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4,582 results for “Gene regulation”
Data from: Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD
DUX4 is a transcription factor whose misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). While DUX4's transcriptional activity has been extensively characterized, the DUX4-induced proteome remains undescribed. Here, we report concurrent measurement of RNA and protein levels in DUX4-expressing cells via RNA-seq and quantitative mass spectrometry. DUX4 transcriptional targets were robustly translated, confirming the likely clinical relevance of proposed FSHD biomarkers. However, a multitude of mRNAs and proteins exhibited discordant expression changes upon DUX4 expression. Our dataset revealed unexpected proteomic, but not transcriptomic, dysregulation of diverse molecular pathways, including Golgi apparatus fragmentation, as well as extensive post-transcriptional buffering of stress response genes. Key components of RNA degradation machineries, including UPF1, UPF3B, and XRN1, exhibited suppressed protein, but not mRNA, levels, explaining the build-up of aberrant RNAs that characterizes DUX4-expressing cells. Our results provide a resource for the FSHD community and illustrate the importance of post-transcriptional processes to DUX4-induced pathology.
Data from: Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress-response and developmental genes when exposed to a biologically realistic heat stress
Oviparous reptile embryos are expected to breach their critical thermal maxima if temperatures reach those predicted under current climate change models due to the lack the maternal buffering processes and parental care. Heat shock proteins (HSPs) are integral in the molecular response to thermal stress, and their expression is heritable, but the roles of other candidate families such as the heat shock factors (HSFs) have not been determined in reptiles. Here we subject embryonic sea turtles (Caretta caretta) to a biologically realistic thermal stress and employ de novo transcriptomic profiling of brain tissue to investigate the underlying molecular response. From a reference transcriptome of 302,293 transcripts, 179 were identified as differentially expressed between treatments. As anticipated, genes enriched in the heat shock treatment were primarily associated with the Hsp families, or were genes whose products play similar protein editing and chaperone functions (e.g. bag3, MYOC and serpinh1). Unexpectedly, genes encoding the HSFs were not significantly upregulated under thermal stress, indicating their presence in unstressed cells in an inactive state. Genes that were downregulated under thermal stress were less well functionally defined but were associated with stress response, development, and cellular organization, suggesting that developmental processes may be compromised at realistically high temperatures. These results confirm that genes from the Hsp families play vital roles in the thermal tolerance of developing reptile embryos, and in addition with a number of other genes, should be targets for evaluating the capacity of oviparous reptiles to respond adaptively to the effects of climate change.
Data from: Seed traits are pleiotropically regulated by the flowering time gene PERPETUAL FLOWERING 1 (PEP1) in the perennial Arabis alpina
The life cycles of plants are characterized by two major life history transitions—germination and the initiation of flowering—the timing of which are important determinants of fitness. Unlike annuals, which make the transition from the vegetative to reproductive phase only once, perennials iterate reproduction in successive years. The floral repressor PERPETUAL FLOWERING 1 (PEP1), an orthologue of FLOWERING LOCUS C, in the alpine perennial Arabis alpina ensures the continuation of vegetative growth after flowering and thereby restricts the duration of the flowering episode. We performed greenhouse and garden experiments to compare flowering phenology, fecundity, and seed traits between A. alpina accessions that have a functional PEP1 allele and flower seasonally and pep1 mutants and accessions that carry lesions in PEP1 and flower perpetually. In the garden, perpetual genotypes flower asynchronously and show higher winter mortality than seasonal ones. PEP1 also pleiotropically regulates seed dormancy and longevity. Seeds from perpetual genotypes have shallow dormancy and reduced longevity regardless of whether they afterripened in plants grown in the greenhouse or in the experimental garden. These results suggest that perpetual genotypes have higher mortality during winter, but compensate by showing higher seedling establishment. Differences in seed traits between seasonal and perpetual genotypes are also coupled with differences in hormone sensitivity and expression of genes involved in hormonal pathways. Our study highlights the existence of pleiotropic regulation of seed traits by hub developmental regulators such as PEP1, suggesting that seed and flowering traits in perennial plants might be optimized in a coordinated fashion.
