Most Caenorhabditis elegans microRNAs Are Individually Not Essential for Development or Viability

“We performed a broad phenotypic study of all available miRNA loss-of-function mutants, including mutants that had been reported earlier [2,4,20,52].”

“]. Because many messages have been under selective pressure to preserve pairing to a 6mer in the 5′ region of the miRNA known as the miRNA seed (nucleotides 2–7), targets of metazoan miRNAs can be predicted above the background of false-positives by searching for conserved matches to the seed region [”

“In animals, miRNAs are transcribed as long RNA precursors (pri-miRNAs), which are processed in the nucleus by the RNase III enzyme complex Drosha-Pasha/DGCR8 to form the approximately 70-base pre-miRNAs [21–25] or are derived directly from introns [26,27].”

“Because many messages have been under selective pressure to preserve pairing to a 6mer in the 59 region of the miRNA known as the miRNA seed (nucleotides 2–7), targets of metazoan miRNAs can be predicted above the background of false-positives by searching for conserved matches to the seed region [41–45].”

“miRNAs have been identified in organisms as diverse as roundworms, flies, fish, frogs, mammals, flowering plants, mosses, and even viruses, using genetics, molecular cloning, and predictions from bioinformatics [7–16].”

“We performed a broad phenotypic study of all available miRNA loss-of-function mutants, including mutants that had been reported earlier [2,4,20,52].”

“elegans and mice (15, 17-19), KOs of 127 either individual members or individual clusters of the miR-506 family induced no 128 discernable phenotypes and did not impact male fertility.”

“Most C.elegans miRNAs are not essential for development and function redundantly (Miska et al., 2007; Alvarez-Saavedra and Horvitz, 2010).”

“Redundancy in microRNA contributions in developing worms is well-described, thought to ensure developmental robustness (Miska et al. 2007; Weaver and Han 2018).”

“A current perception is that many miRNAs act redundantly or combinatorially to sculpt gene expression, buffering the loss of individual miRNAs (Miska et al. 2007; Bartel 2009).”

“Surprisingly, most miRNA genes are individually dispensable for development and viability, at least in the worm Caenorhabditis elegans ​[12]​, but the disruption of miRNA biogenesis impairs the ability of embryonic stem cells to differentiate ​[13]​.”

“Few miRNAs have a mutant phenotype despite pervasive purifying selection, suggesting functional redundancy and/or that miRNA functions become apparent when organisms are subject to environmental and genetic perturbations (Miska et al. 2007; Li et al. 2009; Alvarez-Saavedra and Horvitz 2010; Brenner et al. 2010; Meunie…”

“As numerous deletion strains of single miRNA genes appear to be grossly normal, it has been suggested that redundancy might mask their functions [8].”

“apparent phenotypes; although one negative regulator is deleted, the target mRNAs in question remain under the regulation of additional, functionally redundant miRNAs [82,83].”

“…of miRNAs in Caenorhabditis elegans showed that loss of a single miRNA’s function often had no discernable impacts on the phenotypes assayed (Miska et al. 2007), but more recent work has found that loss of miRNA function can have strong effects on many organismal traits, including viability…”

“Numerous studies have shown that miRNA mutations rarely result in a discernable phenotype 23 .”

“Large scale efforts to identify functions of individual miRNAs or miRNA families provide invaluable insight into the roles these miRNAs play in organism development (Miska et al. 2007, Alvarez-Saavedra and Horvitz 2010), however, some miRNA genes lack deletion alleles.”

“While many miRNA genes and their families have been analyzed for function (Miska et al. 2007, Alvarez-Saavedra and Horvitz 2010), there are microRNA genes for which loss of function alleles have not yet been generated.”

“developmental processes in the Caenorhabditis elegans [60].”

“elegans are essential for survival under lab conditions (Miska et al., 2007).”

“elegans revealing that most are not required for normal development, viability, or behaviour [35], the phenotypic consequences of manipulation are typically challenging to detect.”

“Therefore, to study the function of a particular miRNA in the absence of an overt phenotype, it might be necessary to generate an animal with multiple genetic deletions of the miRNA family members or induce stress in the single knockout model [180-182].”

“elegans (227), but loss of most miRNAs and miRNA families do not exhibit any obvious developmental phenotypes (76, 228), which I think could be explained by several reasons.”

“Even in C. elegans, where it was possible to analyze deletions for about 75% of the miRNAs encoded in the worm genome, the majority of them were found to be non-essential (Miska et al. 2007).”

“Knockdown of many miRNAs in worms and some in flies resulted in no or subtle phenotypes under lab conditions [64], [65].”

“Since the first miRNAs were discovered, very few appear to be similarly essential to developmental processes (Miska et al. 2007) or to participate in targeting interactions that are well conserved, even for miRNAs that are themselves extremely well-conserved (Chen and Rajewsky 2007, Gao 2010).”

“Previous studies have also shown that single (Miska et al. 2007) and compound miRNA mutants (Alvarez-Saavedra et al.”

“The first puzzling observation is that most miRNAs effect very small, often undetectable cellular or behavioral phenotypes ( [Miska et al., 2007]).”

“This is exemplified by the lack of obvious phenotypes in C. elegans deficient for individual miRNAs whose functions are apparently compensated by other similar miRNAs (Miska et al, 2007).”

“Studies have shown that the role of individual miRNAs is limited during development due to compensatory or redundant roles of other expressed miRNAs (Plasterk, 2006; Miska et al., 2007; Wang et al., 2008).”

“The promoter of mir-232 is active exclusively in excretory cells and mir-232 mutants do not show any phenotype in the standard assays (Martinez et al. 2008b; Miska et al. 2007).”