Analysis of 3' 2'-O-methylated small RNAs in Caenorhabditis elegans
ABSTRACT: To identify methylated small RNAs in C. elegans, we deep sequenced both β-eliminated and untreated small RNAs isolated from wild type C. elegans. Small RNAs were isolated from larval and adult stage C. elegans and either subjected to β-elimination or no treatment. Small RNA cDNA libraries were sequenced on an Illumina HiSeq instrument, and enrichment or depletion of small RNAs by β-elimination was assessed after library size normalization based on the number of mappable reads in each library.
Project description:Small RNAs, including piRNAs, miRNAs and endogenous siRNAs, bind Argonaute proteins to form RNA-silencing complexes that target coding genes, transposons and aberrant RNAs. To assess the requirements for endogenous siRNA formation and activity in C. elegans, we developed a GFP-based sensor for the endogenous siRNA 22G siR-1, one of a set of abundant siRNAs processed from a precursor RNA mapping to the X chromosome, the X-cluster. Silencing of the sensor is also dependent on the partially complementary, unlinked 26G siR-O7 siRNA. We show that 26G siR-O7 acts in trans to initiate 22G siRNA formation from the X-cluster. The presence of several mispairs between 26G siR-O7 and the X-cluster mRNA, as well as mutagenesis of the siRNA sensor, indicates that siRNA target recognition is permissive to a degree of mispairing. From a candidate reverse genetic screen, we identified several factors required for 22G siR-1 activity, including the Argonaute ergo-1 and the 3' methyltransferase henn-1. Quantitative RT-PCR of small RNAs in a henn-1 mutant and deep sequencing of methylated small RNAs indicate that siRNAs and piRNAs that associate with PIWI clade Argonautes are methylated by HENN-1, while siRNAs and miRNAs that associate with non-PIWI clade Argonautes are not. Thus, PIWI-class Argonaute proteins are specifically adapted to associate with methylated small RNAs in C. elegans. This SuperSeries is composed of the following subset Series: GSE34320: Analysis of 22G siRNA triggered siRNA amplification in Caenorhabditis elegans GSE34321: Analysis of 3' 2'-O-methylated small RNAs in Caenorhabditis elegans Refer to individual Series
Project description:To determine if an endogenous 22G siRNA sensor transgene is subject to siRNA amplification, small RNAs were deep sequenced from the sensor and from a control transgene that is identical to the sensor but lacks an siRNA target site. Small RNAs were isolated from synchronized young adult C. elegans and subjected to deep sequencing.
Project description:The nematode Caenorhabditis elegans contains each of the broad classes of eukaryotic small RNAs, including microRNAs (miRNAs), endogenous small-interfering RNAs (endo-siRNAs) and piwi-interacting RNAs (piRNAs). To better understand the evolution of these regulatory RNAs, we deep sequenced small RNAs from C. elegans and three closely related nematodes: C. briggsae, C. remanei and C. brenneri. The results reveal a fluid landscape of small RNA pathways with essentially no conservation of individual sequences aside from a subset of miRNAs. We identified 52 miRNA families that are conserved in each of the four species as well as numerous miRNAs that are species specific or shared between only two or three species. Despite a lack of conservation of individual piRNAs and siRNAs many of the features of each pathway, including genomic distribution, are conserved. We show that in each species, 26G siRNAs trigger stage-specific secondary siRNA formation. We also observe that piRNAs trigger siRNA formation from targets containing up to three mismatches in each species. Finally, we show that nematodes produce two distinct sex-specific classes of piRNAs, suggesting different roles for piRNAs in male and female germlines. Sequencing small RNAs from four Caenorhabditis species: C. elegans, C. briggsae, C. remanei and C. brenneri
Project description:To characterize the role of the ERI-6/7 helicase in endogenous small RNA pathways in C. elegans, small RNA populations from null alleles of eri-6 and eri-7, and from mutants of known endogenous RNAi pathway factors, eri-1 and ergo-1, were determined by deep sequencing, and compared to wild type. Small RNA analysis in wild type and eri-1, ergo-1, eri-6 and eri-7 mutant C. elegans strains.
Project description:From a forward genetic screen for C. elegans genes required for RNAi, we identified rde-10 and through proteomic analysis of RDE-10-interacting proteins, we identified a protein complex containing the new RNAi factor RDE-11, the known RNAi factors RSD-2 and ERGO-1, as well as other candidate RNAi factors. The newly identified RNAi defective genes rde-10 and rde-11 encode a novel protein and a RING-type zinc finger domain protein, respectively. Mutations in rde-10 and rde-11 genes cause dosage-sensitive RNAi deficiencies: these mutants are resistant to low dosage, but sensitive to high dosage of double-stranded RNAs. We assessed the roles of rde-10, rde-11, and the dosage-sensitive RNAi defective genes rsd-2, rsd-6 and haf-6 in both exogenous and endogenous small RNA pathways using high-throughput sequencing and qRT-PCR. These genes are required for the accumulation of secondary siRNAs in both exogenous and endogenous RNAi pathways. Small RNA analysis by deep sequencing in various wild type and mutant C. elegans strains.
Project description:Recent work has shown that small non-coding RNAs, including miRNAs, serve an important role in controlling gene expression during development and disease. However, little detailed information exists concerning the relative expression patterns of small RNAs during development of C. elegans. Here we use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs, including miRNAs, changes dynamically during development and in the different sexes of C. elegans; approximately 16% of known miRNAs changed over 10 fold in expression during C. elegans development and about 12% of miRNAs showed major changes in expression between males and hermaphrodites of C. elegans. These results should lead to a better understanding of the expression and function of small RNAs in C. elegans development. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of small RNA expression in six different developmental stages of hermaphrodites (Embryo, mid-L1, mid-L2, mid-L3, mid-L4, young adult), and young adult males (dpy-28;him-8) and spermatogenesis-defective young adult hermaphrodites (spe-9). The number of sequence reads for miRNA was assessed from the raw sequence data from Solexa sequencing using perfect sequence matching to known miRNAs (miRBase Release 11.0).
