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ShareScore release 0.7.1
Dataset results
14 results for “trinucleotide repeat”
Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity
<p>The expansion of DNA trinucleotide repeats (TRs) beyond a threshold often results in neurodegenerative diseases in humans. The mechanisms causing these expansions remain unknown, although the tendency of TR ssDNA to self-associate into hairpins that slip along their length is widely presumed to be related. Here we apply single molecule FRET (smFRET) experiments and molecular dynamics simulations to determine conformational stabilities and slipping dynamics for CAG, CTG, GAC, and GTC hairpins. By developing novel analysis approaches for states with closely spaced FRET efficiencies along with improved transition detection algorithms, we determined the kinetic slipping schemes for these hairpins. Tetraloops are favored in CAG (89%), CTG (89%) and GTC (69%) while GAC favors triloops. We also determined that TTG interrupts near the loop in the CTG hairpin stabilize the hairpin against slipping (as do CAA substitutions in CAG hairpins). The different loop stabilities have implications for intermediate structures that may form when TR-containing duplex DNA opens. Opposing hairpins in the (CAG) ∙ (CTG) duplex would have matched stability whereas opposing hairpins in a (GAC) ∙ (GTC) duplex would have unmatched stability. This unmatched stability would introduce mechanical stress or frustration in the (GAC) ∙ (GTC) opposing hairpins that would be absent in (CAG) ∙ (CTG) structures. Given the biological observation that the CAG and CTG TR can undergo large, disease-related expansion whereas the GAC and GTC sequences do not, the mechanical stability differences we have identified can inform and constrain models of the expansion mechanisms of TR regions.</p>
Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity
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Data from: Spatial and environmental influences on selection in a clock gene coding trinucleotide repeat in Canada lynx (Lynx canadensis)
Clock genes exhibit substantial control over gene expression and ultimately life-histories using external cues such as photoperiod, and are thus likely to be critical for adaptation to shifting seasonal conditions and novel environments as species redistribute their ranges under climate change. Coding trinucleotide repeats (cTNRs) are found within several clock genes, and may be interesting targets of selection due to their containment within exonic regions and elevated mutation rates. Here, we conduct inter-specific characterization of the NR1D1 cTNR between Canada lynx and bobcat, and intra-specific spatial and environmental association analyses of neutral microsatellites and our functional cTNR marker, to investigate the role of selection on this locus in Canada lynx. We report signatures of divergent selection between lynx and bobcat, with the potential for hybrid-mediated gene flow in the area of range overlap. We also provide evidence that this locus is under selection across Canada lynx in eastern Canada, with both spatial and environmental variables significantly contributing to the explained variation, after controlling for neutral population structure. These results suggest that cTNRs may play an important role in the generation of functional diversity within some mammal species, and allow for contemporary rates of adaptation in wild populations in response to environmental change. We encourage continued investment into the study of cTNR markers to better understand their broader relevance to the evolution and adaptation of mammals.
CGG, CAG, and GAA: genome-wide comparison of the disease linked Trinucleotide short tandem repeat
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Data from: Spatial and environmental influences on selection in a clock gene coding trinucleotide repeat in Canada lynx (Lynx canadensis)
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Data from: Signatures of selection in mammalian clock genes with coding trinucleotide repeats: implications for studying the genomics of high-pace adaptation
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Analyzing Presymptomatic Tissue to Gain Insights into Late-Onset Degenerative Trinucleotide Repeat Disease
GEO Series GSE142538. Homo sapiens. 25 samples. Type: Expression profiling by high throughput sequencing.
Nuclear MBL-1 modulates mitochondrial morphology through carnitine palmitoyltransferase in C. elegans with toxic trinucleotide repeats
GEO Series GSE311723. Caenorhabditis elegans. 36 samples. Type: Expression profiling by high throughput sequencing.
A novel approach to investigate tissue-specific trinucleotide repeat instability
GEO Series GSE19780. Mus musculus. 12 samples. Type: Expression profiling by array.
Evidence for toxic CAG trinucleotide repeats contributing to Huntington’s disease though RNA interference
GEO Series GSE201692. Homo sapiens. 10 samples. Type: Other.
A novel approach to investigate tissue-specific trinucleotide repeat instability - A validation set of prediction model
GEO Series GSE9025. Mus musculus. 2 samples. Type: Expression profiling by array.
Evidence for toxic CAG trinucleotide repeats contributing to Huntington’s disease though RNA interference
GEO Series GSE201694. synthetic construct. 8 samples. Type: Other.
Evidence for toxic CAG trinucleotide repeats contributing to Huntington’s disease though RNA interference
GEO Series GSE201691. Mus musculus. 8 samples. Type: Other.
Generation and Characterization of Tcf4 CTG Trinucleotide Repeat Expansion Knock-in Mouse as a Model for Fuchs Endothelial Corneal Dystrophy
GEO Series GSE283422. Mus musculus. 10 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.