Comparative analysis of piRNA sequences, targets and functions in Caenorhabditis nematodes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA839379 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19270784.fastq.gz | Fastqsanger.gz | |||
| SRR19270785.fastq.gz | Fastqsanger.gz | |||
| SRR19270786.fastq.gz | Fastqsanger.gz | |||
| SRR19270787.fastq.gz | Fastqsanger.gz | |||
| SRR19270788.fastq.gz | Fastqsanger.gz |
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Project description:Piwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in C. briggsae, a sibling species of the model organism C. elegans. Our analyses define 25,883 piRNA producing-loci in C. briggsae. piRNA sequences in C. briggsae are extremely divergent from their counterparts in C. elegans, yet both species adopt similar genomic organization and transcription program that drive piRNA expression. By examining production of Piwi-dependent secondary small RNAs, we identified a set of protein-coding genes that are evolutionarily conserved piRNA targets. In contrast to C. elegans, small RNAs mapped to ribosomal RNAs or histone transcripts are not hyper-accumulated in C. briggsae. Instead, we found that fewer introns in transcripts are associated with hyper-accumulation of small RNAs. Together our work highlights evolutionary conservation and divergence of the nematode piRNA pathway and provides insights into its role in endogenous gene regulation.
2022-08-23 | GSE203297 | GEO
Project description:Piwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in C. briggsae, a sibling species of the model organism C. elegans. Our analyses define 25,883 piRNA producing-loci in C. briggsae. piRNA sequences in C. briggsae are extremely divergent from their counterparts in C. elegans, yet both species adopt similar genomic organization that drive piRNA expression. By examining production of Piwi-mediated secondary small RNAs, we identified a set of protein-coding genes that are evolutionarily conserved piRNA targets. In contrast to C. elegans, small RNAs targeting ribosomal RNAs or histone transcripts are not hyper-accumulated in C. briggsae Piwi mutants. Instead, we found that transcripts with few introns are prone to small RNA overamplification. Together our work highlights evolutionary conservation and divergence of the nematode piRNA pathway and provides insights into its role in endogenous gene regulation.
| S-EPMC9683057 | biostudies-literature
Project description:The nematode Caenorhabditis elegans contains each of the broad classes of eukaryotic small RNAs, including microRNAs (miRNAs), endogenous small-interfering RNAs (endo-siRNAs) and piwi-interacting RNAs (piRNAs). To better understand the evolution of these regulatory RNAs, we deep sequenced small RNAs from C. elegans and three closely related nematodes: C. briggsae, C. remanei and C. brenneri. The results reveal a fluid landscape of small RNA pathways with essentially no conservation of individual sequences aside from a subset of miRNAs. We identified 52 miRNA families that are conserved in each of the four species as well as numerous miRNAs that are species specific or shared between only two or three species. Despite a lack of conservation of individual piRNAs and siRNAs many of the features of each pathway, including genomic distribution, are conserved. We show that in each species, 26G siRNAs trigger stage-specific secondary siRNA formation. We also observe that piRNAs trigger siRNA formation from targets containing up to three mismatches in each species. Finally, we show that nematodes produce two distinct sex-specific classes of piRNAs, suggesting different roles for piRNAs in male and female germlines. Sequencing small RNAs from four Caenorhabditis species: C. elegans, C. briggsae, C. remanei and C. brenneri
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Project description:The nematode Caenorhabditis elegans contains each of the broad classes of eukaryotic small RNAs, including microRNAs (miRNAs), endogenous small-interfering RNAs (endo-siRNAs) and piwi-interacting RNAs (piRNAs). To better understand the evolution of these regulatory RNAs, we deep sequenced small RNAs from C. elegans and three closely related nematodes: C. briggsae, C. remanei and C. brenneri. The results reveal a fluid landscape of small RNA pathways with essentially no conservation of individual sequences aside from a subset of miRNAs. We identified 52 miRNA families that are conserved in each of the four species as well as numerous miRNAs that are species specific or shared between only two or three species. Despite a lack of conservation of individual piRNAs and siRNAs many of the features of each pathway, including genomic distribution, are conserved. We show that in each species, 26G siRNAs trigger stage-specific secondary siRNA formation. We also observe that piRNAs trigger siRNA formation from targets containing up to three mismatches in each species. Finally, we show that nematodes produce two distinct sex-specific classes of piRNAs, suggesting different roles for piRNAs in male and female germlines.
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Project description:Analysis of miRNA, piRNA and siRNA in Caenorhabditis species
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Project description:Abstract: Cells express distinct sets of genes in a precise spatio-temporal manner during embryonic development. There is a wealth of information about embryonic development in C. elegans, but much less is known about embryonic development at the molecular level in nematodes from other taxa. We are interested in insect pathogenic nematodes from the genus Steinernema as models of parasitism and symbiosis as well as a satellite model for evolution in comparison to C. elegans. We sequenced the transcriptomes of single embryos of two Steinernema species and two Caenorhabditis species at eleven specific stages during embryonic development for comparative analysis. We found that zygotic transcription initiates at different developmental stages in each species, with the Steinernema species initiating transcription at earlier developmental stages than Caenorhabditis. We found that ortholog expression conservation during development is highest at the later embryonic stages than at the earlier ones. Moreover, we found that the components of the neddylation pathway are highly upregulated during Steinernema early embryonic development contributing further to these early differences seen between the genera at the post-translational level. The surprisingly higher conservation of orthologous gene expression in later embryonic stages strongly suggests a funnel-shaped model of developmental gene expression divergence in nematodes. This work provides novel insight into embryonic development across distantly related nematode species and demonstrates that the mechanisms controlling early development are more diverse than previously thought at both the transcriptional and post-translational level.
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Project description:Hybridization Promotes Asexual Reproduction in Caenorhabditis Nematodes
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Project description:Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, S. glaseri) distantly related to Caenorhabditis elegans. We used these genomes to establish phylogenetic relationships, explore gene conservation across species, identify genes uniquely expanded in insect parasites, and to identify conserved non-coding regulatory motifs that influence similar biological processes. Protein domain analysis of these genomes reveals a striking expansion of numerous putative parasitism genes including certain protease and protease inhibitor families as well as fatty acid- and retinol-binding proteins. We identify rapid evolution and expansion of the important developmental Hox gene cluster and identify novel conserved non-coding regulatory motifs associated with orthologous genes in Steinernema and Caenorhabditis. The deep conservation of the network of non-coding DNA motifs between these two genera for a subset of orthologous genes involved in neurogenesis and embryonic development suggests that a kernel of protein-DNA relationships is conserved through nematode evolution. We analyzed the gene expression of a total of 24 RNA-seq samples from 3 nematode species( S. carpocapsae, S. feltiae, and C. elegans) for comparative analysis. We collected the RNA at four developmental time points (mixed embryo, L1, infective juvenile/dauer, young adult) for each species in replicates.
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