Bombycoidea
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB13955 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR396182_subreads.fastq.gz | Fastqsanger.gz | |||
| DRR396183_1.fastq.gz | Fastqsanger.gz | |||
| DRR396183_2.fastq.gz | Fastqsanger.gz | |||
| DRR396184.fastq.gz | Fastqsanger.gz | |||
| DRR396185.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:The piRNA pathway is an adaptive mechanism for maintaining the stability of the genome by repression selfish genomic elements such as transposons. As a host defense mechanism the piRNA pathway is rapidly evolving with different sets of piRNA silencing different targets in closely-related species. In male germline of D.melanogaster, repression of Stellate genes by piRNA generated from Supressor of Stellate, Su(Ste), locus is required for male fertility, but both Su(Ste) piRNA and their targets are absent in other Drosophila species. Here we showed that D.melanogaster genome contain non-coding genomic repeats that have sequence similarity to vasa, protein-coding host gene essential for germline development. In male germline Vasa Related (Varel) repeats produce abundant piRNA that are anti-sense to vasa, however, vasa mRNA escape silencing due to imperfect complementarity between piRNA and vasa sequences. Unexpectedly, we found that Varel piRNA of D.melanogaster target vasa of closely related D. mauritana species in interspecies hybrids. The same hybrids show derepression of harmful Stellate locus due to the absence of Su(Ste) piRNA. Thus, the piRNA pathway contributes to the reproductive isolation between Drosophila species, causing hybrid male sterility via misregulation of two different host factors.
2019-02-19 | GSE120802 | GEO
Project description:Despite being essential for fertility, genome defence pathway genes often evolve rapidly. However, little is known about the molecular basis of this adaptation. Here, we characterize the evolution of a protein interaction network within the PIWI-interacting small RNA (piRNA) genome defence pathway in Drosophila at unprecedented scale and evolutionary resolution. We uncover pervasive rapid evolution of a protein interaction network anchored at the Heterochromatin Protein 1 (HP1) paralog Rhino. Using complementary phylogenetic analysis, high-throughput yeast-two-hybrid matrix screening, and in vivo interaction analyses in cross-species transgenic flies, we characterized at least three distinct evolutionary protein interaction trajectories across ~40 million years of Drosophila evolution. The comprehensive cross-species interaction data set covering 11 piRNA pathway proteins of five Drosophila species revealed several protein interactions that are fully conserved, indicating functional conservation despite overall rapid amino acid sequence change. Other interactions are preserved through co-evolution and were detected only between proteins in closely related and within species. We also identified sets of species-restricted protein interactions which, through rewiring of a Rhino-anchored transcription factor network, may preserve critical roles in enabling and adapting piRNA production from heterochromatic loci. In sum, our analyses dissected principles of interaction evolution in an adaptively evolving protein-protein interaction network uncovering evolutionary and functional insight into germline piRNA production across Drosophila species. Our work provides key experimental evidence in support of a fundamental model proposing that intermolecular interaction innovation is a major molecular mechanism of evolutionary adaptation in protein-coding genes.
2024-10-05 | PXD053049 | Pride
Project description:In Drosophila, Piwi proteins use guide piRNAs to repress selfish genomic elements, protecting the genomic integrity of gametes and ensuring the fertility of animal species. Efficient transposon repression depends on amplification of piRNA guides in the ping-pong cycle, which in Drosophila entails tight cooperation between two Piwi proteins, Aub and Ago3. Here we show that post-translational modification, symmetric dimethylarginine (sDMA), of Aub is essential for piRNA biogenesis, transposon silencing and fertility. Methylation is triggered by loading of a piRNA guide into Aub, which exposes its unstructured N-terminal region to the PRMT5 methylosome complex. Thus, sDMA modification is a signal that Aub is loaded with piRNA guide. Amplification of piRNA in the ping-pong cycle requires assembly of a tertiary complex scaffolded by Krimper, which simultaneously binds the N-terminal regions of Aub and Ago3. To promote generation of new piRNA, Krimp uses its two Tudor domains to bind Aub and Ago3 in opposite modification and piRNA-loading states. Our results reveal essential functions of post-translational modifications in unstructured regions of Piwi proteins and of Tudor domains capable of discriminating between modification states in piRNA biogenesis and silencing.
2020-06-25 | GSE153156 | GEO
Project description:MicroRNAs (miRNAs) are involved in post-transcriptional regulation of gene expression. Since several miRNAs are known to affect the stability or translation of developmental regulatory genes, the origin of novel miRNAs may have contributed to the evolution of developmental processes and morphology. Lepidoptera (butterflies and moths) is a species-rich clade with a well-established phylogeny and abundant genomic resources, thereby representing an ideal system in which to study miRNA evolution. We sequenced small RNA libraries from developmental stages of two divergent lepidopterans, Cameraria ohridella (Horse chestnut Leafminer) and Pararge aegeria (Speckled Wood butterfly), discovering 90 and 81 conserved miRNAs respectively, and many species-specific miRNA sequences. Mapping miRNAs onto the lepidopteran phylogeny reveals rapid miRNA turnover and an episode of miRNA fixation early in lepidopteran evolution, implying that miRNA acquisition accompanied the early radiation of the Lepidoptera. One lepidopteran-specific miRNA gene, miR-2768, is located within an intron of the homeobox gene invected, involved in insect segmental and wing patterning. We identified cubitus interruptus (ci) as a likely direct target of miR-2768, and validated this suppression using a luciferase assay system. We propose a model by which miR-2768 modulates expression of ci in the segmentation pathway and in patterning of lepidopteran wing primordia. Examination of the small RNA complements pooled across life cycle stages in each of Cameraria ohridella and Pararge aegeria.
