Many families of Caenorhabditis elegans microRNAs are not essential for development or viability

available in PMC 2010 August 23MicroRNAs (miRNAs) are approximately 23 nt regulatory RNAs that posttranscriptionally inhibit the functions of protein-coding mRNAs. We previously found that most C. elegans miRNAs are individually not essential for development or viability and proposed that paralogous miRNAs might often function redundantly . To test this hypothesis, we generated mutant C. elegans strains that each lack multiple or all members of one of 15 miRNA families. Mutants for 12 of these families did not display strong synthetic abnormalities, suggesting that these miRNA families have subtle roles during development. By contrast, mutants deleted for all members of the mir-35 or mir-51 families died as embryos or early larvae, and mutants deleted for four members of the mir-58 family showed defects in locomotion, body size, and egg laying and an inability to form dauer larvae. Our findings indicate that the regulatory functions of most individual miRNAs and most individual families of miRNAs related in sequence are not critical for development or viability. Conversely, because in some cases miRNA family members act redundantly, our findings emphasize the importance of determining miRNA function in the absence of miRNAs related in sequence.Ellison Medical FoundationHoward Hughes Medical Institut

The \u3cem\u3elet-7\u3c/em\u3e MicroRNA Family Members \u3cem\u3emir\u3c/em\u3e-48, \u3cem\u3emir\u3c/em\u3e-84, and mir-241 Function Together to Regulate Developmental Timing in \u3cem\u3eCaenorhabditis elegans\u3c/em\u3e

The microRNA let-7 is a critical regulator of developmental timing events at the larval-to-adult transition in C. elegans. Recently, microRNAs with sequence similarity to let-7 have been identified. We find that doubly mutant animals lacking the let-7 family microRNA genes mir-48 and mir-84 exhibit retarded molting behavior and retarded adult gene expression in the hypodermis. Triply mutant animals lacking mir-48, mir-84, and mir-241 exhibit repetition of L2-stage events in addition to retarded adult-stage events. mir-48, mir-84, and mir-241 function together to control the L2-to-L3 transition, likely by base pairing to complementary sites in the hbl-1 3′ UTR and downregulating hbl-1 activity. Genetic analysis indicates that mir-48, mir-84, and mir-241 specify the timing of the L2-to-L3 transition in parallel to the heterochronic genes lin-28 and lin-46. These results indicate that let-7 family microRNAs function in combination to affect both early and late developmental timing decisions

Most \u3cem\u3eCaenorhabditis elegans\u3c/em\u3e MicroRNAs are Individually Not Essential for Development or Viability

MicroRNAs (miRNAs), a large class of short noncoding RNAs found in many plants and animals, often act to post-transcriptionally inhibit gene expression. We report the generation of deletion mutations in 87 miRNA genes in Caenorhabditis elegans, expanding the number of mutated miRNA genes to 95, or 83% of known C. elegans miRNAs. We find that the majority of miRNAs are not essential for the viability or development of C. elegans, and mutations in most miRNA genes do not result in grossly abnormal phenotypes. These observations are consistent with the hypothesis that there is significant functional redundancy among miRNAs or among gene pathways regulated by miRNAs. This study represents the first comprehensive genetic analysis of miRNA function in any organism and provides a unique, permanent resource for the systematic study of miRNAs

Microarray analysis of microRNA expression in the developing mammalian brain

BACKGROUND: MicroRNAs are a large new class of tiny regulatory RNAs found in nematodes, plants, insects and mammals. MicroRNAs are thought to act as post-transcriptional modulators of gene expression. In invertebrates microRNAs have been implicated as regulators of developmental timing, neuronal differentiation, cell proliferation, programmed cell death and fat metabolism. Little is known about the roles of microRNAs in mammals. RESULTS: We isolated 18-26 nucleotide RNAs from developing rat and monkey brains. From the sequences of these RNAs and the sequences of the rat and human genomes we determined which of these small RNAs are likely to have derived from stem-loop precursors typical of microRNAs. Next, we developed a microarray technology suitable for detecting microRNAs and printed a microRNA microarray representing 138 mammalian microRNAs corresponding to the sequences of the microRNAs we cloned as well as to other known microRNAs. We used this microarray to determine the profile of microRNAs expressed in the developing mouse brain. We observed a temporal wave of expression of microRNAs, suggesting that microRNAs play important roles in the development of the mammalian brain. CONCLUSION: We describe a microarray technology that can be used to analyze the expression of microRNAs and of other small RNAs. MicroRNA microarrays offer a new tool that should facilitate studies of the biological roles of microRNAs. We used this method to determine the microRNA expression profile during mouse brain development and observed a temporal wave of gene expression of sequential classes of microRNAs