Data from: Dynamic expressions of hypothalamic genes regulate seasonal breeding in a natural rodent population
Seasonal breeding is a universal reproductive strategy in many animals. Hypothalamic genes, especially type 2 and 3 iodothyronine deiodinases (Dio2/3), RFamide-related peptide 3 (Rfrp-3), kisspeptin (Kiss-1), and gonadotropin-releasing hormone (GnRH), are involved in a photoperiodic pathway that encodes seasonal signals from day length in many vertebrate species. However, the seasonal expression patterns of these genes in wild mammals are less studied. Here, we present a four-year field investigation to reveal seasonal rhythm and age-dependent reproductive activity in male Brandt's voles (Lasiopodomys brandtii) and to detect relationships among seasonal expression profiles of hypothalamic genes, testicular activity, age, and annual day length. From breeding season (April) to non-breeding season (October), adult male voles displayed a synchronous peak in gonadal activity with annual day length around summer solstice, which was jointly caused by age structure shifts and age-dependent gonadal development patterns. Overwintered males maintained reproductive activity until late in the breeding season, whereas most newborn males terminated gonadal development completely, except for a minority of males born early in spring. Consistently, the synchronous and opposite expression profiles of Dio2/3 suggest their central function to decode photoperiodic signals and to predict the onset of the non-breeding season. Moreover, changes in Dio2/3 signals may guide the actions of Kiss-1 and Rfrp-3 to regulate the age-dependent divergence of reproductive strategy in wild Brandt's vole. Our results provide evidence on how hypothalamic photoperiod genes regulate seasonal breeding in a natural rodent population.
FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 in Billions and billions sold: Pet-feeder crickets (Orthoptera: Gryllidae), commercial cricket farms, an epizootic densovirus, and government regulations make for a potential disaster
FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 individuals of G. locorojo from eight "localities" on three continents. See Appendix A for specimen source data.
Population-level amplification of gene regulation by programmable gene transfer
<p>Source data for Son et al, "Population-level amplification of gene regulation by programmable gene transfer", Nature Chemical Biology.</p>
Differentially regulated genes in the heart of benzene exposed TAC-instrumented mice
<p><span>Benzene is a ubiquitous environmental pollutant abundant in household products, petrochemicals, and cigarette smoke. Benzene is a well-known carcinogen in humans and experimental animals; however, little is known about the cardiovascular toxicity of benzene. Recent population-based studies indicate that benzene exposure is associated with an increased risk for heart failure. Nonetheless, it is unclear whether benzene exposure is sufficient to induce and/or exacerbate heart failure. We examined the effects of benzene (50 ppm, 6 h/day, 5 days/week, 6 weeks) or HEPA-filtered air exposure on transverse aortic constriction (TAC)-induced pressure overload in male C57BL/6J mice. Our data show that benzene exposure had no effect on cardiac function in the Sham group; however, it significantly compromised cardiac function as depicted by a significant decrease in fractional shortening and ejection fraction, as compared with TAC/Air-exposed mice. RNA-seq analysis of the cardiac tissue from the TAC/benzene-exposed mice showed a significant increase in several genes associated with adhesion molecules, cell-cell adhesion, inflammation, and stress response. In particular, neutrophils were implicated in our unbiased analyses. Indeed, immunofluorescence studies showed that TAC/benzene exposure promotes infiltration of CD11b<sup>+</sup>/S100A8<sup>+</sup>/myeloperoxidase<sup>+</sup>-positive neutrophils in the hearts by 3-fold. <i>In vitro</i>, the benzene metabolites, hydroquinone, and catechol, induced the expression of P-selectin in cardiac microvascular endothelial cells by 5-fold and increased the adhesion of neutrophils to these endothelial cells by 1.5-2.0-fold. Benzene metabolite-induced adhesion of neutrophils to the endothelial cells was attenuated by anti-P-selectin antibody. Together, these data suggest that benzene exacerbates heart failure by promoting endothelial activation and neutrophil recruitment. </span></p>
Differential analysis of gene regulation at transcript resolution by RNA-Seqcount table
<p>Expression profiling by high throughput sequencing</p>
Plant circadian clock control of Medicago truncatula nodulation involving regulation of Nodule Cysteine-Rich genes
<p>Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcriptional factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset of Nodule-specific Cysteine Rich peptides (NCRs) that have the LHY-bound conserved Evening Element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis.</p>
GWAS summary statistics pertaining to the publication "Mapping of the gene network that regulates glycan clock of ageing"
<p>Dataset pertaining to the publication "Mapping of the gene network that regulates IgG galactosylation". If you use this dataset, please cite the manuscript in order to fairly acknowledge the contribution of all participating studies and their sponsors.</p> <p>Data consists of three gzipped files corresponding to genome-wide association meta-analysis (GWAMA) of three IgG N-glycome traits describing the percentage of galactosylation: G0, G1 and G2. The files are tab-separated and contain genome-wide association meta-analysis data for the discovery studies. Summary data are given for the meta-analyses of over 15 million directly genotyped or imputed single variant polymorphisms corresponding to the HRC (Haplotype Reference Consortium) r1.1 reference panel. Meta-analysis estimates are corrected for inflation of test statistics using genomic control at the individual study level.</p>
Collection of graphs presenting gene expression for transgressively down-regulated genes in livers.
