Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Small RNA sequencing study of C elegans piRNA biogenesis factors

ABSTRACT: Identification of defects in piRNAs and piRNA precursors Sequencing of small RNAs (18-30nt). Sample treatments: Secondary siRNAs in C. elegans carry a 5' triphosphate and this has to be removed prior to cloning, hence the use of 5' polyphosphatase treatment to reveal this population. TAP (tobacco acid pyrophosphatase) is another enzyme that removes 5' triphosphate but it also removes 5' CAP structures- we used this to look for piRNA precursor sequences in C. elegans that have a 5' cap.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Peter Sarkies

PROVIDER: E-GEOD-49220 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

No evidence for a C. elegans small RNA response to feeding with OxyS-expressing bacteria

Project description:Small RNA sequencing shows that there are no Caenorhabditis elegans endo siRNAs made against the OxyS non-coding RNA. Sequencing of small RNAs from C. elegans fed bacteria overexpressing the non-coding RNA OxyS, control samples fed either standard E. coli or one without the OxyS RNA, an rde-4 deletion mutant deficient in endo siRNA production and the OxyS-overexpressing bacteria itself. 5' independent samples were treated with the enzyme RNA 5' polyphosphatase to remove 5' triphosphate; 5' dependent samples were not treated with 5' polyphosphatase.

2016-07-05 | E-GEOD-64990 | biostudies-arrayexpress

Transgenerational antiviral RNAi does not occur in Orsay virus infection of C. elegans

Project description:Comparison of small RNAs between virus-infected animals and their progeny Sequencing of small RNAs (15-30nt)

2015-01-01 | E-GEOD-60020 | biostudies-arrayexpress

Analysis of small RNA response to viral infection in C.elegans

Project description:Dissection of the small RNA pathway required for generation of an antiviral small RNA response Small non-coding RNA (~15-30nt) was extracted from animals infected with the Orsay virus

2013-06-01 | E-GEOD-41693 | biostudies-arrayexpress

Small RNA sequencing of transgenes silencing by paramutation in C. elegans

Project description:In the nematode Caenorhabditis elegans, different small RNA-dependent gene silencing mechanisms act in the germline to initiate transgenerational gene silencing. Piwi-interacting RNAs (piRNAs) can initiate transposon and gene silencing by acting upstream of endogenous short interfering RNAs (siRNAs), which engage a nuclear RNA interference (RNAi) pathway to trigger transcriptional gene silencing. Once gene silencing has been established, it can be stably maintained over multiple generations without the requirement of the initial trigger and is also referred to as RNAe or paramutation. This heritable silencing depends on the integrity of the nuclear RNAi pathway. However, the exact mechanism by which silencing is maintained across generations is not understood.Here we demonstrate that silencing of piRNA targets involves the production of two distinct classes of small RNAs with different genetic requirements. The first class, secondary siRNAs, are localized close to the direct target site for piRNAs. Nuclear import of the secondary siRNAs by the Argonaute HRDE-1 leads to the production of a distinct class of small RNAs that map throughout the transcript, which we term tertiary siRNAs. Both classes of small RNAs are necessary for full repression of the target gene and can be maintained independently of the initial piRNA trigger. Consistently, we observed a form of paramutation associated with tertiary siRNAs. Once paramutated, a tertiary siRNA generating allele confers dominant silencing in the progeny regardless of its own transmission, suggesting germline-transmitted siRNAs are sufficient for multigenerational silencing. C. elegans strains containing transgenes silenced by piRNAs were crossed to strains with transgenes with similar sequences but without piRNA target sites, to investigate the spreading of silencing between transgenes mediated by small RNAs. Mutant backgrounds were used to investigate the genetic requirements for this process.

