ArticleBMC genetics2010
High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.
Article in BMC genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 70 citations in OpenAlex.
- Allele-specific expression of mutated in colorectal cancer (MCC) gene and alternative susceptibility to colorectal cancer in schizophrenia.Scientific reports · 2016Trial
- Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation.Human molecular genetics · 2023Article
- Spontaneous and ART-induced large offspring syndrome: similarities and differences in DNA methylome.Epigenetics · 2022Article
- Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits-The Hispanic/Latino Anthropometry Consortium.HGG advances · 2022Article
- Feasibility of predicting allele specific expression from DNA sequencing using machine learning.Scientific reports · 2021Article
- Parental bias in expression and interaction of genes in the equine placenta.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Discovering candidate imprinted genes and imprinting control regions in the human genome.BMC genomics · 2020Article
- Tumor suppressor genes and allele-specific expression: mechanisms and significance.Oncotarget · 2020Article
- Molecular Etiology Disclosed by Array CGH in Patients With Silver-Russell Syndrome or Similar Phenotypes.Frontiers in genetics · 2019Article
- Genome-wide survey of parent-of-origin effects on DNA methylation identifies candidate imprinted loci in humans.Human molecular genetics · 2018Article
- Parent of origin gene expression in a founder population identifies two new candidate imprinted genes at known imprinted regions.PloS one · 2018Article
- Associations between imprinted gene expression in the placenta, human fetal growth and preeclampsia.Biology letters · 2017Article
- Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data.Genetics · 2016Article
- A haplotype-based normalization technique for the analysis and detection of allele specific expression.BMC bioinformatics · 2016Article
- Characterization of whole-genome autosomal differences of DNA methylation between men and women.Epigenetics & chromatin · 2015Article
- Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta.Epigenetics · 2014Article
- Whole-genome haplotyping using long reads and statistical methods.Nature biotechnology · 2014Article
- DNMT1 and AIM1 Imprinting in human placenta revealed through a genome-wide screen for allele-specific DNA methylation.BMC genomics · 2013Article
- Imprinting at the PLAGL1 domain is contained within a 70-kb CTCF/cohesin-mediated non-allelic chromatin loop.Nucleic acids research · 2013Article
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15 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundImprinted genes show expression from one parental allele only and are important for development and behaviour. This extreme mode of allelic imbalance has been described for approximately 56 human genes. Imprinting status is often disrupted in cancer and dysmorphic syndromes. More subtle variation of gene expression, that is not parent-of-origin specific, termed 'allele-specific gene expression' (ASE) is more common and may give rise to milder phenotypic differences. Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue.
resultsTwenty-three family trios of placental cDNA, placental genomic DNA (gDNA) and gDNA from both parents were tested for 130 candidate genes with the Sequenom MassArray system. Six genes were found differentially expressed but none imprinted. The Illumina ASE BeadArray platform was then used to test 1536 SNPs in 932 genes. The array was enriched for the human orthologues of 124 mouse candidate genes from bioinformatics predictions and 10 human candidate imprinted genes from EST database mining. After quality control pruning, a total of 261 informative SNPs (214 genes) remained for analysis. Imprinting with maternal expression was demonstrated for the lymphocyte imprinted gene ZNF331 in human placenta. Two potential differentially methylated regions (DMRs) were found in the vicinity of ZNF331. None of the bioinformatically predicted candidates tested showed imprinting except for a skewed allelic expression in a parent-specific manner observed for PHACTR2, a neighbour of the imprinted PLAGL1 gene. ASE was detected for two or more individuals in 39 candidate genes (18%).
conclusionsBoth Sequenom and Illumina assays were sensitive enough to study imprinting and strong allelic bias. Previous bioinformatics approaches were not predictive of new imprinted genes in the human term placenta. ZNF331 is imprinted in human term placenta and might be a new ubiquitously imprinted gene, part of a primate-specific locus. Demonstration of partial imprinting of PHACTR2 calls for re-evaluation of the allelic pattern of expression for the PHACTR2-PLAGL1 locus. ASE was common in human term placenta.
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