknown | United States | 2019-05-31 | Cleavage | Embryo | Embryo Imprecise | All anatomical structures |