Project description:Eukaryotic cells express several classes of small RNAs that regulate gene expression and ensure genome maintenance. Endogenous siRNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) mainly control gene and transposon expression in the germline, while microRNAs (miRNAs) generally function in post-transcriptional gene silencing in both somatic and germline cells. To provide an evolutionary and developmental perspective on small RNA pathways in nematodes, we identified and characterized known and novel small RNA classes through gametogenesis and embryo development in the parasitic nematode Ascaris suum and compared them with known small RNAs of Caenorhabditis elegans. piRNAs, Piwi-clade Argonautes, and other proteins associated with the piRNA pathway have been lost in Ascaris. miRNAs are synthesized immediately following fertilization in utero, prior to pronuclear fusion, and before the first cleavage of the zygote. This is the earliest expression of small RNAs ever described at a developmental stage long thought to be transcriptionally quiescent. A comparison of the two classes of Ascaris endo-siRNAs, 22G-RNAs and 26G-RNAs, to those in C. elegans, suggests great diversification and plasticity in the use of small RNA pathways during spermatogenesis in different nematodes. Our data reveal conserved characteristics of nematode small RNAs as well as features unique to Ascaris that illustrate significant flexibility in the use of small RNAs pathways, some of which are likely an adaptation to Ascaris’ life cycle and parasitism. We constructed and analyzed 51 libraries from discrete regions of gametogenesis and synchronized stages of embryo development in the parasitic nematode Ascaris, using three types of small RNA libraries preparation methods: 1) 28 libraries of 18-34 or 18-40 nt RNAs with a 5’ monophosphate (5’ monophosphate libraries), 2) 4 libraries of 18-34 nt RNAs with a 5’ monophosphate but treated with periodate to enrich for small RNAs with 3’ end modifications (5’ monophosphate, 3’ end modified), and 3) 19 libraries of 18-28 or 18-40 nt RNAs with a 5’ triphosphate, diphosphate, or monophosphate (5’ allphosphate). These libraries enabled us to identify different small RNAs, characterize their different 5’ and 3’ ends, and their expression profiles through gametogenesis and embryogenesis.
Project description:Small endogenous C. elegans RNAs from L4 and young adult worms were prepared for sequencing using a protocol derived from Batista et al., (2008) and Lau et al. (2001). The small-RNA libraries were constructed using a method that does not require a 5’ monophosphate (called 5’ monophosphate-independent method, Ambros et al., 2003) to profile secondary siRNAs that have 5’ triphosphorylated G. All preprocessed small-RNA reads were mapped to genome (ce6), allowing no mismatches. After excluding miRNAs, 21U RNAs, rRNAs, and other structural ncRNAs, the remaining reads were classified as 22G RNAs, 26G RNAs, and other siRNAs, based on their length and 5′ terminal nucleotide. Small-RNA libraries were sequenced in L4 and young adult stages in C.elegans.
Project description:This data series contains small RNA high-throughput sequencing data for each of the mutator class genes. Samples are from stage-matched adult C. elegans grown at 20˚C. Small RNAs were isolated from synchronized wild type and mutant C. elegans and subjected to Illumina HiSeq sequencing. The series contains fastq and tab-separated files for 19 libraries.
Project description:Transposable elements are a serious threat for genome integrity and their control via small RNA mediated silencing pathways is an ancient strategy. The fruit fly Drosophila melanogaster has two silencing mechanisms that repress TEs expression: endogenous siRNAs (esiRNAs or endo-siRNAs) and Piwi-interacting small RNAs (piRNAs). The biogenesis of endo-siRNAs involves Loqs-PD, which acts predominantly during processing of dsRNA by Dcr-2, and R2D2 that primarily helps to direct siRNAs for loading into Ago2. We provide deep sequencing evidence consistent with the idea that R2D2 and Loqs-PD can function in part redundantly. Certain transposons display a preference for either dsRBD-protein for production or loading; this appeared to correlate neither with overall abundance, classification of the transposon or a specific site of genomic origin. The endo-siRNA biogenesis pathway in the germline operates according to the same principles as the existing model for the soma, and its impairment does not significantly affect piRNAs. Expanding the analysis, we confirmed the occurrence of somatic piRNA-like RNAs (pilRNAs) that show a ping-pong signature. We detected expression of the Piwi-family protein mRNAs only barely above background, indicating that the somatic pilRNAs may arise from a small sub-population of somatic cells that express a functional piRNA pathway. small RNA sampling experiment; small RNAs were prepared from head & thorax as well as dissected ovaries of Adult female Drosophila melanogaster. We used homozygous mutants of the dsRBD proteins Loqs and r2d2 to determine their contribution to the biogenesis of transposon-derived small RNAs. Heterozygous mutant animals served as control. For each RNA sample, we performed one deep-sequencing run without any treatment, and in parallel one sequencing run after periodate oxidation and beta-elimination. After this treatment, only Ago2, Piwi, Aub and Ago3-loaded small RNAs remain as they carry a 2'-O-methyl modification at their 3'-end. This helps to determine the loading status of the small RNAs detected. In total 8 different RNA samples were prepared and 16 libraries were sequenced.