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112 results for “Regulatory regions”
A chromosome-level genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes
<p><em>Echinometra</em> is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for <em>Echinometra</em> sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an N50 of 39.5 Mb. From this assembly we determined that the <em>E</em>. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO analysis showed that 95.3% of BUSCO genes were complete. ab initio and transcript-informed gene modeling and annotation identified 29,<span>405</span> genes, including a conserved Hox cluster. <em>E.</em> sp. EZ can be found in high-temperature and high-salinity environments, and we therefore compared gene families and transcription factors associated with environmental stress response ("defensome") with other echinoid species with similar high-quality genomic resources. While the number of defensome genes was broadly similar for all species, we identified strong signatures of positive selection in non-coding elements near genes involved in environmental response pathways as well as losses of transcriptions factors important for environmental response. These data provide key insights into the biology of <em>E</em>. sp. EZ as well as the diversification of <em>Echinometra</em> more widely and will serve as a useful tool for the community to explore questions in this taxonomic group and beyond.</p>
An over-dominant effect associated with an SNP in a TP63 regulatory region is implicated in susceptibility to non-syndromic orofacial clefts.
<p><strong>Background</strong>: Non-syndromic orofacial clefts (NSOC) are complex phenotypes, involving multiple low penetrance genetic and environmental factors. Using a candidate gene approach, we aimed to analyze the role of four single nucleotide polymorphisms (SNPs) in the susceptibility to NSOC.</p> <p><strong>Methods</strong>: A total of 254 individuals, 120 patients with NSOC, and 134 controls, all of Portuguese origin and non-consanguineous, were recruited. About 92% of patients had cleft lip with or without cleft palate (NSCL/P) and 8% had cleft palate (NSCP). Four SNPs in the <em>MTHFR</em>, <em>IRF6</em>, <em>PAX7,</em> and <em>TP63</em> genes were studied, using a real-time approach with TaqMan probes. Statistical analysis was performed with IBM SPSS Statistics and included chi-squared, Cochran test for trend and binomial logistic regression. Bonferroni correction was applied. Statistical significance was set to 0.05.</p> <p><strong>Results: </strong>All SNPs were in Hardy-Weinberg equilibrium. A significant statistical association was found for <em>TP63</em> rs9332461 in an over-dominant model (<em>p</em> = 0.016; OR 1.897 (1.144 - 3.147)).</p> <p><strong>Discussion and conclusion</strong>: Few SNPs have been so far identified in <em>TP63</em> in population association studies. In our sample, a significant association was only highlighted for rs9332461, localized in upstream regulatory region. Mechanisms involved in heterozygous advantage may underlie the association. </p>
A chromosome-level genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes
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Data from: Standing genomic variation within coding and regulatory regions contributes to the adaptive capacity to climate in a foundation tree species
Global climate is rapidly changing and the ability for tree species to adapt is dependent on standing genomic variation; however the distribution and abundance of functional and adaptive variants are poorly understood in natural systems. We test key hypotheses regarding the genetics of adaptive variation in a foundation tree: genomic variation is associated with climate and genomic variation is more likely to be associated with temperature than precipitation or aridity. To test these hypotheses, we used 9,593 independent, genomic single‐nucleotide polymorphisms (SNPs) from 270 individuals sampled from Corymbia calophylla's entire distribution in southwestern Western Australia, spanning orthogonal temperature and precipitation gradients. Environmental association analyses returned 537 unique SNPs putatively adaptive to climate. We identified SNPs associated with climatic variation (i.e. temperature (458), precipitation (75) and aridity (78)) across the landscape. Of these, 78 SNPs were non-synonymous (NS), while 26 SNPs were found within gene regulatory regions. The NS and regulatory candidate SNPs associated with temperature explained more deviance (27.35%) then precipitation (5.93%) and aridity (4.77%), suggesting that temperature provides stronger adaptive signals than precipitation. Genes associated with adaptive variants include functions important in stress responses to temperature and precipitation. Patterns of allelic turnover of NS and regulatory SNPs show small patterns of change through climate space with the exception of an aldehyde dehydrogenase gene variant with 80% allelic-turnover with temperature. Together, these findings provide evidence for the presence of adaptive variation to climate in a foundation species and provide critical information to guide adaptive management practices.
Data from: Standing genomic variation within coding and regulatory regions contributes to the adaptive capacity to climate in a foundation tree species
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Data from: The 5S rDNA gene family in mollusks: characterization of transcriptional regulatory regions, prediction of secondary structures, and long-term evolution, with special attention to Mytilidae mussels
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Data from: Positive selection in coding regions and motif duplication in regulatory regions of bottlenose dolphin MHC class II genes
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Data from: Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)
Latest technological developments in evolutionary biology bring new challenges in documenting the intricate genetic architecture of species in the process of divergence. Sympatric populations of lake whitefish represent one of the key systems to investigate this issue. Despite the value of random genotype-by-sequencing methods and decreasing cost of sequencing technologies, it remains challenging to investigate variation in coding regions, especially in the case of recently duplicated genomes as in salmonids, as this greatly complicates whole genome resequencing. We thus designed a sequence capture array targeting 2773 annotated genes to document the nature and the extent of genomic divergence between sympatric dwarf and normal whitefish. Among the 2728 genes successfully captured, a total of 2182 coding and 10 415 noncoding putative single-nucleotide polymorphisms (SNPs) were identified after applying a first set of basic filters. A genome scan with a quality-refined selection of 2203 SNPs identified 267 outlier SNPs in 210 candidate genes located in genomic regions potentially involved in whitefish divergence and reproductive isolation. We found highly heterogeneous FST estimates among SNP loci. There was an overall low level of coding polymorphism, with a predominance of noncoding mutations among outliers. The heterogeneous patterns of divergence among loci confirm the porous nature of genomes during speciation with gene flow. Considering that few protein-coding mutations were identified as highly divergent, our results, along with previous transcriptomic studies, imply that changes in regulatory regions most likely had a greater role in the process of whitefish population divergence than protein-coding mutations. This study is the first to demonstrate the efficiency of large-scale targeted resequencing for a nonmodel species with such a large and unsequenced genome.
Data from: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations
The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.
Data from: Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)
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Data from: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations
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Data from: Positive selection of the TRIM family regulatory region in primate genomes
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Role of Hmo1 and Nhp6 in SWI/SNF occupancy and nucleosome landscape at gene regulatory regions
GEO Series GSE86279. Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C. 21 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Genome-wide changes in DNase-hypersensitivity during osteoblastogenesis reveal differential usage of DNA motifs and define novel cis-regulatory regions that control gene expression during differentiat
GEO Series GSE55045. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Transcription factor occupancy is linked to DNA methylation turnover at active regulatory regions [Bisulfite-Seq]
GEO Series GSE39736. Mus musculus. 3 samples. Type: Methylation profiling by high throughput sequencing.
Hydroxymethylation at gene regulatory regions directs stem cell commitment during erythropoiesis
GEO Series GSE40243. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells
GEO Series GSE93014. Mus musculus. 29 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Arsenic-induced polyadenylation of canonical histone H3.1 mRNA displaces histone variant H3.3 from critical gene regulatory regions
GEO Series GSE135637. Homo sapiens. 34 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Deciphering the importance of the palindromic architecture of the immunoglobulin heavy chain 3’ regulatory region.
GEO Series GSE76359. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Maternal Malnutrition in Mice Impairs Nephrogenesis by Disrupting DNA Methylation of Regulatory Regions
GEO Series GSE249393. Mus musculus. 8 samples. Type: Methylation profiling by high throughput sequencing.
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Allen Brain Atlas
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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.