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Repertoire and evolution of miRNA genes in four divergent nematode species

ABSTRACT: We have performed small RNA sequencing in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei and Pristionchus pacificus, which have diverged up to 400 million years ago, to establish the repertoire and evolutionary dynamics of miRNAs in these species. In addition to previously known miRNA genes from C. elegans and C. briggsae we demonstrate expression of many of their homologs in C. remanei and P. pacificus, and identified in total more than 100 novel expressed miRNA genes, the majority of which belong to P. pacificus. More than half of all identified miRNA genes were found to be conserved at the seed level in all four nematode species, whereas only a few miRNAs appear to be species-specific. In our compendium of miRNAs we observed evidence for known mechanisms of miRNA evolution, including antisense transcription and arm switching, as well as miRNA family expansion through gene duplication. In addition, we identified a novel mode of miRNA evolution, termed ‘hairpin shifting’, in which an alternative hairpin is formed with up- or downstream sequences, leading to shifting of the hairpin and creation of novel miRNA* species. Finally, we identified 21U-RNAs in all four nematodes, including P. pacificus, where the upstream 21U-RNA motif is more diverged. However, the genomic distribution of 21U-RNA clusters in P. pacificus appears more scattered throughout the genome as compared to C. elegans. The identification and systematic analysis of small RNA repertoire in four nematode species described here provides a valuable resource for understanding the evolutionary dynamics of miRNA-mediated gene regulation.

ORGANISM(S): Caenorhabditis remanei Caenorhabditis briggsae Caenorhabditis elegans Pristionchus pacificus

PROVIDER: GSE15169 | GEO | 2009/09/08

SECONDARY ACCESSION(S): PRJNA114977

REPOSITORIES: GEO

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Repertoire and evolution of miRNA genes in four divergent nematode species

Project description:We have performed small RNA sequencing in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei and Pristionchus pacificus, which have diverged up to 400 million years ago, to establish the repertoire and evolutionary dynamics of miRNAs in these species. In addition to previously known miRNA genes from C. elegans and C. briggsae we demonstrate expression of many of their homologs in C. remanei and P. pacificus, and identified in total more than 100 novel expressed miRNA genes, the majority of which belong to P. pacificus. More than half of all identified miRNA genes were found to be conserved at the seed level in all four nematode species, whereas only a few miRNAs appear to be species-specific. In our compendium of miRNAs we observed evidence for known mechanisms of miRNA evolution, including antisense transcription and arm switching, as well as miRNA family expansion through gene duplication. In addition, we identified a novel mode of miRNA evolution, termed ‘hairpin shifting’, in which an alternative hairpin is formed with up- or downstream sequences, leading to shifting of the hairpin and creation of novel miRNA* species. Finally, we identified 21U-RNAs in all four nematodes, including P. pacificus, where the upstream 21U-RNA motif is more diverged. However, the genomic distribution of 21U-RNA clusters in P. pacificus appears more scattered throughout the genome as compared to C. elegans. The identification and systematic analysis of small RNA repertoire in four nematode species described here provides a valuable resource for understanding the evolutionary dynamics of miRNA-mediated gene regulation. Small RNAs were cloned from mixed stage animals. Sequencing was performed using the 454 GS FLX platform.

2009-09-07 | E-GEOD-15169 | biostudies-arrayexpress

Analysis of miRNA, piRNA and siRNA in Caenorhabditis species

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

2012-10-11 | E-GEOD-41461 | biostudies-arrayexpress

Caenorhabditis sex-specific RNAseq

Project description:This project defines the transcriptomes of XO (male) and XX (female or mutant pseudo-female) Caenorhabditis nematodes. The data allow the overall composition and sexual regulation of the transcriptome within a single species to be determined. In addition, the five related species studied allow meta-comparisons between them. Because two of the five (C. elegans and C. briggsae) produce a self-fertile XX hermaphrodite, while the XX sex in the remaining three (C. japonica, C. remanei, and C. brenneri) are true females, the data are particularly useful for inferring effects of sexual mode on genome-wide gene expression. L4 larvae and adults were pooled for each sex for five species (C. elegans, C. briggsae, C. japonica, C. brenneri, and C. remanei). Each of these 10 species-sex combinations was replicated three times, for a total of 30 samples.

