Changes in expression of microRNAs during C. elegans development
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE13339 | GEO | 2008/12/01
REPOSITORIES: GEO
Similar Datasets
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).
2008-12-01 | E-GEOD-13339 | biostudies-arrayexpress
Project description:We report a significant number of miRNAs and other non-coding small RNAs show dramatic changes in expression during aging in C. elegans. RNAs were prepared from four diffrent timepoints during adulthood of C. elegans hermaphrodites, Day 0, 5, 8 and 12 post-L4 molt, and used for making cDNA libraries for small RNAs. Each library was sequenced using recent advances in high-throughput sequencing technology, Solexa. This study should lead to a better understanding of the aging process and age-related diseases. 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 four timepoints during adulthood of C. elegans hermaphrodites (spe-9 (hc88), cultured at 23dC), Day 0, 5, 8 and 12 post L4-molt.
2009-12-31 | E-GEOD-18634 | biostudies-arrayexpress
Project description:We report a significant number of miRNAs and other non-coding small RNAs show dramatic changes in expression during aging in C. elegans. RNAs were prepared from four diffrent timepoints during adulthood of C. elegans hermaphrodites, Day 0, 5, 8 and 12 post-L4 molt, and used for making cDNA libraries for small RNAs. Each library was sequenced using recent advances in high-throughput sequencing technology, Solexa. This study should lead to a better understanding of the aging process and age-related diseases. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2009-12-31 | GSE18634 | GEO
Project description:Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated. Examination of small RNA expression in six different developmental stages (embryo, L1, L2, L3, L4, young adult) and mRNA expression in four stages (L1,L2,L3,L4) of C. elegans prg-1 mutant (wm161) .
2014-06-09 | E-GEOD-56272 | biostudies-arrayexpress
Project description:Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated. Examination of small RNA expression in six different developmental stages (embryo, L1, L2, L3, L4, young adult) and mRNA expression in four stages (L1,L2,L3,L4) of C. elegans prg-1 mutant (wm161) .
2014-06-09 | E-GEOD-56271 | biostudies-arrayexpress
Project description:Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated.
2014-06-09 | GSE56272 | GEO
Project description:Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated.
2014-06-09 | GSE56271 | GEO
Project description:During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small non-coding RNAs that play important roles in gene regulation during early embryonic development. Here, we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs, the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined. Significant sequence variation was observed at the 5' and 3' ends of miRNAs with a large number of extra nucleotides added in a non-template directed manner. We also identified a large and diverse set of piRNAs expressed during early development, far beyond that expected if piRNA expression is restricted to germ cells. Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis.
2012-03-01 | GSE27722 | GEO
Project description:During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small non-coding RNAs that play important roles in gene regulation during early embryonic development. Here, we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs, the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined. Significant sequence variation was observed at the 5' and 3' ends of miRNAs with a large number of extra nucleotides added in a non-template directed manner. We also identified a large and diverse set of piRNAs expressed during early development, far beyond that expected if piRNA expression is restricted to germ cells. Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through-put sequencing
2012-03-01 | E-GEOD-27722 | biostudies-arrayexpress
Project description:Many species undergo sexual reproduction to distribute the parental genomes and increase the genomic diversity of the progeny. Among such species, sexual dimorphism is often displayed through morphology, size, behavior, and life-span, depending on the survival and reproduction strategies of the species. The nematode Caenorhabditis elegans has two sexes, hermaphrodite and male, and only the hermaphrodites, which produce both oocytes and sperm, are essential for the perpetuation of the species. In this study, we found that dietary restriction, which is the most reproducible way to retard aging in many species, extends the life-span of C. elegans hermaphrodites but not that of males. Our analysis revealed that fasting induces male-enriched genes in hermaphrodites and that the sex determination pathway affects life-span regulation, even after the completion of development, and is regulated by food availability. Furthermore, fasting activates the entire X-chromosome only in hermaphrodites. Our tiling array analysis identified a fasting-inducible, X-linked non-coding RNA for which expression positively correlated with the activation level of the X-chromosome and longevity. These links between the sex determination mechanism and dietary restriction at multiple levels may give priority to the survival of hermaphrodites during food shortages in C. elegans.
2017-12-07 | GSE37303 | GEO