ArticleAmerican journal of human genetics2017
Detection of Imprinted Genes by Single-Cell Allele-Specific Gene Expression.
Article in American journal of human genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 91 citations in OpenAlex.
- Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions.American journal of human genetics · 2026Article
- DAESC + : high-performance, integrated software for single-cell allele-specific expression data.BMC bioinformatics · 2026Article
- Challenges and emerging strategies for genome-wide evaluation of loss of imprinting in cancer.British journal of biomedical science · 2026Review
- Role of CNTN6 in neurodevelopment and neuropathology.Frontiers in neuroscience · 2026Review
- Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions.medRxiv : the preprint server for health sciences · 2025Article
- Mom genes and dad genes: genomic imprinting in the regulation of social behaviors.Epigenomics · 2025Review
- Allelic expression patterns of imprinted and non-imprinted genes in cancer cell lines from multiple histologies.Clinical epigenetics · 2025Article
- Characterization of Loss-of-Imprinting in Breast Cancer at the Cellular Level by Integrating Single-Cell Full-Length Transcriptome with Bulk RNA-Seq Data.Biomolecules · 2024Article
- Computational methods for allele-specific expression in single cells.Trends in genetics : TIG · 2024Review
- Z-DNA formation in promoters conserved between human and mouse are associated with increased transcription reinitiation rates.Scientific reports · 2024Article
- Detection of allele-specific expression in spatial transcriptomics with spASE.Genome biology · 2024Article
- Genetic/epigenetic effects in NF1 microdeletion syndrome: beyond the haploinsufficiency, looking at the contribution of not deleted genes.Human genetics · 2024Article
- Epigenomic states contribute to coordinated allelic transcriptional bursting in iPSC reprogramming.Life science alliance · 2024Article
- A novel imprinted locus on bovine chromosome 18 homologous with human chromosome 16q24.1.Molecular genetics and genomics : MGG · 2024Article
- The role of imprinting genes' loss of imprints in cancers and their clinical implications.Frontiers in oncology · 2024Review
- Imprinted genes and the manipulation of parenting in mammals.Nature reviews. Genetics · 2023Review
- Epigenetic Reprogramming inCells · 2023Review
- FOXI3 pathogenic variants cause one form of craniofacial microsomia.Nature communications · 2023Article
- Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.Genome biology · 2023Article
- Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation.Human molecular genetics · 2023Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Genomic imprinting results in parental-specific gene expression. Imprinted genes are involved in the etiology of rare syndromes and have been associated with common diseases such as diabetes and cancer. Standard RNA bulk cell sequencing applied to whole-tissue samples has been used to detect imprinted genes in human and mouse models. However, lowly expressed genes cannot be detected by using RNA bulk approaches. Here, we report an original and robust method that combines single-cell RNA-seq and whole-genome sequencing into an optimized statistical framework to analyze genomic imprinting in specific cell types and in different individuals. Using samples from the probands of 2 family trios and 3 unrelated individuals, 1,084 individual primary fibroblasts were RNA sequenced and more than 700,000 informative heterozygous single-nucleotide variations (SNVs) were genotyped. The allele-specific coverage per gene of each SNV in each single cell was used to fit a beta-binomial distribution to model the likelihood of a gene being expressed from one and the same allele. Genes presenting a significant aggregate allelic ratio (between 0.9 and 1) were retained to identify of the allelic parent of origin. Our approach allowed us to validate the imprinting status of all of the known imprinted genes expressed in fibroblasts and the discovery of nine putative imprinted genes, thereby demonstrating the advantages of single-cell over bulk RNA-seq to identify imprinted genes. The proposed single-cell methodology is a powerful tool for establishing a cell type-specific map of genomic imprinting.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.