<p>Transgressive gene expression was assessed for Cottus lineager of hybrid origing, compared to its parental species. Data contains graphs illustrating gene expression for genes classified af transgressively down-regulated in liver tissues.</p>
Collection of graphs presenting gene expression for transgressively up-regulated genes in fins.
<p>Transgressive gene expression was assessed for Cottus lineager of hybrid origing, compared to its parental species. Data contains graphs illustrating gene expression for genes classified af transgressively up-regulated in fin tissues.</p>
Collection of graphs presenting gene expression for transgressively up-regulated genes in livers.
<p>Transgressive gene expression was assessed for Cottus lineager of hybrid origing, compared to its parental species. Data contains graphs illustrating gene expression for genes classified af transgressively up-regulated in liver tissues.</p>
Collection of graphs presenting gene expression for transgressively down-regulated genes in fins.
<p>Transgressive gene expression was assessed for Cottus lineager of hybrid origing, compared to its parental species. Data contains graphs illustrating gene expression for genes classified af transgressively down-regulated in fin tissues.</p>
Sub-functionalization and epigenetic regulation of a biosynthetic gene cluster in Solanaceae
<p>Datasets for the code analysis in <em>Priego-Cubero, Knoch et al., 2024 </em>(https://doi.org/10.1101/2024.10.02.615186)</p>
Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs
<div> <div> <h2>Abstract</h2> <a href="https://github.com/christabel-bucao/fish-variability-across-organs/#abstract"></a></div> <p>Phenotypic variation among individuals plays a key role in evolution, since variation provides the material on which natural selection can act. One important link between genetic and phenotypic variation is gene expression. As for other phenotypes, the range of accessible expression variation is limited and biased by different evolutionary and developmental constraints. Gene expression variability broadly refers to the tendency of a gene to vary in expression (i.e., between individuals or cells) due to stochastic fluctuations or differences in genetic, epigenetic, or environmental factors, separately from the differences between e.g. organs. Variability due to biomolecular stochasticity (transcriptional ‘noise’) and cell-to-cell heterogeneity has been well-studied in isogenic populations of unicellular organisms such as bacteria and yeasts. However, for more complex organisms with multiple cells, tissues, and organs sharing the same genetic background, the interplay between inter-individual expression variability, gene and organ function, and gene regulation remains an open question. In this study, we used highly multiplexed 3’-end Bulk RNA Barcoding and sequencing (BRB-seq) to generate transcriptome profiles spanning at least nine organs in outbred individuals of three ray-finned fish species: zebrafish, Northern pike, and spotted gar. For each condition, we measured expression variation per gene independent of mean expression level. We observed that lowly variable genes are enriched in cellular housekeeping functions whereas highly variable genes are enriched in stimulus-response functions. Furthermore, genes with highly variable expression between individuals evolve under weaker purifying selection at the coding sequence level, indicating that intra-species gene expression variability predicts inter-species protein sequence divergence. Genes that are broadly expressed across organs tend to be both highly expressed and lowly variable between individuals, whereas organ-biased genes are typically highly variable within their top organ of expression. For genes with organ-biased expression profiles, we inferred differences in selective pressure on gene regulation depending on their top organ. We found that genes with peak expression in the brain have low inter-individual expression variability across non-nervous organs, suggesting stabilizing selection on regulatory evolution of brain-biased genes. Conversely, liver-biased genes have highly variable expression across organs, implying weaker regulatory constraints. These patterns show that gene regulatory mechanisms evolved differently based on constraints on the primary organ.