RNAi-dependent expression of sperm genes in ADL chemosensory neurons is required for olfactory responses in Caenorhabditis elegans
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ABSTRACT:
PROVIDER: PRJNA1118763 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29250208.fastq.gz | Fastqsanger.gz | |||
| SRR29250209.fastq.gz | Fastqsanger.gz | |||
| SRR29250210.fastq.gz | Fastqsanger.gz | |||
| SRR29250211.fastq.gz | Fastqsanger.gz | |||
| SRR29250212.fastq.gz | Fastqsanger.gz |
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Project description:Environmental conditions experienced early in the life of an animal can result in gene expression changes later in its life history. We have previously shown that C. elegans animals that experienced the developmentally arrested and stress resistant dauer stage (postdauers) retain a cellular memory of early-life stress that manifests during adulthood as genome-wide changes in gene expression, chromatin states, and altered life history traits. One consequence of developmental reprogramming in C. elegans postdauer adults is the downregulation of osm-9 TRPV channel gene expression in the ADL chemosensory neurons resulting in reduced avoidance to a pheromone component, ascr#3. This altered response to ascr#3 requires the principal effector of the somatic nuclear RNAi pathway, the Argonaute (AGO) NRDE-3. To investigate the role of the somatic nuclear RNAi pathway in regulating the developmental reprogramming of ADL due to early-life stress, we profiled the mRNA transcriptome of control and postdauer ADL in wild-type and nrde-3 mutant adults. We found 711 differentially expressed (DE) genes between control and postdauer ADL neurons, 90% of which are dependent upon NRDE-3. Additionally, we identified a conserved sequence that is enriched in the upstream regulatory sequences of the NRDE-3-dependent DE genes. Surprisingly, 214 of the ADL DE genes are considered “germline-expressed”, including 21 genes encoding the Major Sperm Proteins and two genes encoding the sperm-specific PP1 phosphatases, GSP-3 and GSP-4. Loss of function mutations in gsp-3 resulted in both aberrant avoidance and attraction behaviors. We also show that an AGO pseudogene, Y49F6A.1 (wago-11), is expressed in ADL and is required for ascr#3 avoidance. Overall, our results suggest that small RNAs and reproductive genes program the ADL mRNA transcriptome during their developmental history and highlight a nexus between neuronal and reproductive networks in calibrating animal neuroplasticity.
2024-07-11 | GSE268801 | GEO
Project description:Environmental conditions experienced early in the life of an animal can result in gene expression changes later in its life history. We have previously shown that C. elegans animals that experienced the developmentally arrested and stress resistant dauer stage (postdauers) retain a cellular memory of early-life stress that manifests during adulthood as genome-wide changes in gene expression, chromatin states, and altered life history traits. One consequence of developmental reprogramming in C. elegans postdauer adults is the downregulation of osm-9 TRPV channel gene expression in the ADL chemosensory neurons resulting in reduced avoidance to a pheromone component, ascr#3. This altered response to ascr#3 requires the principal effector of the somatic nuclear RNAi pathway, the Argonaute (AGO) NRDE-3. To investigate the role of the somatic nuclear RNAi pathway in regulating the developmental reprogramming of ADL due to early-life stress, we profiled the mRNA transcriptome of control and postdauer ADL in wild-type and nrde-3 mutant adults. We found 711 differentially expressed (DE) genes between control and postdauer ADL neurons, 90% of which are dependent upon NRDE-3. Additionally, we identified a conserved sequence that is enriched in the upstream regulatory sequences of the NRDE-3-dependent differentially expressed genes. Surprisingly, 214 of the ADL DE genes are considered "germline-expressed", including 21 genes encoding the Major Sperm Proteins and two genes encoding the sperm-specific PP1 phosphatases, GSP-3 and GSP-4. Loss of function mutations in gsp-3 resulted in both aberrant avoidance and attraction behaviors. We also show that an AGO pseudogene, Y49F6A.1 (wago-11), is expressed in ADL and is required for ascr#3 avoidance. Overall, our results suggest that small RNAs and reproductive genes program the ADL mRNA transcriptome during their developmental history and highlight a nexus between neuronal and reproductive networks in calibrating animal neuroplasticity.
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Project description:Aims of the project is the identification of soluble chemosensory proteins in the olfactory organs of the honeybee mite Varroa destructor. Different families of soluble proteins acting as carriers for odorants have been identified in hexapods, while very limited information is available for other terrestrial Arthropoda. In mites and ticks olfactory organs are located on the distal part of the forelegs and on the capitulum appendages. These two body tagmata and the second pair of legs as control, have been dissected out of phoretics and reproductives Varroa destructor females and protein extracts have been analysed through shotgun proteomics. Protein identification and relative quantification (Label-free quantification, LFQ) has been performed using MaxQuant (version 1.5.8.3). Among the proteins more abundant in appendages bearing chemosensory organs, considering as a model hexapoda soluble olfactory proteins, we have searched for small secreted proteins whose structure include a hydrophobic binding pocket.
