2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
June 4th, 2025
Version: 2
National Heart, Lung, and Blood Institute
genetics
biorxiv

Abundant Parent-of-origin Effect eQTL in Humans: The Framingham Heart Study

Guan, Y.Open in Google Scholar•Huan, T.Open in Google Scholar•Levy, D.Open in Google Scholar

Parent-of-origin effect (POE) is a phenomenon whereby an allele's effect on a phenotype depends both on its allelic identity and parent from whom the allele is inherited, as exemplified by the polar overdominance in the ovine callypyge locus and the human obesity DLK1 locus. Systematic studies of POE of expression quantitative trait loci (eQTL) are lacking. In this study we use trios among participants in the Framingham Heart Study to examine to what extend POE exists for gene expression of whole blood using whole genome sequencing and RNA sequencing. For each gene and the SNPs in cis, we performed eQTL analysis using genotype, paternal, maternal, and joint models, where the genotype model enforces the identical effect sizes on paternal and maternal alleles, and the joint model allows them to have different effect sizes. We compared models using Bayes factors to identify paternal, maternal, and opposing eQTL, where paternal and maternal effects have opposite directions. The resultant variants are collectively called POE eQTL. The highlights of our study include: 1) There are more than 2,000 genes harbor POE eQTL and majority POE eQTL are not in the vicinity of known imprinted genes; 2) Among 180 genes harboring opposing eQTL, 99 harbor exclusively opposing eQTL, and 58 of the 99 are phosphoprotein coding genes, reflecting significant enrichment; 3) Paternal eQTL are enriched with GWAS hits, and genes harboring paternal eQTL are enriched with drug targets. Our study demonstrates the abundance of POE in gene expression, illustrates the complexity of gene expression regulation, and provides a resource that is complementary to existing resources such as GTEx. We revisited two previous POE findings in light of our POE results. A SNP residing in KCNQ1 that is maternally associated with diabetes is a maternal eQTL of CDKN1C, not KCNQ1. A SNP residing in DLK1 that showed paternal polar overdominance for human obesity is a maternal eQTL of MEG3, offering an explanation for the baseline risk of homozygous samples through association between MEG3 expression and obesity. Finally, we advised caution on conducting Mendelian randomization using gene expression as the exposure.

Similar Papers

biorxiv
Fri Jun 06 2025
Unlocking the Forgotten Dimension of Biodiversity: A Scalable Genetic Diversity Index for Multi-Species Analysis
Conservation strategies and biodiversity assessments have long prioritized taxonomic metrics such as species richness and endemism, often neglecting intraspecific genetic diversity, a key driver of population adaptability and long-term resilience. Here, we present a scalable framework for quantifying and mapping multi-species genetic diversity using publicly available DNA sequence data. By calcula...
Karunarathne, P.
•
Kluempen, M.
•
Rose, L.
biorxiv
Fri Jun 06 2025
Comprehensive molecular impact mapping of common and rare variants at GWAS loci
Deep learning sequence to function models can predict the molecular effects of genetic variants, but their predictions are limited to the cell types and assays they are trained on. Here we describe DNACipher, a deep learning model that predicts the effects of genetic variants across diverse biological contexts-including those not directly measured. DNACipher takes 196 kb of genome sequences as inp...
Balderson, B.
•
Tule, S.
•
Okino, M.-L.
•
Rieger, W. J.
...•
McVicker, G.
biorxiv
Thu Jun 05 2025
Establishing a DNA reference library for the identification of elasmobranchs in the Indian Ocean using Oxford Nanopore Sequencing
Elasmobranchs, comprising sharks and rays, are among the most threatened species globally. The first elasmobranchs were added to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) in 2002. Since then, the number of species listed has increased to 151, highlighting the urgent conservation challenges faced by these species. In Sri Lanka, where over 100 specie...
Anjani, L.
•
Tanna, A.
•
Humble, E.
•
Sandamalika, G.
...•
Fernando, D.
biorxiv
Thu Jun 05 2025
Isolation of Cyclotide Gene from Solanaceae Family and Its Bioinformatics Analysis
Abstract: Cyclotides are highly tolerant of sequence variability, aside from the conserved residues forming the cystine knot. Cyclotides have attractive natural movement capabilities including cytotoxicity, harmfulness to HIV, antimicrobials, insecticides, uterine contraction and inhibition of proteases, making them very important in pharmacy and horticulture. The medicinal cyclotides may be able ...
Hussain, M.
•
Ahmad, M.
biorxiv
Thu Jun 05 2025
Leech Speciation and Detection of Hirudin Gene among the Leech Population in Asejire Oyo State, Nigeria
Leeches are segmented, parasitic and sanguivorous worms of the family Hirudinae and phylum Annelida. Various ailments have been treated with them since ancient times. Recent evidence has established the presence of over 100 medicinally useful bioactive substances in their saliva. Based on the therapeutic properties of the substances, they have been used in different areas of medical care and most ...
Olajide, T. H.
•
Ajileye, A. O.
•
Bamikole, O. J.
•
Olufeagba, M.-d. B.
...•
Amodu, O. k.
biorxiv
Thu Jun 05 2025
Natural variation in phospholipase IPLA2-VIA contributes to starvation sensitivity in Drosophila melanogaster
Resistance to starvation is a classic complex trait where genetic and environmental variables can greatly modify an animals ability to survive without nutrients. Genetic analyses in Drosophila have shown that starvation resistance is highly polygenic with different genetic architectures in different mapping populations. In this study we sought to dissect the genetic basis of starvation resistance ...
Rand, D. M.
•
Williams, S. B.
•
Franklin, B.
•
Lemieux, F. A.
biorxiv
Wed Jun 04 2025
The Insertion of an ATTTC Repeat in an Alu Element Hyperactivates a Primate-Specific Neurodevelopmental Enhancer in Spinocerebellar Ataxia Type 37
Alu are evolutionarily very old primate-specific interspersed repeat elements that constitute ~11% of the human genome. They are a source of short tandem repeats (STRs), which often expand in size and originate inherited neuromuscular and neurodegenerative disorders. How expanded STR insertion mutations within Alu STRs culminate in disease remains unknown. Here we report an Alu STR located in an i...
Loureiro, J. R.
•
Castro, A. F.
•
Figueiredo, A. S.
•
Eufrasio, A.
...•
Silveira, I.
biorxiv
Wed Jun 04 2025
A cross-species rescue by mating method to interrogate gene essentiality across the Saccharomyces genus.
The field of budding yeast research has long been empowered by the vast array of genetic tools and community resources available. Rescue by mating is one useful tool that entails mating of meiotic spores directly post-germination. This minimal cell division mating process facilitates mating based screens studying the effects of otherwise haploid lethal gene deletions. In this study, we describe th...
Wang, T. K.
•
Keller, A.
•
Kunjo, S. O.
•
Dunham, M. J.
biorxiv
Wed Jun 04 2025
Impact of trait measurement error on quantitative genetic analysis of computer vision derived traits
Background: Quantitative genetic analysis of image- or video-derived phenotypes is increasingly being performed for a wide range of traits. Pig body weight values estimated by a conventional approach or a computer vision system can be considered as two different measurements of the same trait, but with different sources of phenotyping error. Previous studies have shown that trait measurement error...
Bi, Y.
•
Huang, Y.
•
Yu, H.
•
Morota, G.