2015-04-01 | E-GEOD-66344 | biostudies-arrayexpress

C. elegans piRNAs are processed from capped-small RNAs transcribed at promoters throughout the genome

Project description:Piwi-interacting (pi) RNAs are a class of germline-expressed small RNAs that have been linked to epigenetic programming in metazoa. C. elegans piRNAs known as 21U-RNAs are defined by more than 15,000 genome-encoded species. To explore the origin of 21U-RNAs we employed methods to enrich the 5' ends of Pol II transcripts. We show that a species of capped-short (cs) RNA is frequently expressed bidirectionally at Pol II loci in C. elegans. Interestingly, at annotated 21U-RNA loci, csRNAs originate precisely 2 nt upstream of the mature piRNA species suggesting that csRNAs are piRNA precursors. In addition, we show that csRNAs associated with TS sites genome-wide define a previously overlooked class of 21U-RNA loci, and nearly double the number of piRNA species available for genome surveillance. Our methods should be of general utility in TS site identification and 5' anchored RNA-expression profiling. Identification of capped RNA including capped small RNA and long capped RNA in C. elegans. The mouse data are independent data to test the CapSeq sequencing protocol.

2012-12-22 | E-GEOD-40053 | biostudies-arrayexpress

Function, targets and evolution of Caenorhabditis elegans piRNAs (small RNA-Seq)

Project description:piRNAs are required to maintain germline integrity and fertility but their mechanism of action is poorly understood. Here we demonstrate that C. elegans piRNAs silence transcripts in trans through imperfectly complementary sites. We find that target silencing is independent of Piwi endonuclease activity or “slicing”. Instead, we show that piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. Endogenous protein-coding gene, pseudogene and transposon transcripts exhibit Piwi-dependent endo-siRNAs at sites complementary to piRNAs and are derepressed in Piwi mutants. Genomic loci of piRNA biogenesis are depleted of protein-coding genes but not pseudogenes or transposons. Our data suggest that nematode piRNA clusters are evolving to generate piRNAs against active mobile elements. Thus, piRNAs provide heritable, sequence-specific triggers for RNAi in C. elegans. 7 small RNA libraries were sequenced as part of 25 flow cell lanes on the Illumina GA II platform. Samples were treated with tobacco acid pyrophosphatase to allow cloning of small RNAs with a 5'-triphosphate. Samples were labelled for multiplexing using 4-bp 5'-barcodes or barcodes included in Illumina TruSeq adapters. In most cases a single flow cell lane included several multiplexed libraries.

2012-06-18 | E-GEOD-28617 | biostudies-arrayexpress

Implication of small sperm RNAs in the inheritance of the effect of early traumatic stress in mice

Project description:Small non-coding RNAs (sncRNAs) have been proposed as potential vectors of the interface between genes and environment. Here, we report that environmental conditions involving traumatic stress in early life, alter miRNA and piRNA composition in sperm of adult males in mice. Examination of small RNA content of sperm from males, that experienced early chronic stress during their first two weeks of life versus small RNA content of sperm from control males.

2014-04-13 | E-GEOD-50132 | biostudies-arrayexpress

Transgenerational profiling of small non-coding RNAs in C.elegans RSD mutants

Project description:Attempt to identify progressive changes in small non-coding RNA levels in C.elegans lacking RSD-2 or RSD-6. Small non-coding RNA (18-30nt) was extracted from animals the indicated number of generations after homozygosity was established

2013-06-01 | E-GEOD-40457 | biostudies-arrayexpress

Changes in small RNAs upon Viral infection of C.elegans

Project description:Attempt to identify small non-coding RNAs that change in levels as a result of viral infection of C.elegans Small non-coding RNA (18-30nt) was extracted from animals either infected with Orsay virus or uninfected as indicated.

2013-06-01 | E-GEOD-41057 | biostudies-arrayexpress

Transgenerational changes in small RNA profiles of C.elegans mutants lacking PRG-1

Project description:An attempt to identify small non-coding RNAs that change with increasing generations after becoming homozygous for the loss of PRG-1 Small non-coding RNA (18-30nt) was extracted from animals the indicated number of generations after homozygosity was established

2013-06-01 | E-GEOD-40572 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data