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EGO-1, an essential C. elegans RdRP, modulates gene expression through the mRNA-templated production of short antisense effector RNAs

ABSTRACT: EGO-1, an essential C. elegans RdRP, modulates gene expression through the mRNA-templated production of short antisense effector RNAs

PROVIDER: PRJNA136471 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR097477.fastq.gz	Fastqsanger.gz
	SRR097478.fastq.gz	Fastqsanger.gz
	SRR097479.fastq.gz	Fastqsanger.gz
	SRR097480.fastq.gz	Fastqsanger.gz
	SRR097481.fastq.gz	Fastqsanger.gz

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

2011-06-01 | E-GEOD-26579 | 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

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

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

2011-06-01 | GSE26579 | 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

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

2011-06-01 | GSE26580 | GEO

EGO-1, an essential C. elegans RdRP, modulates gene expression through the mRNA-templated production of short antisense effector RNAs

Project description:This SuperSeries is composed of the SubSeries listed below.

2011-06-01 | GSE26582 | GEO

EGO-1, a C. elegans RdRP, modulates gene expression via production of mRNA-templated short antisense RNAs.

Project description:The development of the germline in Caenorhabditis elegans is a complex process involving the regulation of thousands of genes in a coordinated manner. Several genes required for small RNA biogenesis and function are among those required for the proper organization of the germline. EGO-1 is a putative RNA-directed RNA polymerase (RdRP) that is required for multiple aspects of C. elegans germline development and efficient RNA interference (RNAi) of germline-expressed genes. RdRPs have been proposed to act through a variety of mechanisms, including the posttranscriptional targeting of specific mRNAs, as well as through a direct interaction with chromatin. Despite extensive investigation, the molecular role of EGO-1 has remained enigmatic.Here we use high-throughput small RNA and messenger RNA sequencing to investigate EGO-1 function. We found that EGO-1 is required to produce a distinct pool of small RNAs antisense to a number of germline-expressed mRNAs through several developmental stages. These potential mRNA targets fall into distinct classes, including genes required for kinetochore and nuclear pore assembly, histone-modifying activities, and centromeric proteins. We also found several RNAi-related genes to be targets of EGO-1. Finally, we show a strong association between the loss of small RNAs and the rise of mRNA levels in ego-1(-) animals.Our data support the conclusion that EGO-1 produces triphosphorylated small RNAs derived from mRNA templates and that these small RNAs modulate gene expression through the targeting of their cognate mRNAs.

| S-EPMC3073447 | biostudies-literature

RPA and Rad27 limit templated and inverted insertions at DNA breaks

Project description:Formation of templated insertions at DNA double-strand breaks (DSBs) is very common in cancer cells. The mechanisms and enzymes regulating these events are largely unknown. Here, we investigated templated insertions in yeast at DSBs using amplicon sequencing across a repaired locus. We document very short (most ~5-34 bp), templated inverted duplications at DSBs. They are generated through a foldback mechanism that utilizes microhomologies adjacent to the DSB. Enzymatic requirements suggest a hybrid mechanism wherein one end requires Polδ-mediated synthesis while the other end is captured by nonhomologous end joining (NHEJ) or rarely by alternative end joining (Alt-EJ). This process is exacerbated in mutants with low levels or mutated RPA (rtt105Δ; rfa1-t33) or extensive resection mutant (sgs1Δ exo1Δ). Templated insertions from various distant genomic locations also increase in these mutants as well as in rad27 and originate from fragile regions of the genome. Among complex insertions, common events are insertions of two sequences, originating from the same locus and with inverted orientation. We propose that these inversions are also formed by microhomology-mediated template switching. Taken together, we propose that a shortage of RPA typical in cancer cells is one possible factor stimulating the formation of templated insertions.

2024-03-07 | GSE260753 | GEO

Set2-mediated H3K36 methylation states redundantly repress the production of antisense transcripts:: role in transcription regulation

Project description:Histone H3K36 can be added up to three methyl groups to form mono-, di-, and tri-methylation states. Recent study has shown that Set2 can suppress a specific group of antisense transcripts, which largely depends on the presence of H3K36 methylation. However, whether different methylation states possess distinct regulatory mechanisms on antisense transcripts is still unclear. In this study, we identified two yeast mutants that lack H3K36 di-methylation and tri-methylation, respectively. We also identified novel antisense transcripts in the absence of Set2 with own bioinformatics pipeline. Our study showed that the expression of these antisense transcripts does not affect the expression of corresponding sense genes. Different H3K36 methylation states (me2/me3) are not specific for the regulation of antisense expression, implying a co-regulation mechanism between them. Altogether, our study developed a method to identify new antisense transcripts, examined the potential effect of H3K36 di-methylation and tri-methylation on production of antisense transcripts. This study would shed light on the mechanism underlying how H3K36 methylation functions in the production of antisense transcripts.

2021-06-19 | GSE167338 | GEO

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