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Series GSE256488 Query DataSets for GSE256488
Status Public on Feb 26, 2024
Title Catalytic residues of microRNA Argonautes play a modest role in microRNA star strand destabilization in C. elegans
Organism Caenorhabditis elegans
Experiment type Expression profiling by high throughput sequencing
Summary Many Argonaute proteins can cleave RNA (“slicing”) as part of the microRNA-induced silencing complex (miRISC), even though miRNA-mediated target repression is generally independent of target cleavage. Here we use C. elegans to examine the role of catalytic residues of miRNA Argonautes in organismal development. In contrast to previous work, mutations in presumed catalytic residues did not interfere with normal development when introduced by CRISPR. We find that unwinding and decay of miRNA star strands is weakly defective in the catalytic residue mutants, with the largest effect observed in embryos. Argonaute-Like Gene 2 (ALG-2) is more dependent on slicing for unwinding than ALG-1. The miRNAs that displayed the greatest (albeit minor) dependence on catalytic residues for unwinding tend to form stable duplexes with their star strand, and in some cases, lowering duplex stability alleviates dependence on catalytic residues. While a few miRNA guide strands are reduced in the mutant background, the basis of this is unclear since changes were not dependent on EBAX-1, an effector of Target-Directed miRNA Degradation (TDMD). Overall, this work defines a role for the catalytic residues of miRNA Argonautes in star strand decay; future work should examine whether this role may contribute to the selection pressure to conserve catalytic activity of miRNA Argonautes across the metazoan phylogeny.
 
Overall design To test the role of miRISC-mediated slicing in invertebrates, we used CRISPR/Cas9-mediated genome editing to mutate the DEDH catalytic tetrad to AEDH in the major C. elegans microRNA Argonautes, ALG-1 and ALG-2 (alg-1(AEDH); alg-2(AEDH)). We performed total RNAseq from these mutants or wild type in young adults (4 replicates), L4s (3 replicates), and mixed stage embryos (4 replicates).
Web link https://doi.org/10.1093/nar/gkae170
 
Contributor(s) Kotagama K, Grimme AL, Braviner L, Yang B, Sakhawala RM, Yu G, Benner LK, Joshua-Tor L, McJunkin K
Citation(s) 38471816
NIH grant(s)
Grant ID Grant title Affiliation Name
ZIA DK075147 Biological functions and post-transcriptional regulation of microRNAs National Institute of Diabetes and Digestive and Kidney Diseases Katherine Han Needles McJunkin
BioProject PRJNA922944
Submission date Feb 23, 2024
Last update date May 31, 2024
Contact name Katherine McJunkin
E-mail(s) mcjunkin@nih.gov
Phone 3048811944
Organization name National Institutes of Health
Street address 50 South Drive, Building 50 Room 3148
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL26672 Illumina NovaSeq 6000 (Caenorhabditis elegans)
Samples (22)
GSM8101428 alg-1(AEDH); alg-2(AEDH) young adult experiment 1rep1
GSM8101429 wild type young adult experiment 1rep1
GSM8101430 wild type L4 experiment 1rep1

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE256488_gene_featurecounts_KM.xlsx 4.6 Mb (ftp)(http) XLSX
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Raw data are available in SRA
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