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Series GSE268809 Query DataSets for GSE268809
Status Public on Jun 01, 2024
Title Screening by deep sequencing reveals mediators of microRNA tailing in C. elegans
Organism Caenorhabditis elegans
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary microRNAs are frequently modified by addition of untemplated nucleotides to the 3' end, but the role of this tailing is often unclear. Here we characterize the prevalence and functional consequences of microRNA tailing in vivo, using Caenorhabditis elegans. MicroRNA tailing in C. elegans consists mostly of mono-uridylation of mature microRNA species, with rarer mono-adenylation which is likely added to microRNA precursors. Through a targeted RNAi screen, we discover that the TUT4/TUT7 gene family member CID-1/CDE-1/PUP-1 is required for uridylation, whereas the GLD2 gene family member F31C3.2-here named GLD-2-related 2 (GLDR-2)-is required for adenylation. Thus, the TUT4/TUT7 and GLD2 gene families have broadly conserved roles in miRNA modification. We specifically examine the role of tailing in microRNA turnover. We determine half-lives of microRNAs after acute inactivation of microRNA biogenesis, revealing that half-lives are generally long (median = 20.7 h), as observed in other systems. Although we observe that the proportion of tailed species increases over time after biogenesis, disrupting tailing does not alter microRNA decay. Thus, tailing is not a global regulator of decay in C. elegans. Nonetheless, by identifying the responsible enzymes, this study lays the groundwork to explore whether tailing plays more specialized context- or miRNA-specific regulatory roles.
 
Overall design To determine the role of microRNA tailing (i.e. untemplated addition of nucleotides to the 3' end), an RNAi screen was performed to identify enzymes required for microRNA tailing in C. elegans (screen group samples). To determine the role of tailing in rates of microRNA decay, decay rates were profiled in the presence of tailing (sample group 1), or in the context of disrupted tailing by knockdown of tailing enzymes CID-1 or F31C3.2/GLDR-2 (sample group 2). To further determine redundancy of CID-1 or F31C3.2/GLDR-2 with their paralogs, tailing was profiled in double mutant conditions for CID-1/PUP-1 and PUP-2 (sample group 3) or in F31C3.2/GLDR-2 mutant with GLD-2 RNAi (sample group 4). Additional experiments were performed, which were ultimately inconclusive due to technical limitations, to determine requirements for TDMD in C. elegans (sample group 5).
 
Contributor(s) Vieux K, Prothro KP, Kelley LH, Palmer C, Maine EM, Veksler-Lublinsky I, McJunkin K
Citation(s) 34586415
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 PRJNA703306
Submission date May 31, 2024
Last update date Sep 03, 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 (2)
GPL19757 Illumina NextSeq 500 (Caenorhabditis elegans)
GPL24892 Illumina HiSeq 3000 (Caenorhabditis elegans)
Samples (94)
GSM8299744 wild type adult hermaphrodite, sample group 1 rep 1
GSM8299745 wild type adult hermaphrodite, sample group 1 rep 2
GSM8299746 wild type adult hermaphrodite, sample group 1 rep 3

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE268809_081921_Supplemental_Tables_Prothro.xlsx 589.6 Kb (ftp)(http) XLSX
GSE268809_Rawreads_df_compile_samples_Selected.xlsx 216.4 Kb (ftp)(http) XLSX
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