2012-10-25 | E-GEOD-41367 | biostudies-arrayexpress

Male and Female DNA and RNA sequencing in several nematode species

Project description:The overall goal of this investigation was to investigate X-content of sex-biased genes in several nematode species. The following species of nematode were investigated: *C. elegans, *N2; *C. brenneri, *PB2801; *C. briggsae, *AF16; *C. remanei*, PB4641; *P. **pacificus, *PS312*.* Genomic DNA sequencing data was used to assign X and autosomal - linkage to unassembled sequencing contigs. Male and female RNA seq data was then generated and used to determine sex-biased expression. For both DNA and RNA experiments, 50bp paired-end (DNA) or single-end (RNA) reads were generated on the Illumina HiSeq 2500. Sequencing lanes were multiplexed. Genomic DNA was isolated from 50-100 hand-picked young adult worms. At least two replicates for each sex were prepared. DNA was sheared via sonication and 350-500 bp sequencing libraries were prepared following the Illumina protocol. Total RNA was isolated from at least 1000 hand-picked L4/young adult worms (*C. **elegans, *N2) or J4/young adult worms (*P. pacificus, *PS312*). *PolyA beads were used to enrich for mRNA. Stranded RNAseq libraries were prepared via incorporation of dUTPs during cDNA synthesis, following the protocol detailed in Parkhomchuk et al, 2009. DNAseq and RNAseq reads were aligned to the appropriate WS228 reference genomes. DNA sequencing data (2-3 replicates) from male and female YA worms are included along with RNAseq data from C.elegans YA hermaphrodites and P.pacificus YA males and hermaphrodites.

2014-04-17 | E-GEOD-53144 | biostudies-arrayexpress

Male and Female DNA and RNA sequencing in several nematode species

2014-04-17 | GSE53144 | GEO

Transcription profiling of C. elegans daf-19(+) and daf-19(-) mutants

Project description:By screening for genes possessing canonical X-box sequences in promoters of three Caenorhabditis species, namely C. elegans, C. briggsae and C. remanei, we identified 93 genes (including known X-box regulated genes) that encode putative components of ciliated neurons in C. elegans and are subject to the same regulatory control. For many of these genes, restricted anatomical expression in ciliated cells was confirmed, and control of transcription by the ciliogenic DAF-19 RFX transcription factor was demonstrated by comparative transcriptional profiling of daf-19(+) and daf-19(-) animals. Experiment Overall Design: There 4 samples.

2008-06-14 | E-GEOD-6563 | biostudies-arrayexpress

Analysis of expression of genes regulated by DAF-19

2006-12-21 | GSE6563 | GEO

Caenorhabditis sex-specific RNAseq

2012-10-25 | GSE41367 | GEO

Analysis of miRNA, piRNA and siRNA in Caenorhabditis species

2012-10-11 | GSE41461 | GEO

C. elegans piRNAs are processed from capped-small RNAs transcribed at promoters throughout the genome

Project description:Piwi-interacting (pi) RNAs are a class of germline-expressed small RNAs that have been linked to epigenetic programming in metazoa. C. elegans piRNAs known as 21U-RNAs are defined by more than 15,000 genome-encoded species. To explore the origin of 21U-RNAs we employed methods to enrich the 5' ends of Pol II transcripts. We show that a species of capped-short (cs) RNA is frequently expressed bidirectionally at Pol II loci in C. elegans. Interestingly, at annotated 21U-RNA loci, csRNAs originate precisely 2 nt upstream of the mature piRNA species suggesting that csRNAs are piRNA precursors. In addition, we show that csRNAs associated with TS sites genome-wide define a previously overlooked class of 21U-RNA loci, and nearly double the number of piRNA species available for genome surveillance. Our methods should be of general utility in TS site identification and 5' anchored RNA-expression profiling.

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