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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Defining soma-specific/enriched and germline-specific/enriched transcripts

ABSTRACT: To define what genes are predominantly or specifically expressed in either soma or germline in C. elegans adults, total RNA was extracted from germline-less glp-4 mutant animals or from dissected gonads, respectively. Total RNA sequencing was peformed in duplicates. Four samples in total.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Dimos Gaidatzis

PROVIDER: E-GEOD-62857 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Functional characterization of C. elegans Y-box-binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes.

Arnold Andreas A Rahman Md Masuder MM Lee Man Chun MC Muehlhaeusser Sandra S Katic Iskra I Gaidatzis Dimos D Hess Daniel D Scheckel Claudia C Wright Jane E JE Stetak Attila A Boag Peter R PR Ciosk Rafal R

Nucleic acids research 20141105 21

The cold shock domain is one of the most highly conserved motifs between bacteria and higher eukaryotes. Y-box-binding proteins represent a subfamily of cold shock domain proteins with pleiotropic functions, ranging from transcription in the nucleus to translation in the cytoplasm. These proteins have been investigated in all major model organisms except Caenorhabditis elegans. In this study, we set out to fill this gap and present a functional characterization of CEYs, the C. elegans Y-box-bind ...[more]

PMID: 25378320

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Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (RNA-Seq)

Project description:We present a basic characterization of the function of Y-box binding proteins in C. elegans. Besides playing an important role for fertility in the germline (all four CEY proteins), we found that the presence of CEY-1 and CEY-4 is essential for the assembly of larger polysomes in the soma. We therefore performed ribosome-profiling in combination with total RNA sequencing in wild type and cey-1,-4 double mutant animals to globally compare mRNA levels and their translation status. Total RNA sequencing was peformed on RNA extacted from wild type and cey-1,-4 mutant animals in duplicates. Four samples in total.

2015-01-08 | E-GEOD-62858 | biostudies-arrayexpress

Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (ribosome)

Project description:We present a basic characterization of the function of Y-box binding proteins in C. elegans. Besides playing an important role for fertility in the germline (all four CEY proteins), we found that the presence of CEY-1 and CEY-4 is essential for the assembly of larger polysomes in the soma. We therefore performed ribosome-profiling in combination with total RNA sequencing in wild type and cey-1,-4 double mutant animals to globally compare mRNA levels and their translation status. Ribosome-profiling analysis was peformed on wild type and cey-1,-4 mutant animals in duplicates. Four samples in total.

2015-01-08 | E-GEOD-62859 | biostudies-arrayexpress

Extensive oscillatory gene expression during C. elegans larval development [RNA-seq for polyA enriched mRNAs]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Examination of three timecourses that were collected over C. elegans development and analyzed by RNA-seq of mRNA libraries

2014-03-01 | E-GEOD-52861 | biostudies-arrayexpress

Developmental Timecourses total-RNA sequencing [Ribosome repleted total RNA]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Examination of two timecourses that were collected over C. elegans development and analyzed by RNA-seq of "RiboMinus" libraries

2014-03-01 | E-GEOD-52864 | biostudies-arrayexpress

Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (RIP-Seq)

Project description:We present a basic characterization of the function of Y-box binding proteins (YBPs) in C. elegans. YBPs in other organisms are known RNA-binding proteins. Our global analysis of associated mRNAs supports a role of YBPs as general mRNA binders in C.elegans. FLAG IPs were performed on transgenic animals expressing FLAG-tagged versions of either CEY-1, CEY-2, or CEY-4. MYC IPs served as controls. All IPs were performed in duplicates. 12 samples in total.

2015-01-08 | E-GEOD-62856 | biostudies-arrayexpress

Extensive oscillatory gene expression during C. elegans larval development [Ribosome footprinting]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Ribosome-profiling analysis of a timecourse that was collected over C. elegans development

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RNA-seq for monitoring expression changes in absence of chromatin anchoring

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2015-12-11 | E-GEOD-74067 | biostudies-arrayexpress

LEM-2 ChIP-seq to study chromatin anchoring

Project description:Chromatin Immunoprecipitation against the nuclear envelope protein LEM-2 to detect association to the nuclear periphery. LEM-2 ChIP was performed on early embryo fixed extracts for wild-type and two mutants that have altered position of a perinuclear chromatin reporter. LEM-2 ChIP on early embryo chromatin extracts of three different genotypes: wild-type, met-2 set-25_delta_delta and cec-4_delta, in two independent biological replicas

2015-12-11 | E-GEOD-74133 | biostudies-arrayexpress

The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans

Project description:RNA interference (RNAi) is a potent mechanism for down-regulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi and other eukaryotes. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary siRNAs. Exogenous double stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition. The RDE-10/RDE-11 complex and the RNA dependent RNA polymerase RRF-1 then engage the target mRNA for secondary siRNA synthesis. However, the molecular link between primary siRNA production and secondary siRNA synthesis remains largely unknown. Furthermore, it is unclear if the sub-cellular sites for target mRNA recognition and degradation coincide with sites where siRNA synthesis and amplification occur. In the C. elegans germline, cytoplasmic P granules at the nuclear pores and perinuclear Mutator foci contribute to target mRNA surveillance and siRNA amplification, respectively. We report that RDE-12, a conserved FG domain containing DEAD-box helicase, localizes in P-granules and cytoplasmic foci that are enriched in RSD-6 but are excluded from the Mutator foci. Our results suggest that RDE-12 promotes secondary siRNA synthesis by orchestrating the recruitment of RDE-10 and RRF-1 to primary siRNA targeted mRNA in distinct cytoplasmic compartments. Examination of exogenous dsRNA trigger derived siRNA in wildtype and rde-12 mutant animals

2014-03-27 | E-GEOD-53830 | biostudies-arrayexpress

Degradome sequencing reveals an endogenous microRNA target in C. elegans

Project description:Total poly(A) RNAs from wild-type adult stage worms were subjected to high-throughput sequencing using an Illumina platform to detect RNA cleavage fragment. Wild-type (N2) C. elegans

2013-02-19 | E-GEOD-44336 | biostudies-arrayexpress

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