Small-RNAs in L4 and young adult stages
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE36394 | GEO | 2012/06/13
SECONDARY ACCESSION(S): PRJNA159607
REPOSITORIES: GEO
Similar Datasets
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 5M-bM-^@M-^Y monophosphate (called 5M-bM-^@M-^Y monophosphate-independent method, Ambros et al., 2003) to profile secondary siRNAs that have 5M-bM-^@M-^Y 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 5M-bM-^@M-2 terminal nucleotide. Small-RNA libraries were sequenced in L4 and young adult stages in C.elegans.
2012-06-12 | E-GEOD-36394 | biostudies-arrayexpress
Project description:These datasets profile the expression of small RNAs with 3p hydroxyls (including endo-siRNAs, miRNAs, and 21U-RNAs) in young adult worms from the wt and prg-1 mutant backgrounds. They were prepared using an approach that captures small RNAs independent of the covalent status of their 5p termini, as described in Ambros et al. (2003) Curr Biol 13:807-18. These datasets were prepared in the Craig C. Mello laboratory. Keywords: endo-siRNA mutant expression profiling
2008-06-16 | GSE11736 | GEO
Project description:These datasets examine the association of small RNAs with 3p hydroxyls (including endo-siRNAs, miRNAs, and 21U-RNAs) with the PRG-1 protein through co-immunoprecipitation. Two datasets are provided; one sequences small RNAs that co-IP with PRG-1; the other sequences small RNAs from the IP input sample. These RNA samples were prepared using an approach that captures small RNAs independent of the covalent status of their 5p termini, as described in Ambros et al. (2003) Curr Biol 13:807-18. These datasets were prepared in the Craig C. Mello laboratory. Keywords: identification of PRG-1-associated small RNAs
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Project description:High throughput seqeuncing of small RNAs (PAGE isolated from total RNA or Argonaute immunoprecipitates) from Drosophila melanogaster using the Illumina platform. Adapter ligation requires 5' monophosphate and 3' OH. Full analysis of all libraries in this set is published (Czech B. et al. 2008), leading to the description of endogenous siRNAs in flies. Keywords: Solexa sequences
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Project description:Adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that convert adenosine to inosine in double-stranded RNA (dsRNA). To evaluate effects of ADARs on small RNAs that derive from dsRNA precursors, we performed deep-sequencing, comparing small RNAs from wildtype and ADAR mutant C. elegans. While editing in small RNAs was rare, at least 40% of microRNAs had altered levels in at least one ADAR mutant strain, and miRNAs with significantly altered levels had mRNA targets with correspondingly affected levels. About 40% of siRNAs derived from endogenous genes (endo-siRNAs) also had altered levels in at least one mutant strain, including 63% of Dicer-dependent endo-siRNAs. The 26G class of endo-siRNAs was significantly affected by ADARs, and many altered 26G loci had intronic reads, and histone modifications associated with transcriptional silencing. Our data indicate ADARs, through both direct and indirect mechanisms, are important for maintaining wildtype levels of many small RNAs in C. elegans.
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Project description:Eukaryotic cells regulate 5’ triphosphorylated (ppp) RNAs to promote cellular functions and to prevent recognition by viral RNA sensors. For example, the triphosphatase domain of RNA capping enzymes removes the γ phosphate of ppp-RNAs in RNA capping reactions. Members of a related RNA polyphosphotase family including human PIR1 remove both the β and γ phosphates from ppp-RNAs. Here we demonstrate that C. elegans PIR-1, previously identified as a Dicer-interacting protein, dephosphorylates single and double-stranded ppp-RNAs, and is required for the maturation of 26G-RNAs, which regulate thousands of genes during spermatogenesis and embryogenesis. We find that 26G-RNAs are generated in a unique semi-phasing manner in which primary 26G-RNAs are required for generating secondary 26G-RNAs and PIR-1 is required for removing a diphosphate group from each triphosphorylated precursor, which only generates one 26G-RNA. Our findings also implicate PIR-1 in regulating ppp-RNAs in Dicer-independent pathways, supporting PIR-1 as a master phosphatase regulating ppp-RNAs.
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Project description:These datasets profile the expression of small RNAs with 3p hydroxyls (including endo-siRNAs, miRNAs, and 21U-RNAs) in young adult worms from the wt and prg-1 mutant backgrounds. They were prepared using an approach that captures small RNAs independent of the covalent status of their 5p termini, as described in Ambros et al. (2003) Curr Biol 13:807-18. These datasets were prepared in the Craig C. Mello laboratory. Keywords: endo-siRNA mutant expression profiling CE-prg1-endoSiRNAs-Illumina 1 flowcell each for the wt and prg-1 mutant
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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 AscarisM-bM-^@M-^Y 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 5M-bM-^@M-^Y monophosphate (5M-bM-^@M-^Y monophosphate libraries), 2) 4 libraries of 18-34 nt RNAs with a 5M-bM-^@M-^Y monophosphate but treated with periodate to enrich for small RNAs with 3M-bM-^@M-^Y end modifications (5M-bM-^@M-^Y monophosphate, 3M-bM-^@M-^Y end modified), and 3) 19 libraries of 18-28 or 18-40 nt RNAs with a 5M-bM-^@M-^Y triphosphate, diphosphate, or monophosphate (5M-bM-^@M-^Y allphosphate). These libraries enabled us to identify different small RNAs, characterize their different 5M-bM-^@M-^Y and 3M-bM-^@M-^Y ends, and their expression profiles through gametogenesis and embryogenesis.
2011-06-16 | E-GEOD-26955 | biostudies-arrayexpress
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 SubSeries listed below.
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