Unravelling functions of a novel miRNA-aquaporin module linked to rice domestication
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PROVIDER: PRJNA822657 | ENA |
REPOSITORIES: ENA
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Project description:Background Understanding the genetic basis of phenotypic diversity is a challenge in contemporary biology. Domestication provides a model for unravelling aspects of this, for example with respect to stress sensitivity. Ancestral Red Junglefowl (RJF) show more fearful behaviour and a more pronounced HPA-axis reactivity than its domesticated descendant White Leghorn (WL). By comparing adrenal global gene transcription profiles between WL and RJF as well as their plasma levels of adrenal hormones in response to an acute stress event, we aimed at investigating the molecular basis for the altered physiological stress responsiveness in domesticated chicken.
2015-10-30 | E-MTAB-3622 | biostudies-arrayexpress
Project description:Aquaporin-11 (AQP11), a new member of the aquaporin family, is localized in the endoplasmic reticulum (ER). Aqp11–/– mice neonatally suffer from polycystic kidneys derived from the proximal tubule. Its onset is proceeded by the vacuolization of ER. However, the mechanism for the formation of vacuoles and the development of cysts remain to be clarified. Here, we show that Aqp11–/– mice and polycystic kidney disease animals share a common pathogenic mechanism of cyst formation. Keywords: Geneexpression profile of Aqp11 knokout mouse kidney
2008-10-01 | GSE10634 | GEO
Project description:Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. A wealth of archeological and population genetic data has established maize as a model system for studying domestication , genome evolution and the genetics and evolution of complex traits. We used expression profiling of 18,242 genes for 38 diverse maize genotypes and 18 teosinte genotypes to examine how domestication has re-shaped the transcriptome of maize seedlings. We detected evidence for more than 600 genes having significantly different expression levels in maize compared to teosinte as well as 800 genes with significantly altered co-expression profiles reflective of substantial rewiring of the transcriptome since domestication. These genes likely include loci with altered expression due to domestication. The genes with altered expression show a significant enrichment for genes located in regions that previous population genetic analyses have identified as having undergone a selective sweep during maize domestication; thirty-two genes previously identified as putative targets of selection also exhibit altered expression levels and co-expression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to out-crossed teosinte. These genes are over-represented for genes that function in response to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication and identifies several genes that may have contributed to the evolution of maize but also highlights the complementary information that can be gained by combining gene expression with population genetic analyses.
2012-04-01 | GSE30036 | GEO
Project description:Improving the yield by modifying plant architecture is key to progressive crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 promotes the critical transition from semi-prostrate growth and low yield in wild rice (Oryza rufipogon), to erect growth and high yield in Asian cultivated rice (O. sativa). The microdeletion harbors a tandem repeat of seven putative Cys2-His2 zinc-finger genes. Three of these genes regulate the plant architecture in O. rufipogon and are closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene. Therefore, we refer to this locus as RICE PLANT ARCHITECTURE DOMESTICATION (RPAD). Furthermore, a similar but independent 113-kb deletion was detected at the RPAD locus in African cultivated rice. These results indicate that the deletions, coupled with the loss of a tandem repeat of zinc-finger genes, drove the parallel domestication of plant architecture in Asian and African rice.
2018-07-04 | GSE116423 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE16889: Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the brain transcriptome GSE16897: Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the liver transcriptome GSE16901: Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the muscle transcriptome Refer to individual Series
2010-05-16 | E-GEOD-16903 | biostudies-arrayexpress
Project description:This experiment compared aRNA derived from the kidney inner medula of three mice lacking a functional aquaporin-1 gene to three wild type mice. Each sample was hybridized 4 times, against 4 of the other 5 samples, using an interwoven loop experimental design. Keywords: repeat sample
2004-05-05 | GSE1298 | GEO
Project description:Integrated microRNA and secretome analysis of human endometrial organoid reveal the miR-3194-5p/Aquaporin/S100A9 module in regulating trophoblast functions
| PRJNA811793 | ENA
Project description:The leaf transcriptome of the Arabidopsis thaliana aquaporin gene PIP1;2 T-DNA insertion line was compared to that of control plants. In total 730 genes were found to be differentially regulated. This regulation pattern was compared to mild drought stress and low CO2 Affymetrix data to elucidate whether loss of the aquaporin resembles transcriptomic changes of drought stress or lack of CO2 supply. Mild drought stress data were obtained from Harb A, Krishnan A, Ambavaram MMR, Pereira A (2010) Molecular and Physiological Analysis of Drought Stress in Arabidopsis Reveals Early Responses Leading to Acclimation in Plant Growth. Plant Physiology 154: 1254-1271 (GSE24177). Low CO2 data were obtained from Oliver E. Bläsing, Yves Gibon, Manuela Günther, Melanie Höhne, Rosa Morcuende, Daniel Osuna, Oliver Thimm, Björn Usadel, Wolf-Rüdiger Scheible, and Mark Stitt (2005) Sugars and Circadian Regulation Make Major Contributions to the Global Regulation of Diurnal Gene Expression in Arabidopsis. The Plant Cell, Vol. 17, 3257-3281 (GSE3423).
2015-01-10 | GSE34984 | GEO
Project description:Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection.
2018-03-08 | GSE79155 | GEO
Project description:Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection.
2018-03-08 | GSE79154 | GEO