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MRNA sequencing from ego-1(om84) and control L3, L4, and adult C. elegans hermaphrodites

ABSTRACT: Cellular RdRPs play a critical role in the development of many organisms. Using high-throughput small RNA and messenger RNA sequencing we found that the Caenorhabditis elegans RdRP, EGO-1, is required to produce small RNAs antisense to a number of germline-expressed genes through several developmental stages. We found that these genes fall into distinct classes including genes required for kinetochore and nuclear pore assembly, as well as the production of histone-modifying and centromeric proteins. We also found several RNAi-related genes to be targets of EGO-1. Finally, we show a strong correlation between the loss of small RNAs and the rise of mRNA levels in ego-1 mutant animals. mRNA sequencing from ego-1(om84) and control L3, L4, and adult C. elegans hermaphrodites

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Jay Maniar

PROVIDER: E-GEOD-26579 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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5'-monophosphate-dependent small RNA sequencing from ego-1(om84) and control adult C. elegans hermaphrodites

Project description:Cellular RdRPs play a critical role in the development of many organisms. Using high-throughput small RNA and messenger RNA sequencing we found that the Caenorhabditis elegans RdRP, EGO-1, is required to produce small RNAs antisense to a number of germline-expressed genes through several developmental stages. We found that these genes fall into distinct classes including genes required for kinetochore and nuclear pore assembly, as well as the production of histone-modifying and centromeric proteins. We also found several RNAi-related genes to be targets of EGO-1. Finally, we show a strong correlation between the loss of small RNAs and the rise of mRNA levels in ego-1 mutant animals. 5'-monophosphate-dependent small RNA sequencing from ego-1(om84) and control adult C. elegans hermaphrodites

2011-06-01 | E-GEOD-26580 | biostudies-arrayexpress

5'-monophosphate-independent small RNA sequencing from ego-1(om84) and control L3, L4, and adult C. elegans hermaphrodites

Project description:Cellular RdRPs play a critical role in the development of many organisms. Using high-throughput small RNA and messenger RNA sequencing we found that the Caenorhabditis elegans RdRP, EGO-1, is required to produce small RNAs antisense to a number of germline-expressed genes through several developmental stages. We found that these genes fall into distinct classes including genes required for kinetochore and nuclear pore assembly, as well as the production of histone-modifying and centromeric proteins. We also found several RNAi-related genes to be targets of EGO-1. Finally, we show a strong correlation between the loss of small RNAs and the rise of mRNA levels in ego-1 mutant animals. 5'-monophosphate-independent small RNA sequencing from ego-1(om84) and control L3, L4, and adult C. elegans hermaphrodites

2011-06-01 | E-GEOD-26581 | biostudies-arrayexpress

mRNA sequencing from ego-1(om84) and control L3, L4, and adult C. elegans hermaphrodites

2011-06-01 | GSE26579 | GEO

5'-monophosphate-dependent small RNA sequencing from ego-1(om84) and control adult C. elegans hermaphrodites

2011-06-01 | GSE26580 | GEO

5'-monophosphate-independent small RNA sequencing from ego-1(om84) and control L3, L4, and adult C. elegans hermaphrodites

2011-06-01 | GSE26581 | GEO

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Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in ERGO-1/Argonaute pathway

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Project description:RNA interference was first described in the nematode Caenorhabditis elegans. Ever since, several new endogenous small RNA pathways have been described and characterized to different degrees. Much like plants, but unlike Drosophila and mammals, worms have RNA-dependent RNA Polymerases (RdRPs) that directly synthesize small RNAs using other transcripts as a template. The very prominent secondary small interfering RNAs, also called 22G-RNAs, produced by the RdRPs RRF-1 and EGO-1 in C. elegans, maintain the 5’ triphosphate group, stemming from RdRP activity, also after loading into an Argonaute protein. This creates a technical issue, since 5’PPP groups decrease cloning efficiency for small RNA sequencing. To increase cloning efficiency of these small RNA species, a common practice in the field is the treatment of RNA samples, prior to library preparation, with Tobacco Acid pyrophosphatase (TAP). Recently, TAP production and supply was discontinued, so an alternative must be devised. We turned to RNA 5’ pyrophosphohydrolase (RppH), a commercially available pyrophosphatase isolated from E. coli. Here we directly compare TAP and RppH in their use for small RNA library preparation.

2018-03-20 | GSE111995 | GEO

RNA-dependent RNA polymerases in the black-legged tick produce Argonaute-dependent small RNAs and regulate genes

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2021-09-11 | GSE183810 | GEO

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