PIF transposases are recurrently domesticated as ovary and nervous system regulatory proteins in Drosophila
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ABSTRACT:
PROVIDER: PRJNA683611 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13218833.fastq.gz | Fastqsanger.gz | |||
| SRR13218834.fastq.gz | Fastqsanger.gz | |||
| SRR13218835.fastq.gz | Fastqsanger.gz | |||
| SRR13218836.fastq.gz | Fastqsanger.gz | |||
| SRR13218837.fastq.gz | Fastqsanger.gz |
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Project description:Proteins encoded by transposable elements (TEs) play a vital role in their proliferation in host genomes. In recent years, an increasing number of studies have shown that TE proteins have contributed to the emergence of novel host proteins. In Drosophila, there are several proteins derived from the PIF/Harbinger transposase superfamily called Drosophila PIF Like Genes (DPLGs). Here, we investigated the function of four DPLGs (DPLG1-4) in D. melanogaster that are highly conserved and present across Drosophila but are deeply diverged from each other, and likely originated through independent domestication of the transposase from distinct PIF-like TE families. We have analyzed transcript localization of DPLG 1-4, tagged DPLG3 and DPLG4 and studied their protein localization and, produced null alleles for DPLG1 and DPLG4. RNA in situ hybridization reveals that DPLG1-4 have strikingly similar pattern of transcript localization in the gonads, and in the nervous system during embryogenesis, suggesting their domestication for related functions. DPLGs show co-expression enrichment with transcription factors in ovaries and during embryogenesis supporting that they may be domesticated as regulatory proteins in flies. DPLG3 and DPLG4 tagged proteins localize with DNA in the nucleus of the ovaries consistent with this hypothesis. Loss of DPLG1 or DPLG4 results in viability and/or fertility effects, while loss of both DPLG1 and DPLG4 resulted in no effect in viability or fertility suggesting genetic interaction between these two genes. Further, loss of DPLG4 showed increased survival in flies, and increased fertility in older females indicating its involvement in the process of ageing. Transcriptional analyses in the ovaries showed that the loss of either DPLG1 or DPLG4 protein leads to modest changes in transcription of a large and significantly overlapping set of genes, and also affects transposable elements activity. The observed functional overlap of independently domesticated transposases from the same TE family and genetic interaction between them suggests a stepping stone model in which domestication of a PIF/Harbinger transposase might promote the domestication of related transposases for gonad and nervous system regulatory functions.
2021-12-31 | GSE162866 | GEO
Project description:Light-induced phosphorylation is necessary and essential for the degradation of phytochrome-interacting factors (PIFs), the central repressors of photomorphogenesis. Although the kinases responsible for PIF phosphorylation have been extensively studied, the phosphatases underlying PIF dephosphorylation are largely unknown. Here, we real that mutation of FyPP1 and FyPP3, two catalytic subunits of PP6 phosphatases, promoted photomorphogenesis of seedlings in the dark. PP6 and PIFs functioned synergistically to repress photomorphogenesis. FyPP1 and FyPP3 directly interacted with and dephosphorylated PIF3 and PIF4. The light-induced degradation of PIF4 and the PIF transcriptional activities were dependent on PP6 activity. These data demonstrate that PP6 phosphatases repress photomorphogenesis through regulation of PIF phosphorylation, protein stability and transcriptional activity.
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Project description:Pregnancy is an immune paradox: where the mother accepts a semi-allograft/allograft (donor embryo), while avoiding maternal immune suppression. Indeed, impaired development of maternal immune tolerance towards the conceptus may be an important cause of implantation failure and pregnancy loss. Successful implantation rates for allogenic donor embryos are unexpectedly high, while abnormal embryos may be unable to initiate maternal tolerance, suggesting that embryo-specific compounds can play a vital role in this process. Both a tolerant T-suppressor (TH2), and inflammatory, T-helper 1 (TH1) cytokine profiles are an integral part of pregnancy and the viable embryo/fetus plays a critical role in creating this delicate balance. Maternal recognition of pregnancy occurs prior to implantation. There were several embryo derived factors reported. However, we previously found that preimplantation factor (PIF) is distinct from the other non-pregnancy-specific embryo-derived factors. Herein we aimed to characterize PIF and examine its role in early pregnancy events by observing the isolated novel peptide's effect on human Peripheral Blood Mononuclear Cell (PBMC). We did affymetrix, GeneChip Human Genome U133 plus 2.0 array on RNA isolated from normal human PBMC cultured for 24hrs in the presence or absence of PIF to study the genes modulated by PIF. Experiment Overall Design: Blood was collected from a male volunteer and PBMC were separated using the Ficoll Hypaque method. Cells were cultured in RPMI culture media for 24 hours in four different groups in duplicate viz., Media alone, Media + 50 nM PIF, Media + 50nM PIF +CD3 (10µg/ml)+ CD28 (10µg/ml) and Media + CD3 (10µg/ml) +CD28 (10µg/ml). At the end of incubation cells were removed from the media, washed and collected in RNAlater (Qiagen) and transferred to Biocodon Sciences (Tx, USA) for Gene array analysis on dry ice. Samples were analyzed using the Agilent Bioanalyzer Process found to be adequate. Each 100 µl contained 2.7-5.4 µg RNA (Nanodrop analyzer). Each sample was tested integrity. RNA from duplicate samples was combined and array was performed on an Affymetrix chip (Human Genome U 133 Plus 2.0 Array). Subsequently, arrays were processed, scanned, data was extracted and statistical evaluation was carried out comparing the various groups. Data generated were categorized as robust changes or mild changes based on differences in expression.
