ArticleBMC biology2019
RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting.
Article in BMC biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Uncovering transcriptomic biomarkers for enhanced diagnosis of methamphetamine use disorder: a comprehensive review.Frontiers in psychiatry · 2023Pooled it
- Species-Specific Parent-Of-Origin Expression of Adam23 in the Mammalian Brain.Genes to cells : devoted to molecular & cellular mechanisms · 2026Article
- Article
- Abundant Parent-of-origin Effect eQTL: The Framingham Heart Study.bioRxiv : the preprint server for biology · 2025Article
- Article
- Ornaments for efficient allele-specific expression estimation with bias correction.American journal of human genetics · 2024Article
- A novel imprinted locus on bovine chromosome 18 homologous with human chromosome 16q24.1.Molecular genetics and genomics : MGG · 2024Article
- Single‑nucleotide polymorphism rs6592645 confers asthma risk through regulatingExperimental and therapeutic medicine · 2023Article
- Characterizing the landscape of gene expression variance in humans.PLoS genetics · 2023Article
- Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation.Human molecular genetics · 2023Article
- KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition.International journal of molecular sciences · 2022Article
- Fcα Receptor-1-Activated Monocytes Promote B Lymphocyte Migration and IgA Isotype Switching.International journal of molecular sciences · 2022Article
- Genome-wide detection of imprinted differentially methylated regions using nanopore sequencing.eLife · 2022Article
- Human genetic diversity regulating theHGG advances · 2022Article
- Genomic Imprinting in the New Omics Era: A Model for Systems-Level Approaches.Frontiers in genetics · 2022Review
- Breast cancer-associated SNP rs72755295 is a cis-regulatory variation for human EXO1.Genetics and molecular biology · 2022Article
- Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas.G3 (Bethesda, Md.) · 2021Article
- Review
- Joint modeling of eQTLs and parent-of-origin effects using an orthogonal framework with RNA-seq data.Human genetics · 2020Article
- Loss of Imprinting in Human Placentas Is Widespread, Coordinated, and Predicts Birth Phenotypes.Molecular biology and evolution · 2020Article
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Authors and funding
15 authors.
Funding
Abstract
backgroundIdentification of imprinted genes, demonstrating a consistent preference towards the paternal or maternal allelic expression, is important for the understanding of gene expression regulation during embryonic development and of the molecular basis of developmental disorders with a parent-of-origin effect. Combining allelic analysis of RNA-Seq data with phased genotypes in family trios provides a powerful method to detect parent-of-origin biases in gene expression.
resultsWe report findings in 296 family trios from two large studies: 165 lymphoblastoid cell lines from the 1000 Genomes Project and 131 blood samples from the Genome of the Netherlands (GoNL) participants. Based on parental haplotypes, we identified > 2.8 million transcribed heterozygous SNVs phased for parental origin and developed a robust statistical framework for measuring allelic expression. We identified a total of 45 imprinted genes and one imprinted unannotated transcript, including multiple imprinted transcripts showing incomplete parental expression bias that was located adjacent to strongly imprinted genes. For example, PXDC1, a gene which lies adjacent to the paternally expressed gene FAM50B, shows a 2:1 paternal expression bias. Other imprinted genes had promoter regions that coincide with sites of parentally biased DNA methylation identified in the blood from uniparental disomy (UPD) samples, thus providing independent validation of our results. Using the stranded nature of the RNA-Seq data in lymphoblastoid cell lines, we identified multiple loci with overlapping sense/antisense transcripts, of which one is expressed paternally and the other maternally. Using a sliding window approach, we searched for imprinted expression across the entire genome, identifying a novel imprinted putative lncRNA in 13q21.2. Overall, we identified 7 transcripts showing parental bias in gene expression which were not reported in 4 other recent RNA-Seq studies of imprinting.
conclusionsOur methods and data provide a robust and high-resolution map of imprinted gene expression in the human genome.
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