2018-04-12 | PXD008679 | Pride
Project description:miRNA seq of sperm RNA after olfactory stress
| PRJNA591183 | ENA
Project description:In this study, we evaluated the role of the gnathosomoa (mouthpart) in chemosensing of the most devastating honey bee parasite, Varroa destructor mite. Through transcriptomic analysis, we compared the expression of putative chemosensory genes between the body parts containing the main chemosensory organs (the forelegs), gnathosoma and the rest of the body devoid of these two body parts. Furthermore, we checked the presence of chemosensory-related transcripts in the proteome of the gnathosoma. Our comparative transcriptomic analysis revealed the presence of 83 transcripts with known characteristic conserved domains belonging to eight chemosensory gene families in the three Varroa transcriptomes. Among these transcripts, 11 were significantly upregulated in the mite’s forelegs, compared to 8 and 10 in the gnathosoma and body devoid of both organs, respectively. Whilst the gnathosoma and the forelegs share similar expression of some putative lipid carrier proteins, membrane-bound receptors, and associated proteins, they also differ in the expression profiles of some transcripts belonging to these protein families. This suggests two functional chemosensory organs that may differ in their chemosensory function according to specific characteristics of compounds they detect. Moreover, the higher expression of some chemosensory transcripts in the body devoid of forelegs and gnathosoma compared to the gnathosoma alone, may suggest the presence of additional function of these transcripts or alternatively presence of additional external or internal chemosensory organs. Insights into the functional annotation of a highly expressed gustatory receptor present in both organs using RNA interference (RNAi) are also revealed.
2025-05-07 | PXD053065 | Pride
Project description:The olfactory gene repertoire is largely species-specific, shaped by the nature and necessityof chemosensory information for survival in each species' niche. We are intrigued by thisinterspecific variation and aim to investigate the olfactory transcriptome across mammals forevidence of selection at the level of receptor gene choice. Having collected this data frommice and rats, we now wish to extend the analysis to cows, and three primates. All of whichhave a well annotated olfactory sub-genome.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2015-01-14 | E-ERAD-320 | biostudies-arrayexpress
Project description:The olfactory gene repertoire is largely species-specific, shaped by the nature and necessityof chemosensory information for survival in each species' niche. We are intrigued by thisinterspecific variation and aim to investigate the olfactory transcriptome across mammals forevidence of selection at the level of receptor gene choice. Having collected this data from mice, rats, cows, and two primates, we now wish to extend the analysis to humans.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2015-07-07 | E-ERAD-373 | biostudies-arrayexpress
Project description:We report the first RNAseq study of human olfactory epithelium, aimed at obtaining a whole transcriptome overview of the sensory tissue. Our work reveals nearly 200 olfactory-enriched non-receptor transcripts, 80% of which have not yet been implicated in chemosensory function, thus providing a platform for future discovery. Our study further allowed us to quantitate the expression levels of most (90%) of the ~400 intact human olfactory receptor (OR) genes. The expression levels of different paralogous members of the OR repertoire span a 1000-fold range, suggesting a strong imbalance among different odorant specificities. Further, we obtained convincing hints that different human beings show different cross-repertoire expression patterns. Having successfully assembled transcripts for 100 OR genes, we observed prevalent genome-encoded mutations that render some transcripts inactive despite the fact that the protein coding region is intact, an unreported mechanism for OR pseudogenization. In sum, our transcriptome study offers important observations on genes that underlie olfactory function and provides a basis for significant future work.
2016-09-13 | GSE80249 | GEO
Project description:Chemosensation (olfaction, taste) is essential for detecting and assessing foods, such that dietary shifts elicit evolutionary changes in vertebrate chemosensory genes. The transition from hunting and gathering to agriculture dramatically altered how humans acquire food. Recent genetic and linguistic studies suggest agriculture may have precipitated olfactory degeneration. Here, we explore the effects of subsistence behaviors on olfactory (OR) and taste (TASR) receptor genes among rainforest foragers and neighboring agriculturalists in Africa and Southeast Asia. We analyze 378 functional OR and 26 functional TASR genes in 133 individuals across populations in Uganda (Twa, Sua, BaKiga) and the Philippines (Agta, Mamanwa, Manobo) with differing subsistence histories. We find no evidence of relaxed selection on chemosensory genes in agricultural populations. However, we identify subsistence-related signatures of local adaptation on chemosensory genes within each geographic region. Our results highlight the importance of culture, subsistence economy, and drift in human chemosensory perception.
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Project description:To better understand the olfactory mechanisms in G. mellonella, we established six transcriptomes from the antennae of male and female adults. A total of 226 chemosensory gene transcripts were identified, which included 36 chemosensory proteins, 52 odorant-binding proteins, 2 sensory neuron membrane proteins, 80 olfactory receptors, and 56 ionotropic receptors. The expression patterns of these genes were calculated from the estimated fragments per kilobase of transcript sequence per million fragments mapped, and the differentially expressed genes (DEGs) related to olfaction were validated by qRT-PCR. Among the 114 DEGs identified, 66 were exclusively or primarily expressed in the female antenna, whereas the rest were specifically expressed in the male antenna. These antenna-specific genes may provide useful subjects for advanced studies of their biological functions; this may provide a theoretical basis for the control of G. mellonella and the prevention of damage caused by this species using the male pheromone as a bait.
2020-12-06 | GSE107887 | GEO