</p> <h2>Directory Structure</h2> </div> <ul> <li> <p><code>config/</code>: Contains YAML file indicating package versions for conda environment</p> </li> <li> <p><code>data/</code>: Contains input data</p> <ul> <li><code>counts/</code>: Contains counts and UMI-deduplicated counts. Currently under embargo and will be made available upon acceptance for publication.</li> <li><code>gene_metadata/</code>: Contains gene biotype information from Ensembl</li> <li><code>sample_metadata/</code>: Contains sample metadata files for each species</li> <li><code>selectome/</code>: Contains selection statistics from the <a href="https://selectome.org/" rel="nofollow">Selectome</a> database<br><br></li> </ul> </li> <li> <p><code>results/</code>: Contains output files sorted by subfolders labeled after each step of the analysis pipeline. Only R notebook HTML files are available on the Git repository, please check Zenodo for R data files.</p> <ul> <li><code>run_pipeline.Rdata</code>: Contains all parameters used for each step of the analysis pipeline<br><br></li> </ul> </li> <li> <p><code>workflow/</code>: Contains scripts used for the analysis pipeline</p> <ul> <li><code>analysis/</code>: Contains all steps of the analysis pipeline, available as .Rmd files</li> <li><code>functions/</code>: Contains all functions used for analysis/</li> <li><code>renv/</code>: Used for package management in R</li> <li><code>run_pipeline.R</code>: Runs all the steps under analysis/</li> <li><code>run_go_figure.sh</code>: Runs <a href="https://gitlab.com/evogenlab/GO-Figure" rel="nofollow">GO-Figure!</a> 1.0.0 (downloaded separately)</li> <li><code>demultiplex_brbseq_fastq.sh</code>: Used for demultiplexing BRB-seq fastq files using <a href="https://github.com/DeplanckeLab/BRB-seqTools">BRB-seqTools</a> 1.6.1 (downloaded separately) for uploading to NCBI SRA</li> <li><code>rename_fastq_files.sh</code>: Used for renaming demultiplexed fastq files by mapping each barcode to their corresponding sample name</li> <li><code>renv.lock</code>: Lockfile for managing R package versions. Run <code>renv::restore()</code> to set up the R environment based on packages specified in the lockfile. All package versions used are also specified in the output HTML files under results/.</li> </ul> </li> </ul> <div> <h2>Species Codes</h2> </div> <ul> <li><strong>LOC</strong>: <em>Lepisosteus oculatus</em> (spotted gar)</li> <li><strong>ELU</strong>: <em>Esox lucius</em> (Northern pike)</li> <li><strong>DRE</strong>: <em>Danio rerio</em> (zebrafish)</li> </ul>
Data from: Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin
Across heterogeneous landscapes, populations may have adaptive differences in gene regulation that adjust their physiologies to match local environments. Such differences could have origins in acclimation or in genetically fixed variation between habitats. Here we use common garden experiments to evaluate differences in gene expression between populations of the purple sea urchin, Strongylocentrotus purpuratus, spanning 1700 km and average temperature differences of 5 °C to 8 °C. Across expression profiles from 18,883 genes after three years of common conditions, we find highly correlated expression patterns (Pearson's r = 0.992) among most genes. However, sixty-six genes were differentially expressed, including many ribosomal protein and biomineralization genes, all of which had higher expression in urchins originally from the southern population. Gene function analyses revealed slight but pervasive expression differences in genes related to ribosomal function, metabolism, transport, "bone" development, and response to stimuli. In accord with gene expression patterns, a post-hoc spine re-growth experiment revealed that urchins of southern origin re-grew spines at a faster rate than northern urchins. These results suggest that there may be genetically controlled, potentially adaptive differences in gene regulation across habitats and that gene expression differences may be under strong enough selection to overcome high dispersal-mediated gene flow in this marine species.
