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4,582 results for “Gene regulation”
Data from: An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics
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Growth hormone pulses are differentially regulated by the circadian clock gene Bmal1
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Data from: Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation
Variation in the presence or absence of transposable elements (TEs) is a major source of genetic variation between individuals. Here, we identified 23,095 TE presence/absence variants between 216 Arabidopsis accessions. Most TE variants were rare, and we find these rare variants associated with local extremes of gene expression and DNA methylation levels within the population. Of the common alleles identified, two thirds were not in linkage disequilibrium with nearby SNPs, implicating these variants as a source of novel genetic diversity. Many common TE variants were associated with significantly altered expression of nearby genes, and a major fraction of inter-accession DNA methylation differences were associated with nearby TE insertions. Overall, this demonstrates that TE variants are a rich source of genetic diversity that likely plays an important role in facilitating epigenomic and transcriptional differences between individuals, and indicates a strong genetic basis for epigenetic variation.
Data from: Diurnal transcriptional regulation of endosymbiotically derived genes in the chlorarachniophyte Bigelowiella natans
Chlorarachniophyte algae possess complex plastids acquired by the secondary endosymbiosis of a green alga, and the plastids harbor a relict nucleus of the endosymbiont, the so-called nucleomorph. Due to massive gene transfer from the endosymbiont to the host, many proteins involved in plastid and nucleomorph are encoded by the nuclear genome. Genome sequences have provided a blueprint for the fate of endosymbiotically derived genes; however, transcriptional regulation of these genes remains poorly understood. To gain insight into the evolution of endosymbiotic genes, we performed genome-wide transcript profiling along the cell cycle of the chlorarachniophyte Bigelowiella natans, synchronized by light and dark cycles. Our comparative analyses demonstrated that transcript levels of 7,751 nuclear genes (35.7% of 21,706 genes) significantly oscillated along the diurnal/cell cycles, and those included 780 and 147 genes for putative plastid and nucleomorph-targeted proteins, respectively. Clustering analysis of those genes revealed the existence of transcriptional networks related to specific biological processes such as photosynthesis, carbon metabolism, translation, and DNA replication. Interestingly, transcripts of many plastid-targeted proteins in B. natans were induced before dawn, unlike other photosynthetic organisms. In contrast to nuclear genes, 99% nucleomorph genes were found to be constitutively expressed during the cycles. We also found that the nucleomorph DNA replication would be controlled by a nucleus-encoded viral-like DNA polymerase. The results of this study suggest that nucleomorph genes have lost transcriptional regulation along the diurnal cycles, and nuclear genes exert control over the complex plastid including the nucleomorph.
Data from: Evidence for parallel evolution of a gene involved in the regulation of spermatogenesis
PHD finger protein 7 (Phf7) is a male germline specific gene in Drosophila melanogaster that can trigger the male germline sexual fate and regulate spermatogenesis, and its human homologue can rescue fecundity defects in male flies lacking this gene. These findings prompted us to investigate conservation of reproductive strategies through studying the evolutionary origin of this gene. We find that Phf7 is present only in select species including mammals and some insects, whereas the closely related G2/M-phase specific E3 ubiquitin protein ligase (G2e3) is in the genome of most metazoans. Interestingly, phylogenetic analyses showed that vertebrate and insect Phf7 genes did not evolve from a common Phf7 ancestor but rather through independent duplication events from an ancestral G2e3. This is an example of parallel evolution in which a male germline factor evolved at least twice from a pre-existing template to develop new regulatory mechanisms of spermatogenesis.
Data from: Tandem-running and scouting behavior are characterized by up-regulation of learning and memory formation genes within the ant brain
Tandem-running is a recruitment behavior in ants that has been described as a form of teaching, where spatial information possessed by a leader is conveyed to following nestmates. Within Temnothorax ants, tandem-running is used within a variety of contexts, from foraging and nest relocation to – in the case of slavemaking species – slave raiding. Here, we elucidate the transcriptomic basis of scouting, tandem-leading, and tandem-following behavior across two species with divergent lifestyles: the slavemaking Temnothorax americanus and its primary, non-parasitic host T. longispinosus. Analysis of gene expression data from brains revealed that only a small number of unique differentially-expressed genes are responsible for scouting and tandem-running. Comparison of orthologous genes between T. americanus and T. longispinosus suggests that tandem-running is characterized by species-specific patterns of gene usage. However, within both species, tandem-leaders showed gene expression patterns median to those of scouts and tandem-followers, which was expected, as leaders can be recruited from either of the other two behavioral states. Most importantly, a number of differentially-expressed behavioral genes were found, with functions relating to learning and memory formation in other social and non-social insects. This includes a number of up-regulated receptor genes such as a glutamate and dopamine receptor, as well as serine/threonine protein phosphatases and kinases. Learning and memory genes were specifically up-regulated within scouts and tandem-followers, not only reinforcing previous behavioral studies into how Temnothorax navigate novel environments and share information, but also providing insight into the molecular underpinnings of teaching and learning within social insects.
