Gene expression comparisons between captive and wild shrew brains reveal captivity effects

Biology Letters, Journal Year: 2025, Volume and Issue: 21(1)

Published: Jan. 1, 2025

Compared with their free-ranging counterparts, wild animals in captivity experience different conditions lasting physiological and behavioural effects. Although shifts gene expression are expected to occur upstream of these phenotypes, we found no previous comparisons captive versus mammals. We assessed profiles three brain regions (cortex, olfactory bulb hippocampus) shrews ( Sorex araneus ) compared kept for two months undertook sample dropout examine robustness given limited sizes. Consistent effects, hundreds differentially expressed genes all regions, 104 overlapping across three, that enriched pathways associated neurodegenerative disease, oxidative phosphorylation encoding ribosomal proteins. In the shrew, transcriptomic changes detected under resemble responses several human pathologies, including major depressive disorder neurodegeneration. While interpretations individual tempered by small sizes, propose influences function can confound analyses natural processes individuals conditions.

Language: Английский

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Stress Reactivity, Susceptibility to Hypertension, and Differential Expression of Genes in Hypertensive Compared to Normotensive Patients

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(5), P. 2835 - 2835

Published: March 4, 2022

Although half of hypertensive patients have parents, known hypertension-related human loci identified by genome-wide analysis explain only 3% hypertension heredity. Therefore, mainstream transcriptome profiling subjects addresses differentially expressed genes (DEGs) specific to gender, age, and comorbidities in accordance with predictive preventive personalized participatory medicine treating according their symptoms, individual lifestyle, genetic background. Within this paradigm, here, we determined whether, among the DEGs that could find, there is any theranostic molecular marker applicable everyone, everywhere, anytime. sequenced hippocampal tame aggressive rats, corresponding low high stress reactivity, an increase which raises risk; stress-reactivity-related rat compared them homologous animal DEGs. This yielded significant correlations between reactivity-related fold changes (log2 values) these DEG homologs. We found principal components, PC1 PC2, a half-difference half-sum log2 values. Using versus normotensive (as control), verified components. highlighted downregulation β-protocadherins hemoglobin as whole-genome markers associated wide vascular inner diameter blood viscosity, respectively.

Language: Английский

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Transcription Factors as Important Regulators of Changes in Behavior through Domestication of Gray Rats: Quantitative Data from RNA Sequencing

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(20), P. 12269 - 12269

Published: Oct. 14, 2022

Studies on hereditary fixation of the tame-behavior phenotype during animal domestication remain relevant and important because they are both basic research applied significance. In model animals, gray rats Rattus norvegicus bred for either an enhancement or reduction in defensive response to humans, first time, we used high-throughput RNA sequencing investigate differential expression genes tissue samples from tegmental region midbrain 2-month-old showing tame aggressive behavior. A total 42 differentially expressed (DEGs; adjusted p-value < 0.01 fold-change > 2) were identified, with 20 upregulated 22 downregulated compared rats. Among them, three encoding transcription factors (TFs) detected: Ascl3 was upregulated, whereas Fos Fosb brains brain. Other DEGs annotated as associated extracellular matrix components, transporter proteins, neurotransmitter system, signaling molecules, immune system proteins. We believe that these encode proteins constitute a multifactorial determining behavior which have been artificially selected. demonstrated several structural subtypes E-box motifs—known binding sites many developmental TFs bHLH class, including ASCL subfamily TFs—are enriched set promoters rats’. Because ASCL3 may act repressor target other hypothesize TF gene indicates longer neurogenesis (as rats), is sign neoteny domestication. Thus, our shows new function ASCL3: it play most role behavioral changes animals.

Language: Английский

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Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(4), P. 3996 - 3996

Published: Feb. 16, 2023

Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) is focused on differentially expressed genes (DEGs) specific gender, age, and pathogeneses. This approach fits in well with predictive, preventive, personalized, participatory medicine helps understand how, why, when, what ARDs one can develop depending their genetic background. Within this mainstream paradigm, we wanted find out whether the known ARD-linked DEGs available PubMed reveal a molecular marker that will serve purpose anyone’s any tissue at time. We sequenced periaqueductal gray (PAG) tame aggressive rats, identified rat-behavior-related DEGs, compared them homologous animal DEGs. analysis yielded statistically significant correlations between behavior-related ARD-susceptibility-related fold changes (log2 values) expression these DEG homologs. found principal components, PC1 PC2, corresponding half-sum half-difference log2 values, respectively. With linked ARD humans used as controls, verified components. only common for ARDs: an excess Fcγ receptor IIb suppressing immune cell hyperactivation.