2009-10-03 | E-GEOD-18291 | biostudies-arrayexpress
Project description:We sequenced mRNA from WT and PhytochromeInteractingFactor (pif) mutant seedlings grown for 2d in darkness. Transcriptome profiles of the wild-type (WT), pif1, pif3, pif, pif5 monogenic mutants, pif3pif4pif5 (pif345), pif1pif4pif5(pif145), pif1pif3pif5 (pif135) and pif1pif3pif4 (pif134) triple mutants and pif1pif3pif4pif5 (pifq) quadruple mutant seedlings. Biological triplicate samples were analyzed from libraries constructed using a 3'-capture, 5' to 3' directional method.
2014-10-02 | E-GEOD-42665 | biostudies-arrayexpress
Project description:Pregnancy is an immune paradox: where the mother accepts a semi-allograft/allograft (donor embryo), while avoiding maternal immune suppression. Indeed, impaired development of maternal immune tolerance towards the conceptus may be an important cause of implantation failure and pregnancy loss. Successful implantation rates for allogenic donor embryos are unexpectedly high, while abnormal embryos may be unable to initiate maternal tolerance, suggesting that embryo-specific compounds can play a vital role in this process. Both a tolerant T-suppressor (TH2), and inflammatory, T-helper 1 (TH1) cytokine profiles are an integral part of pregnancy and the viable embryo/fetus plays a critical role in creating this delicate balance. Maternal recognition of pregnancy occurs prior to implantation. There were several embryo derived factors reported. However, we previously found that preimplantation factor (PIF) is distinct from the other non-pregnancy-specific embryo-derived factors. Herein we aimed to characterize PIF and examine its role in early pregnancy events by observing the isolated novel peptide's effect on human Peripheral Blood Mononuclear Cell (PBMC). We did affymetrix, GeneChip Human Genome U133 plus 2.0 array on RNA isolated from normal human PBMC cultured for 24hrs in the presence or absence of PIF to study the genes modulated by PIF.
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Project description:Transcriptional profiling of Arabidopsis dark-induced senescence comparing wild type (Col-0) with pif quadruple (pif1/3/4/5) mutant. After synchronized germination, the plants were grown under continuous white light for 7 days and transferred to darkness for 2 days to induce senescence. Goal was to determine the effect of PIFs on transcriptomic regulation during dark-induced senescence. Two-condition experiment, wild type vs. pif quadruple mutant. Biological replicates: 3 wild type replicates, 3 mutant replicates.
2014-08-04 | E-GEOD-52646 | biostudies-arrayexpress
Project description:We sequenced mRNA from WT and PhytochromeInteractingFactor (pif) mutant seedlings grown for 2d in darkness.
2014-10-02 | GSE42665 | GEO
Project description:Induction of somatic oncogenic mutations by the domesticated DNA transposase PGBD5 in cerebellar progenitor cells promotes medulloblastoma development.
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Project description:Zebrafish populations recently collected from the wild differ from domesticated populations in anxiety-related behaviors. We measured anxiety-related behaviors in wild and domesticated zebrafish populations and performed a multi-brain region transcriptional comparison using microarrays to try to understand the genetic changes that accompany behavioral adaptation to domestication.
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Project description:A 44K salmonid oligoarray was used to examine the influence of genotype and developmental stage on mRNA expression in wild-type (age matched and size matched to domesticated), domesticated and wild-domesticated hybrid populations. Significant differences were found in mRNA expression between genotypes. The largest proportion of differentially expressed mRNAs were found in comparisons of domesticated and wild-type groups. Significant differences were also noted in pairings of wild-domesticated hybrid progeny to both parental strains. Differences in gene expression were found in comparison of both wild-type age and size matched to each other and in combination with genotype analysis, showing a strong effect of fish developmental stage on differential gene expression. Domestication was found to modify biological pathways associated with transport, metabolism, cell tissue structure and development, stress and immune response and protein synthesis. Genotype analysis of hybrid progeny inheritance patterns showed similar levels of recessive, dominant and additive effects.
2013-03-18 | GSE45151 | GEO