Phenomenology of a light gluon resonance in top-physics at Tevatron and LHC

We present a phenomenological analysis of the recent Tevatron results on the $t \bar t$ forward-backward asymmetry and invariant-mass spectrum assuming a new contribution from an s-channel gluon resonance with a mass in the range from 700 to 2500 GeV. In contrast to most of the previous works, this analysis shows that for masses below ~1 TeV resonant New Physics could accommodate the experimental data. In general, we find that axial-like couplings are preferred for light and top quark couplings, and that only top quark couples strongly to New Physics. We find that composite model scenarios arise naturally from only phenomenological analyses of the experimental results. We show that our results are compatible with recent LHC limits in dijet and $t \bar t$ production, and find some tension for large resonance mass ~2.5 TeV. We indicate as best observables for discriminating a relatively light new gluon a better resolution in CDF forward-backward asymmetry, as well as the $t \bar t$ charge asymmetry and invariant-mass spectrum at the LHC.Comment: 22 pages with 5 figure

Functional analysis of the miRNA genes of C. elegans

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2008.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. 231-252).MicroRNAs (miRNAs) were discovered in C. elegans during studies of the control of developmental timing. MicroRNAs are a large class of short non-coding RNAs found in many viruses, plants and animals that regulate gene expression through sequence-specific base-pairing with target mRNAs. Initial studies since the identification of many miRNAs only six years ago, have revealed their very diverse roles in biology. Yet, few miRNAs have been studied using loss-of-function mutations. We have generated deletion mutations in 87 miRNA genes in C. elegans, and performed an initial characterization of the 95 miRNA mutants available (86% of known C. elegans miRNAs). We found that the majority of miRNAs are not essential for the viability or development of C. elegans, and mutations in most miRNA genes do not result in grossly abnormal phenotypes. Within species, many miRNAs can be grouped into families according to their sequence similarities. We generated a collection of 12 multiply mutant C. elegans strains that each lacks an entire miRNA family. We found that at least four families display synthetic abnormalities, indicating that miRNAs within a family can have redundant functions. While single mutants are superficially wild-type, mutants deleted for all members of the mir-35 or the mir-51 families show embryonic or early larval lethality, mutants deleted for all members of the mir-58 family show an egglaying defect, and mutants deleted for some members of the let-7 family show defects in developmental timing. We developed a microarray technology suitable for detecting microRNAs and used this microarray to determine the profile of microRNAs expressed in the developing mouse brain. We observed a temporal wave of expression of microRNAs, suggesting that microRNAs play important roles in the development of the mammalian brain.(cont.) We also performed a systematic expression analysis of 334 samples covering diverse human cancers, using a bead-based flow cytometric miRNA expression profiling method we developed. The miRNA profiles reflect the developmental lineage and differentiation state of the tumors, and reveal a general down-regulation of miRNAs in tumors compared to normal tissues.by Ezequiel Alvarez-Saavedra.Ph.D

Report Many Families of C. elegans MicroRNAs Are Not Essential for Development or Viability

Summary MicroRNAs (miRNAs) are approximately 23 nt regulatory RNAs that posttranscriptionally inhibit the functions of protein-coding mRNAs. We previously found that most C. elegans miRNAs are individually not essential for development or viability and proposed that paralogous miRNAs might often function redundantly Results and Discussion Genetic, computational, and genome-wide expression analyses indicate that microRNAs (miRNAs) function primarily by targeting sites in the 3 0 -untranslated regions (UTRs) of their target genes To investigate functional redundancy among miRNA family members, we constructed double, triple, or quadruple multiply mutant strains that each carried mutations in members of a given family for 15 of the 23 known C. elegans miRNA families The mir-35 family comprises eight miRNAs, mir-35 through mir-42, located in two genomic miRNA clusters separated by 350 kb on LGII. One cluster contains mir-35 through mir-41 (mir-35-41), and the other contains mir-42, mir-43, and mir-44 (mir-42-44) ( We obtained three deletions that affect mir-35 family members in the mir-35-41 or mir-42-44 clusters and constructed strains lacking most or all mir-35 family members ( The mir-35 family contains members that are tightly clustered in the genome, and the deletions we isolated affected all or multiple members of each cluster ( We examined the mir-35 family mutant phenotype in more detail. Most animals deleted for all mir-35 family members underwent developmental arrest at the two-fold or three-fol