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Genetic Variants Influence on the Placental-specific Regulatory Landscape

ABSTRACT: Genetic Variants Influence on the Placental-specific Regulatory Landscape

PROVIDER: PRJNA497169 | ENA |

REPOSITORIES: ENA

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Genetic Variants Influence on the Placental-specific Regulatory Landscape

Project description:Genetic Variants Influence on the Placental-specific Regulatory Landscape

| PRJNA497170 | ENA

Genetic variants influence on the placenta regulatory landscape.

Project description: Not available

| S-EPMC6277118 | biostudies-literature

Genetic Variants Influence on the Placenta Regulatory Landscape

Project description:<p>This study of the regulatory landscape of the placenta relies on the identification of associations between genetic variant and gene expression changes (eQTLs); genetic variant and DNA methylation changes (mQTLs); and, gene expression change and DNA methylation change (eQTMs). It involves the analysis of DNA sequence variation (n=303), DNA methylation (n=303) and mRNA expression data (n=80) from placentas from healthy women. Such studies are crucial to fully apprehend the complexity of the regulatory landscape and to support further analysis focusing and disease driven phenotype.</p>

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Genetic Risk Variants for Autoimmune Diseases that Influence Gene Expression in Thymus

Project description:Genome-wide association studies (GWAS) have boosted our knowledge of genetic risk variants in autoimmune diseases (AIDs). Most of the risk variants are located within or near genes with immunological functions, and the majority is found to be non-coding, pointing towards a regulatory role. We have performed a cis expression quantitative trait locus (eQTL) screen to investigate whether single nucleotide polymorphisms (SNPs) associated with AIDs influence gene expression in thymus. Genotyping was performed using the Immunochip and 353 AID associated SNPs were tested against expression of surrounding genes (+/- 1 Mb) from human thymic tissue (N=42). We identified eight genes where the expression was associated with AID risk SNPs at a study-wide level of significance (P < 2.57x10-5). Five genes (FCRL3, RNASET2, C2orf74, SIRPG and SYS1) displayed cis eQTL signals also in other tissues, while for two loci (NPIPB8 and LOC388814), the eQTL signal appear to be thymus-specific. Since many AID risk variants from GWAS have been subsequently fine-mapped in recent Immunochip projects, we explored the overlap between these novel AID risk variants and the thymic eQTL regions. Moreover, we examined the functional annotation of the seven expression altering SNPs (eSNPs). Our study reveals autoimmune risk variants that act as eQTLs in thymus. We have highlighted functional variants within these genetic regions that potentially can represent causal autoimmune risk variants. Total RNA from 42 human thymic samples were obtained from children undergoing cardiac surgery.

2016-01-21 | E-GEOD-77052 | biostudies-arrayexpress

Genetic variants affecting RNA stability influence complex traits and disease risk

Project description:Genetic variants affecting RNA stability influence complex traits and disease risk

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Genetic variants affecting RNA stability influence complex traits and disease risk II

Project description:Genetic variants affecting RNA stability influence complex traits and disease risk II

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Genetic variants affecting RNA stability influence complex traits and disease risk I

Project description:Genetic variants affecting RNA stability influence complex traits and disease risk I

| PRJNA1268379 | ENA

HCMV infection mitigate the ability of placental EVs to potentiate neurogenesis by altering their miRNA landscape

Project description:Human cytomegalovirus (HCMV) is the most common virus transmitted in utero and a leading cause of infectious brain malformations and deafness, yet prognosis methods remain unreliable. Although certain central nervous system lesions caused by HCMV are explained, the neuropathogenesis of congenital infection remains poorly understood. The placenta, a key target of HCMV, plays a critical role during infection due to its involvement in maternal-fetal exchanges, particularly via the secretion of extracellular vesicles (EVs). Placental EVs mediate maternal-fetal communication, carrying proteins and RNAs, including microRNAs, that influence placental function, maternal immune tolerance, and viral defense. Our study explored the effects of placental EVs on fetal neural stem cell phenotype, demonstrating that EVs secreted from HCMV-infected placenta alter neurogenesis. Analysis of EV microRNA profiles revealed infection-induced alterations with predicted interference in brain development pathways. These findings highlight the critical role of placental EVs in fetal brain development and their contribution to HCMV neuropathogenesis.

2026-02-02 | PXD060921 | Pride

Genetic variants affecting RNA stability influence complex traits and disease risk

Project description:Gene expression is jointly modulated by transcriptional regulation and mRNA stability, yet the latter is often overlooked in studies on genetic variants. Leveraging metabolic labeling data (Bru/BruChase-seq) and a new computational pipeline, RNAtracker, we distinguished allele-specific RNA stability (asRS) from allele-specific RNA transcription (asRT) events. Our analysis identified >5,000 asRS variants, revealing comparable impact of stability on allelic imbalance as transcriptional regulation. This study highlights RNA stability as a critical, yet understudied mechanism linking genetic variation and disease.

2025-05-21 | GSE276016 | GEO

Fucntional genetic variants mediate their regulatory effects through altered transcription factor binding. [miRNA-seq]

Project description:The extensive molecular characterization of the transcriptional regulatory landscape within the LCLs of a 3-generation, 17-member kindred was performed to allow for the identification of functional variants. A variant associated with changes in multiple molecular phenotypes was selected for validation through precise CRISPR/Cas9 editing. Edited clones were subsequently tested for reconstitution of function through CRISPR/dCas9 targeted TF activation.

2019-06-04 | GSE117574 | GEO

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