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791 results for “noncoding”
Alignments of chloroplast noncoding regions for context-dependency analysis
<p>Substitutions between closely related noncoding chloroplast DNA sequences are studied with respect to the composition of the three bases on each side of the substitution, that is the hexanucleotide context. There is about 100-fold variation in rate, amongst the contexts, particularly on substitutions of A and T. Rate heterogeneity of transitions differs from that of transversions, resulting in a more than 200-fold variation in the transitions:transversion bias. The data are consistent with a CpG effect, and it is shown that both the A+T content and the arrangement of purines/pyrimidines along the same DNA strand are correlated with rate variation. Expected equilibrium A+T content ranges from 36.4% to 82.8% across contexts, while G-C skew ranges from -77.4 to 72.2 and A-T skew from -63.9 to 68.2. The predicted equilibria are associated with specific features of the content of the hexanucleotide context, and also show close agreement with the observed context-dependent compositions. Finally, by controlling for the content of nucleotides closer to the substitution site it is shown that both the third and fourth nucleotide removed on each side of the substitution directly influence substitution dynamics at that site. Overall, the results demonstrate that noncoding sites in different contexts are evolving along very different evolutionary trajectories and that substitution dynamics are far more complex than typically assumed. This has important implications for a number of types of sequence analysis, particularly analyses of natural selection, and the context-dependent substitution matrices developed here can be applied in future analyses.</p>
Coding and noncoding genes involved in atrophy and compensatory muscle growth in Nile Tilapia
<p><strong>Electronic Supplementary Material</strong><strong>: </strong>Supplementary Table S1;Supplementary Table S2;Supplementary Table S3</p>
FIGURE 1. A–B. Veltheimia capensis. A in Genetic diversity and species limits in Veltheimia (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data
FIGURE 1. A–B. Veltheimia capensis. A. Flowering plant in situ. B. Plant in fruit, also showing the papery tunic at the exposed part of the bulb. C–F. Veltheimia bracteata. C. Yellow form in cultivation. D. Common colour form. E. Striated leaved form from Baviaanskloof. F. Whole plant showing the globose bulb and fleshy scales. Photographs: A, B: L. Mucina; C: J. Sampson; D: T. Dold; E: G. Schafer; F: N. Barker.
FIGURE 2 in Genetic diversity and species limits in Veltheimia (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data
FIGURE 2. Specimen distribution of species of Veltheimia. Red dots = known localities of V. bracteata, blue triangles = known locations of V. capensis (based on data from the BODATSA database of the National Herbarium, South Africa, http://posa.sanbi.org/). The inserted frame shows the Bayesian Inference phylogeny of the combined chloroplast non-coding data set (numbers shown below the branches indicate Posterior Probability values, the number above the red branch is the parsimony Bootstrap Support value). The branch with the thick red line indicates the "bracteata clade". Numbers preceding sample names link to specimens listed in Table 1, and are also (where the locality is known) indicated on the map. The Median Joining Network (MJN) is shown overlaid on the distribution to indicate the location of the samples (and haplotypes) used in the MJN analysis. The numbers in parentheses next to the lines linking the haplotypes indicate the number of mutational differences between the haplotypes, and the solid black circle indicate an un-sampled or hypothesised missing haplotype.
Association of SNPs in Long Intergenic Noncoding RNA 00511 (LINC00511) With Breast Cancer Among the Egyptian Population
ClinicalTrials.gov study NCT06357689. IPD Sharing: UNDECIDED. Countries: 1. Publications: 17.
Alignments of chloroplast noncoding regions for context-dependency analysis
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Data from: Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis
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Evolution of conserved noncoding sequences in Arabidopsis thaliana
<p>Recent pangenome studies have revealed that a large fraction (>20%) of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana accessions from multiple distinct habitats and characterized species level variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered not only evidence for PAV and Positional Variation (PosV) but that diversity in CNS is non-random, with variants shared across different accessions. Using evolutionary analyses and chromatin accessibility data, we provide further evidence supporting conserved and variable CNS roles in gene regulation. Characterizing species-level diversity in all functional genomic sequences may later uncover previously unknown mechanistic links between genotype and phenotype.<span> </span></p>
Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness
<p><span>Body hair is a defining mammalian characteristic, but several mammals, such as whales, naked mole-rats, and humans, have notably less hair than others. To find the genetic basis of reduced hair quantity, we used our evolutionary-rates-based method, RERconverge, to identify coding and noncoding sequences that evolve at significantly different rates in so-called hairless mammals compared to hairy mammals. Using RERconverge, we performed an unbiased, genome-wide scan over 62 mammal species using 19,149 genes and 343,598 conserved noncoding regions to find genetic elements that evolve at significantly different rates in hairless mammals compared to hairy mammals. We show that these rate shifts resulted from relaxation of evolutionary constraint on hair-related sequences in hairless species. In addition to detecting known and potential novel hair-related genes, we also discovered hundreds of putative hair-related regulatory elements. Computational investigation revealed that genes and their associated noncoding regions show different evolutionary patterns and influence different aspects of hair growth and development. Many genes under accelerated evolution are associated with the structure of the hair shaft itself, while evolutionary rate shifts in noncoding regions also included the dermal papilla and matrix regions of the hair follicle that contribute to hair growth and cycling. Genes that were top-ranked for coding sequence acceleration included known hair and skin genes KRT2, KRT35, PKP1, and PTPRM that surprisingly showed no signals of evolutionary rate shifts in nearby noncoding regions. Conversely, accelerated noncoding regions are most strongly enriched near regulatory hair-related genes and microRNAs, such as mir205, ELF3, and FOXC1, that themselves do not show rate shifts in their protein-coding sequences. Such dichotomy highlights the interplay between the evolution of protein sequence and regulatory sequence to contribute to the emergence of a convergent phenotype.</span></p>
Assessment Of Long Noncoding RNA CCAT1 In Colorectal Cancer Patients
ClinicalTrials.gov study NCT04269746. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Data from: Timing transantarctic disjunctions in the Atherospermataceae (Laurales): evidence from coding and noncoding chloroplast sequences
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Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness
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Evolution of conserved noncoding sequences in Arabidopsis thaliana
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A transcribed ultra-conserved noncoding RNA, uc.285+, promotes colorectal cancer proliferation via directly binding mRNA
GEO Series GSE167326. Homo sapiens. 2 samples. Type: Non-coding RNA profiling by array.
Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of Ets-1 promoter-associated noncoding RNA (pancEts-1)
GEO Series GSE104950. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
A long noncoding RNA regulates sister chromatid cohesion
GEO Series GSE81602. Homo sapiens. 15 samples. Type: Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Senescence-associated lncRNAs: senescence-associated long noncoding RNAs.
GEO Series GSE77675. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Angiogenic patterning by STEEL, an endothelial-enriched long noncoding RNA
GEO Series GSE108321. Homo sapiens. 32 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
Oncogenic HPV E7 promotes the expression of a long noncoding RNA lnc-FANCI-2 via YY1 and miR-29a
GEO Series GSE150227. Homo sapiens. 18 samples. Type: Non-coding RNA profiling by high throughput sequencing.
The Long Noncoding RNA Lncenc1 Regulates Glycolysis in Naive Mouse ES Cells II
GEO Series GSE116462. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
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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.