Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genetic Variants Influence on the Placental-specific Regulatory Landscape

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

PROVIDER: PRJNA497170 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Genetic Variants Influence on the Placental-specific Regulatory Landscape

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

| PRJNA497169 | ENA

Genetic variants influence on the placenta regulatory landscape.

Project description:From genomic association studies, quantitative trait loci analysis, and epigenomic mapping, it is evident that significant efforts are necessary to define genetic-epigenetic interactions and understand their role in disease susceptibility and progression. For this reason, an analysis of the effects of genetic variation on gene expression and DNA methylation in human placentas at high resolution and whole-genome coverage will have multiple mechanistic and practical implications. By producing and analyzing DNA sequence variation (n = 303), DNA methylation (n = 303) and mRNA expression data (n = 80) from placentas from healthy women, we investigate the regulatory landscape of the human placenta and offer analytical approaches to integrate different types of genomic data and address some potential limitations of current platforms. We distinguish two profiles of interaction between expression and DNA methylation, revealing linear or bimodal effects, reflecting differences in genomic context, transcription factor recruitment, and possibly cell subpopulations. These findings help to clarify the interactions of genetic, epigenetic, and transcriptional regulatory mechanisms in normal human placentas. They also provide strong evidence for genotype-driven modifications of transcription and DNA methylation in normal placentas. In addition to these mechanistic implications, the data and analytical methods presented here will improve the interpretability of genome-wide and epigenome-wide association studies for human traits and diseases that involve placental functions.

| 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>

| phs001717 | dbGaP

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

| PRJNA1154281 | ENA

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

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

2019-06-04 | GSE117484 | GEO

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

2019-06-04 | GSE117565 | GEO

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

2019-06-04 | GSE117490 | GEO

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data