Combinatorial expression of neurexin genes regulates glomerular targeting by olfactory sensory neurons
<p>This deposit contains the MERFISH data used in this study.</p>
Accurate Spatial Heterogeneity Dissection and Gene Regulation Interpretation for Spatial Transcriptomics using Dual Graph Contrastive Learning
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Cuproptosis-related genes in colorectal cancer: prognostic significance, immune function, methylation, and regulation
<p>Despite recent advances in therapeutic options, colorectal cancer (CRC) continues to be a lethal disease with a poor prognosis. A recently identified mode of cell death, cuproptosis is yet to be understood in the context of CRC. Herein, we identified a cuproptosis-related three-gene signature that correlates with CRC survival in the Cancer Genome Atlas (TCGA) cohort. With this signature, a nomogram was constructed with new prognostic values, and CDKN2A was identified as an independent risk factor for CRC. Furthermore, CDKN2A expression was significantly correlated with both immune cell infiltration and the immune response. A pan-cancer analysis also revealed the prognostic value and immunological correlations of CDKN2A in other tumor types. Additionally, downregulation of CDKN2A was associated with methylation of m6A. Last but not least, we constructed a ceRNA network to discover the lncRNA KCNQ1OT1/miR-125b-5p/CDKN2A regulatory pathway in CRC. In this study, we provided insights into the role of cuproptosis in CRC and identified CDKN2A as an important cuproptosis-related gene. These results need to be verified by further research.</p>
Study on the Regulation Mechanism of TBX5 Gene and Gegen Qinlian Decoction on Colorectal Cancer
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Data from: Yeast adapts to a changing stressful environment by evolving cross-protection and anticipatory gene regulation.
Organisms can protect themselves against future environmental change. An example is cross-protection, where physiological adaptation against a present environmental stressor can protect an organism against a future stressor. Another is anticipation, where an organism uses information about its present environment to trigger gene expression and other physiological changes adaptive in future environments. "Predictive" abilities like this exist in organisms that have been exposed to periodic changes in environments. It is unknown how readily they can evolve. To answer this question, we carried out laboratory evolution experiments in the yeast Saccharomyces cerevisiae. Specifically, we exposed three replicate populations of yeast to environments that varied cyclically between two stressors, salt stress and oxidative stress, every 10 generations, for a total of 300 generations. We evolved six replicate control populations in only one of these stressors for the same amount of time. We analyzed fitness changes and genome-scale expression changes in all these evolved populations. Our populations evolved asymmetric cross protection, where oxidative stress protects against salt stress but not vice versa. Gene expression data also suggest the evolution of anticipation and basal gene expression changes that occur uniquely in cyclic environments. Our study shows that highly complex physiological states that are adaptive in future environments can evolve on very short evolutionary time scales.
Comprehensive characterization of HNF4A and HNF1A genomic targets in pancreatic beta cells and hepatic cells reveals common and tissue-specific gene regulation
<p>Molecular dynamics simulation input files, initial and final coordinate files</p>
Efficacy and Safety of Vamifeport in Adult Participants With Homeostatic Iron Regulator Gene (HFE)-Related Hereditary Hemochromatosis
ClinicalTrials.gov study NCT07332091. IPD Sharing: YES. Countries: 17. Publications: 0.
Analysis of Mother-child Interaction and Regulation of Candidate Genes of Stress Signaling Pathways in Mature Infants
ClinicalTrials.gov study NCT03926923. IPD Sharing: NO. Countries: 1. Publications: 0.
Gene Regulation by Thiazolidinediones
ClinicalTrials.gov study NCT00567593. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Relationship Between Genes Important in Blood Pressure Regulation and Blood Pressure Therapy in Hypertension
ClinicalTrials.gov study NCT02524873. IPD Sharing: NO. Countries: 0. Publications: 0.
Data from: Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation
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Data from: Y-linked variation for autosomal immune gene regulation has the potential to shape sexually dimorphic immunity
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Data from: The clock gene Period1 regulates innate routine behaviour in mice
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Data from: Diurnal transcriptional regulation of endosymbiotically derived genes in the chlorarachniophyte Bigelowiella natans
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ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.