Singh et al. 2021 (PRJNA648380)

General Details

Title Translation and codon usage regulate Argonaute slicer activity to trigger germline small RNA biogenesis [Ribo-Seq]
Organism
Number of Samples 14
Release Date 2020/07/24 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP273441
ENA SRP273441
GEO GSE155073
BioProject PRJNA648380

Publication

Title
Authors Singh M, Cornes E, Li B, Quarato P, Bourdon L, Dingli F, Loew D, Proccacia S, Cecere G
Journal Nature communications
Publication Date 2021 Jun 9
Abstract In the Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remains unknown. Here, we show that CSR-1 slicer activity is primarily involved in triggering the synthesis of small RNAs on the coding sequences of germline mRNAs and post-transcriptionally regulates a fraction of targets. CSR-1-cleaved mRNAs prime the RNA-dependent RNA polymerase, EGO-1, to synthesize 22G-RNAs in phase with translating ribosomes, in contrast to other 22G-RNAs mostly synthesized in germ granules. Moreover, codon optimality and efficient translation antagonize CSR-1 slicing and 22G-RNAs biogenesis. We propose that codon usage differences encoded into mRNA sequences might be a conserved strategy in eukaryotes to regulate small RNA biogenesis and Argonaute targeting.
PMC PMC8190271
PMID 34108460
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR12318105 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318106 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318107 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318108 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318109 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318110 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318111 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318112 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318113 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318114 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318115 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318116 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318117 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR12318118 PRJNA648380 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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