Genetic variants have potential influence on DNA methylation and thereby regulate mRNA expression. This study aimed to comprehensively reveal the relationships among SNP, methylation and mRNA, and identify methylation-mediated regulation patterns in human peripheral blood mononuclear cells (PBMCs). Based on in-house multi-omics datasets from 43 Chinese Han female subjects, genome-wide association trios were constructed by simultaneously testing the following three association pairs: SNP-methylation, methylation-mRNA and SNP-mRNA. Causal inference test (CIT) was used to identify methylation-mediated genetic effects on mRNA. A total of 64,184 significant cis-methylation quantitative trait loci (meQTLs) were identified (FDR < 0.05). Among the 745 constructed trios, 464 trios formed SNP-methylation-mRNA regulation chains (CIT). Network analysis (Cytoscape 3.3.0) constructed multiple complex regulation networks among SNP, methylation and mRNA (eg a total of 43 SNPs simultaneously connected to cg22517527 and further to PRMT2, DIP2A and YBEY). The regulation chains were supported by the evidence from 4DGenome database, relevant to immune or inflammatory related diseases/traits, and overlapped with previous eQTLs from dbGaP and GTEx. The results provide new insights into the regulation patterns among SNP, DNA methylation and mRNA expression, especially for the methylation-mediated effects, and also increase our understanding of functional mechanisms underlying the established associations.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584519 | PMC |
| http://dx.doi.org/10.1111/jcmm.14315 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Differential Expression of miR-26b-5p, EGR1, and STAT1 in Peripheral Blood of Schizophrenia Patients.
Psychiatry Clin Psychopharmacol
December 2024
The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China.
Background: This study aimed to investigate miRNAs and upstream regulatory transcription factors involved in schizophrenia (SZ) pathogenesis.
Methods: Differential expression of miRNAs and genes in SZ patients was investigated utilizing the gene expression omnibus dataset, gene ontology annotations, and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis. Real-time quantitative polymerase chain reaction experiments were conducted to validate the predictive screening of regulatory genes in peripheral blood samples from 20 SZ patients and 20 healthy controls.
Circulating MicroRNAs Related to Arterial Stiffness in Adults with HIV Infection.
Viruses
December 2024
1st Internal Medicine Department, AHEPA University Hospital, School of Medicine, Aristotle University of Thessaloniki, 55436 Thessaloniki, Greece.
People with HIV (PWH) have an elevated risk of cardiovascular disease compared to those without HIV. This study aimed to investigate the relative serum expression of microRNAs (miRNAs) associated with arterial stiffness, a significant marker of cardiovascular disease. A total of 36 male PWH and 36 people without HIV, matched for age, body mass index, pack years, and dyslipidemia, were included in the study.
View Article and Find Full Text PDFPeripheral B Lymphocyte Serves as a Reservoir for the Persistently Covert Infection of Mandarin Fish Ranavirus.
Viruses
December 2024
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
Mandarin fish ranavirus (MRV) is a distinctive member among the genus of the family . The persistently covert infection of MRV was previously observed in a natural outbreak of MRV, but the underlying mechanism remains unclear. Here, we show that mandarin fish peripheral B lymphocytes are implemented as viral reservoirs to maintain the persistent infection.
View Article and Find Full Text PDFTissue-Specific DNA Methylation Changes in CD8 T Cells During Chronic Simian Immunodeficiency Virus Infection of Infant Rhesus Macaques.
Viruses
November 2024
Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA.
Robust CD8 T cell responses are critical for the control of HIV infection in both adults and children. Our understanding of the mechanisms driving these responses is based largely on studies of cells circulating in peripheral blood in adults, but the regulation of CD8 T cell responses in tissue sites is poorly understood, particularly in pediatric infections. DNA methylation is an epigenetic modification that regulates gene transcription.
View Article and Find Full Text PDFHorse Innate Immunity in the Control of Equine Infectious Anemia Virus Infection: A Preliminary Study.
Viruses
November 2024
Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Via Appia Nuova 1411, 00178 Rome, Italy.
The mechanisms of the innate immunity control of equine infectious anemia virus in horses are not yet widely described. Equine monocytes isolated from the peripheral blood of three Equine infectious anemia (EIA) seronegative horses were differentiated in vitro into macrophages that gave rise to mixed cell populations morphologically referable to M1 and M2 phenotypes. The addition of two equine recombinant cytokines and two EIA virus reference strains, Miami and Wyoming, induced a more specific cell differentiation, and as for other species, IFNγ and IL4 stimulation polarized horse macrophages respectively towards the M1 and the M2 phenotypes.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!