Data from: Phenotypic plasticity through transcriptional regulation of the evolutionary hotspot gene tan in Drosophila melanogaster
Phenotypic plasticity is the ability of a given genotype to produce different phenotypes in response to distinct environmental conditions. Phenotypic plasticity can be adaptive. Furthermore, it is thought to facilitate evolution. Although phenotypic plasticity is a widespread phenomenon, its molecular mechanisms are only beginning to be unravelled. Environmental conditions can affect gene expression through modification of chromatin structure, mainly via histone modifications, nucleosome remodelling or DNA methylation, suggesting that phenotypic plasticity might partly be due to chromatin plasticity. As a model of phenotypic plasticity, we study abdominal pigmentation of Drosophila melanogaster females, which is temperature sensitive. Abdominal pigmentation is indeed darker in females grown at 18°C than at 29°C. This phenomenon is thought to be adaptive as the dark pigmentation produced at lower temperature increases body temperature. We show here that temperature modulates the expression of tan (t), a pigmentation gene involved in melanin production. t is expressed 7 times more at 18°C than at 29°C in female abdominal epidermis. Genetic experiments show that modulation of t expression by temperature is essential for female abdominal pigmentation plasticity. Temperature modulates the activity of an enhancer of t without modifying compaction of its chromatin or level of the active histone mark H3K27ac. By contrast, the active mark H3K4me3 on the t promoter is strongly modulated by temperature. The H3K4 methyl-transferase involved in this process is likely Trithorax, as we show that it regulates t expression and the H3K4me3 level on the t promoter and also participates in female pigmentation and its plasticity. Interestingly, t was previously shown to be involved in inter-individual variation of female abdominal pigmentation in Drosophila melanogaster, and in abdominal pigmentation divergence between Drosophila species. Sensitivity of t expression to environmental conditions might therefore give more substrate for selection, explaining why this gene has frequently been involved in evolution of pigmentation.
Data from: Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Background: Life history traits like developmental time, age and size at maturity are directly related to fitness in all organisms and play a major role in adaptive evolution and speciation processes. Comparative genomic or transcriptomic approaches to identify positively selected genes involved in species divergence can help to generate hypotheses on the driving forces behind speciation. Here we use a bottom-up approach to investigate this hypothesis by comparative analysis of orthologous transcripts of four closely related European Radix species. Results: Snails of the genus Radix occupy species specific distribution ranges with distinct climatic niches, indicating a potential for natural selection driven speciation based on ecological niche differentiation. We then inferred phylogenetic relationships among the four Radix species based on whole mt-genomes plus 23 nuclear loci. Three different tests to infer selection and changes in amino acid properties yielded a total of 134 genes with signatures of positive selection. The majority of these genes belonged to the functional gene ontology categories "reproduction" and "genitalia" with an overrepresentation of the functions "development" and "growth rate". Conclusions: We show here that Radix species divergence may be primarily enforced by selection on life history traits such as (larval-) development and growth rate. We thus hypothesise that life history differences may confer advantages under the according climate regimes, e.g., species occupying warmer and dryer habitats might have a fitness advantage with fast developing susceptible life stages, which are more tolerant to habitat desiccation.
Supporting data for: Gene-rich UV sex chromosomes harbor conserved regulators of sexual development (Carey et al., 2021)
<p>Non-recombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here we generate and use nearly gapless female and male chromosome-scale reference genomes of the moss <i>Ceratodon purpureus </i>to test for degeneration in the bryophyte UV sex chromosome system. We show the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes show signs of weaker purifying selection than autosomes, we find suppressed recombination alone is insufficient to drive gene loss on sex-specific chromosomes. Instead, the U and V sex chromosomes harbor thousands of broadly-expressed genes, including numerous key regulators of sexual development across land plants.</p>
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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.