Candidate SNP Markers Significantly Altering the Affinity of the TATA-Binding Protein for the Promoters of Human Genes Associated with Primary Open-Angle Glaucoma

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(23), P. 12802 - 12802

Published: Nov. 28, 2024

Primary open-angle glaucoma (POAG) is the most common form of glaucoma. This condition leads to optic nerve degeneration and eventually blindness. Tobacco smoking, alcohol consumption, fast-food diets, obesity, heavy weight lifting, high-intensity physical exercises, many other bad habits are lifestyle-related risk factors for POAG. By contrast, moderate-intensity aerobic exercise Mediterranean diet can alleviate In this work, we first time estimated phylostratigraphic age indices (PAIs) all 153 POAG-related human genes in NCBI Gene Database. allowed us separate them into two groups: that appeared before after phylum Chordata, is, ophthalmologically speaking, camera-type eye evolved. Next, genes’ promoters, silico predicted 3835 candidate SNP markers significantly change TATA-binding protein (TBP) affinity these promoters and, through molecular mechanism, expression levels genes. Finally, verified our results against five independent web services—PANTHER, DAVID, STRING, MetaScape, GeneMANIA—as well as ClinVar database. It was concluded POAG likely be a symptom self-domestication syndrome, downside being civilized.

Language: Английский

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Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly.

F1000Research, Journal Year: 2022, Volume and Issue: 11, P. 120 - 120

Published: Jan. 31, 2022

Background: De novo assembly is often required for analysing short-read RNA sequencing data. An under-characterized aspect of the contigs produced chimerism, extent to which affects mapping, differential expression analysis and annotation. Despite long-read negating this issue, short-reads remain in use through on-going research archived datasets created during last two decades. Consequently, there still a need quantify chimerism its effects. Methods: Effects on mapping were quantified by simulating reads off Drosophila melanogaster cDNA library these related reference sets containing increasing levels chimerism. Next, ten read simulated divided into conditions where, within one, representing 1000 randomly selected transcripts over-represented across replicates. Differential was performed iteratively with set. Finally, an expectation r-squared values describing relationship between alignment transcript lengths matches involving those incrementing created. Similar calculated three graph-based assemblers, relative from input simulated, or sequenced (relative species represented), compared. Results: At 5% 95% sets, 100% 77% mapped, making success poor indicator over-representation, 953 identified analysis; at 10% 936 identified, while it 510. This indicates that despite success, per-transcript counts are unpredictably altered. R-squared obtained assemblers suggest 5-15% chimeric. Conclusions: Although not evident based had significant impact megablast identification. will have consequences past present experiments short-reads.

Language: Английский

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Large captivity effect based on gene expression comparisons between captive and wild shrew brains

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 3, 2023

ABSTRACT Compared to their free-ranging counterparts, wild animals in captivity are subject different conditions with lasting effects on physiology and behavior. Alterations gene expression response environmental changes occur upstream of physiological behavioral phenotypes, but there no experiments analyzing differential captive vs. mammals. We assessed profiles three brain regions (cortex, olfactory bulb, hippocampus) juvenile shrews ( Sorex araneus ) comparison kept for two months. found hundreds differentially expressed genes all regions, suggesting a large uniform effect. Many the downregulated significantly enrich pathways associated neurodegenerative disease (p<0.001), oxidative phosphorylation encoding ribosomal proteins (p<0.001). Transcriptomic shrew resemble responses identified several human pathologies, such as major depressive disorder neurodegeneration. Thus, not only does impact function expression, may also confound analyses natural processes individuals under conditions. NEW & NOTEWORTHY To our knowledge, this is first study that identifies effect transcriptomic mammalian species, identifying 4,094 (p<0.05) at least one region implications experimental comparisons.

Language: Английский

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