2014-11-26 | E-GEOD-63644 | biostudies-arrayexpress
Project description:The PIWI-interacting small RNA (piRNA) pathway silences transposons in the germline of almost all animals. Contrary to the conservation of the pathway, piRNA-producing loci turn over fast between species, even though some of these loci are found in syntenic regions and even when the sequences of the piRNA precursor transcripts are conserved. The evolution of piRNAs is a remarkable, yet poorly understood, characteristic of this class of small RNAs. In order to learn about the sequence changes that contribute to the fast evolution of piRNAs, we set out to analyse piRNA expression between genetically different mice. Here we report the sequencing and analysis of small RNAs from the mouse male germline of four classical inbred strains, one inbred wild-derived strain and one outbred strain. We show that the majority of piRNAs are produced from the same loci, with similar levels, in different mice, with notable exceptions. We find that genetic differences between individuals cause variation in piRNA expression from specific loci. We report differences in piRNA production at loci of the mouse genome with endogenous retrovirus insertions in the same strand as the piRNA-precursor transcripts. These results suggest that at least one of the piRNA biogenesis pathways identifies transcripts as piRNA precursors when these transcripts are post-transcriptionally controlled by strand-specific regulatory elements of endogenous retroviruses. Our findings provide evidence that transposable elements are major – although not the only – drivers of piRNA diversification in mammals.
2023-09-22 | GSE215030 | GEO
Project description:MicroRNAs (miRNAs) are involved in post-transcriptional regulation of gene expression. Since several miRNAs are known to affect the stability or translation of developmental regulatory genes, the origin of novel miRNAs may have contributed to the evolution of developmental processes and morphology. Lepidoptera (butterflies and moths) is a species-rich clade with a well-established phylogeny and abundant genomic resources, thereby representing an ideal system in which to study miRNA evolution. We sequenced small RNA libraries from developmental stages of two divergent lepidopterans, Cameraria ohridella (Horse chestnut Leafminer) and Pararge aegeria (Speckled Wood butterfly), discovering 90 and 81 conserved miRNAs respectively, and many species-specific miRNA sequences. Mapping miRNAs onto the lepidopteran phylogeny reveals rapid miRNA turnover and an episode of miRNA fixation early in lepidopteran evolution, implying that miRNA acquisition accompanied the early radiation of the Lepidoptera. One lepidopteran-specific miRNA gene, miR-2768, is located within an intron of the homeobox gene invected, involved in insect segmental and wing patterning. We identified cubitus interruptus (ci) as a likely direct target of miR-2768, and validated this suppression using a luciferase assay system. We propose a model by which miR-2768 modulates expression of ci in the segmentation pathway and in patterning of lepidopteran wing primordia.
2014-11-26 | GSE63644 | GEO
Project description:To elucidate potential roles of piRNA in lung cancer, we analyzed global piRNA expression profiles in 8 NSCLC and 3 HBE cell lines. RNA-seq results showed that >99% of the approximately 4.5 million reads were between 26 and 32 bases. Most of the piRNA loci are represented by two or more identical reads. We observed a total 555 expressed mature piRNAs, distributed among chromosomes and mitochondria with bias in chromosomes 1 and 6. 99% of the piRNAs are mapped to intergenic regions (64%) or introns (35%) and 1% to exons. Of the 555 mature piRNAs, 260 (47%) have been recorded in NCBI whereas 295 (53%) are novel. These results provide a comprehensive view of piRNA expressed in human bronchial epithelial cells and NSCLC cells.
2016-06-27 | GSE57681 | GEO
Project description:Argonaute proteins of the PIWI clade are central to transposon silencing in animal gonads. Their target specificity is defined by 22-30nt PIWI interacting RNAs (piRNAs), which mostly originate from discrete genomic loci termed piRNA clusters. Here we show that the RDC complex composed of Rhino, Deadlock and Cutoff defines dual-strand piRNA clusters genome-wide in Drosophila ovaries. The RDC complex is anchored to H3K9me3-marked chromatin in part via Rhino’s chromo-domain. Depletion of Piwi results in loss of the RDC and small RNAs at euchromatic piRNA source loci, demonstrating a feedback loop between Piwi and genomic piRNA sources. Intriguingly, profiles of RNA Polymerase II occupancy, nascent transcription and steady-state RNA levels reveal that the RDC licenses non-canonical transcription of dual-stranded piRNA clusters. Likely, this process involves 5’end protection of nascent RNAs and subsequent suppression of transcription termination. Together, our data provide a comprehensive model for the regulation and evolution of piRNA clusters.
2014-06-08 | GSE55824 | GEO
Project description:Piwi-interacting RNA (piRNA) are small RNA abundant in the germline across animal species. In fruit flies and mice, piRNA were implicated in maintenance of genomic integrity by transposable elements silencing. Outside of the germline, piRNA have only been found in Drosophila ovarian follicle cells. Previous studies further reported the presence of multiple piRNA-like small RNA (pilRNA) in fly heads and a small number of pilRNA in mouse tissues and human NK cells. Here, by analyzing high-throughput small RNA sequencing data in more than 130 fruit fly, mouse and rhesus macaque samples, we show widespread presence of pilRNA displaying all known characteristics of piRNA in multiple somatic tissues of these three species. In mouse pancreas and macaque epididymis, pilRNA abundance was compatible with piRNA abundance in the germline. Using in situ hybridizations, we further demonstrate pilRNA co-localization with mRNA expression of Piwi-family genes in all macaque tissues. These findings indicate that piRNA-like molecules might play important roles outside of the germline.
2011-06-01 | GSE27369 | GEO