Language: Английский

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Editorial: Bioinformatics of Genome Regulation, Volume II

Frontiers in Genetics, Journal Year: 2021, Volume and Issue: 12

Published: Nov. 8, 2021

EDITORIAL article Front. Genet., 08 November 2021Sec. Computational Genomics https://doi.org/10.3389/fgene.2021.795257

Language: Английский

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Candidate SNP Markers Significantly Altering the Affinity of TATA-Binding Protein for the Promoters of Human Hub Genes for Atherogenesis, Atherosclerosis and Atheroprotection

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(10), P. 9010 - 9010

Published: May 19, 2023

Atherosclerosis is a systemic disease in which focal lesions arteries promote the build-up of lipoproteins and cholesterol they are transporting. The development atheroma (atherogenesis) narrows blood vessels, reduces supply leads to cardiovascular diseases. According World Health Organization (WHO), diseases leading cause death, has been especially boosted since COVID-19 pandemic. There variety contributors atherosclerosis, including lifestyle factors genetic predisposition. Antioxidant diets recreational exercises act as atheroprotectors can retard atherogenesis. search for molecular markers atherogenesis atheroprotection predictive, preventive personalized medicine appears be most promising direction study atherosclerosis. In this work, we have analyzed 1068 human genes associated with atherogenesis, atherosclerosis atheroprotection. hub regulating these processes found ancient. silico analysis all 5112 SNPs their promoters revealed 330 candidate SNP markers, statistically significantly change affinity TATA-binding protein (TBP) promoters. These made us confident that natural selection acts against underexpression At same time, upregulation one promotes health.

Language: Английский

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RatDEGdb: a knowledge base of differentially expressed genes in the rat as a model object in biomedical research

Vavilov Journal of Genetics and Breeding, Journal Year: 2023, Volume and Issue: 27(7), P. 794 - 806

Published: Dec. 11, 2023

The animal models used in biomedical research cover virtually every human disease. RatDEGdb, a knowledge base of the differentially expressed genes (DEGs) rat as model object is collection published data on gene expression strains simulating arterial hypertension, age-related diseases, psychopathological conditions and other afflictions. current release contains information 25,101 DEGs representing 14,320 unique that change transcription levels 21 tissues 10 genetic 11 diseases based 45 original scientific papers. RatDEGdb novel that, unlike any database, it offers manually curated annotations rats with use independent clinical equal changes homologous revealed people pathologies. put were annotated their homologs affected people. In its release, 94,873 such for 321 836 959 papers found PubMed. may be interesting first all to geneticists, molecular biologists, physicians, advisors well experts biopharmaceutics, bioinformatics personalized genomics. publicly available at https://www.sysbio.ru/RatDEGdb.

Language: Английский

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AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(1), P. 607 - 607

Published: Jan. 3, 2024

The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, this work, we used Web-service Plant_SNP_TATA_Z-tester, which have previously developed, to run a uniform silico analysis transcriptional alterations 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located proximal promoter region. identified 54,993 significantly decreasing or increasing gene expression through changes TATA-binding protein affinity promoters. existence these highly conserved promoters may be explained intraspecific diversity kept stabilizing natural To support this, hand-annotated papers on some possessing their orthologs other and demonstrated effects expressions vital traits. We integrated estimates TBP-promoter AtSNP_TATAdb knowledge base showed significant correlations independent vivo experimental data. These appeared robust variations statistical criteria, genomic environment TATA box regions, plants growing conditions.

Language: Английский

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A Principal Components Analysis and Functional Annotation of Differentially Expressed Genes in Brain Regions of Gray Rats Selected for Tame or Aggressive Behavior

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(9), P. 4613 - 4613

Published: April 23, 2024

The process of domestication, despite its short duration as it compared with the time scale natural evolutionary process, has caused rapid and substantial changes in phenotype domestic animal species. Nonetheless, genetic mechanisms underlying these remain poorly understood. present study deals an analysis transcriptomes from four brain regions gray rats (Rattus norvegicus), serving experimental model object domestication. We gene expression profiles hypothalamus, hippocampus, periaqueductal matter, midbrain tegmental region between tame domesticated aggressive revealed subdivisions differentially expressed genes by principal components that explain main part variance. Functional (in DAVID (Database for Annotation, Visualization Integrated Discovery) Bioinformatics Resources database) allowed us to identify describe key biological processes can participate formation different behavioral patterns seen two groups rats. Using STRING- DB (search tool recurring instances neighboring genes) web service, we built a association network. engaged broad network interactions have been identified. Our offers data on whose levels change response artificial selection behavior during

Language: Английский

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Epigenetics and the evolution and feralization of domestic animals

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 187 - 215

Published: Jan. 1, 2024

Language: Английский

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