Extensive oscillatory gene expression during C. elegans larval development [RNA-seq for polyA enriched mRNAs]
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ABSTRACT: 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
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
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.
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.
Project description: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.
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
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.
Project description:Transcriptome profiling of three models with impaired insulin/IGF1 signaling. 1. Deep sequencing of endogenous mRNA from Caenorhabditis elegans N2 var. Bristol (wildtype) and daf-2(e1370) mutant; 2. Deep sequencing of endogenous mRNA from murine embryonic fibroblasts (MEF) wildtype and irs1-/- knockout; 3. Deep sequencing of endogenous mRNA from murine embryoinic fibroblast (MEF) insr+/- -lox and insr+/- knockout 14 samples examined: C. elegans N2 var. Bristol (wildtype) vs. daf-2(e1370) mutant; MEF wildtype vs. irs1-/- knockout; MEF insr+/- -lox vs. insr +/- knockout
Project description:We compare whole-animal RNA-seq transcriptomes for C. elegans males and hermaphrodites from the late L3 larval stage to young adulthood. During this interval, male sexual structures develop, including extensive neurogenesis and synaptogenesis that nearly doubles the size of the nervous system. Previous genome-wide expression studies in C. elegans have usually focused on only one sex â the hermaphrodite, and there are a relatively large number of predicted genes that still remain without meaningful annotation. In the present study, differential expression analysis of the RNA-seq data revealed 1,751 genes expressed at a higher level in the male. By differential expression analysis, unbiased gene correlation analysis, and a guilt-by-association approach, we identified new transcription factors required for differentiation of male genital structures, semen proteins, and candidates for previously-unknown components for synapse function. The results validate the dataset as a rich resource for future gene discovery in C. elegans. To analyze gene expression during sexual maturation in C. elegans, we performed RNA-seq for five samples for each sex ranging at 6 hr intervals from late L3 to young adult stages
Project description:Background: Arsenite is one of the most toxic chemical substances known and is assumed to exert detrimental effects on viability even at lowest concentrations. By contrast and unlike higher concentrations, we here find that exposure to low-dose arsenite promotes growth of cultured mammalian cells. In the nematode C. elegans, low-dose arsenite promotes resistance against thermal and chemical stressors, and extends lifespan of this metazoan, whereas higher concentrations reduce longevity. While arsenite causes a transient increase in reactive oxygen species (ROS) levels in C. elegans, co-exposure to ROS scavengers prevents the lifespan-extending capabilities of arsenite, indicating that transiently increased ROS levels act as transducers of arsenite effects on lifespan, a process known as mitohormesis. The RNA-seq data comprises 2 biological replicates for worms exposed to 100nM Arsenite 48h after L4 and 2 biological replicates of the same age as controls 4 samples: 2 mRNA profiles of C.elegans 48h after L4 exposed to Arsenite; 2 mRNA profiles of C.elegans 48h after L4 as controls (H20). The N2 wild type (var. Bristol) strain was used.
Project description:This SuperSeries is composed of the following subset Series: GSE30977: C. elegans: Dauers and Dauer-Exit at 12 hour time-point vs. Mix-stage worms GSE31861: P. pacificus : Dauers and Dauer-Exit at 12 hour time-point vs. Mix-stage worms Refer to individual Series