Novel parent-of-origin specific differentially methylated loci on chromosome 16
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA516879 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8482550_1.fastq.gz | Fastqsanger.gz | |||
| SRR8482550_2.fastq.gz | Fastqsanger.gz | |||
| SRR8482551_1.fastq.gz | Fastqsanger.gz | |||
| SRR8482551_2.fastq.gz | Fastqsanger.gz | |||
| SRR8482552_1.fastq.gz | Fastqsanger.gz |
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Project description:To identify parent-of-origin biased DNA methylation, we performed high-resolution bisulfite sequencing of chromosome 16 on peripheral blood and cultured skin fibroblasts from individuals with maternal and paternal UPD(16) as well as lung tissue from patients with 16q24.1 ACDMPV-causative deletions and a normal control. We identified 22 differentially methylated regions (DMRs) with ≥5 consecutive CpG methylation sites and varying tissue-specificity, including the known DMRs associated with the established imprinted gene ZNF597 and DMRs supporting maternal methylation of PRR25, thought to be paternally expressed in lymphoblastoid cells. Lastly, we found evidence of paternal methylation on 16q24.1 near LINC01082 mapping to the FOXF1 enhancer. Using high-resolution bisulfite sequencing to evaluate DNA methylation across chromosome 16, we found evidence of novel candidate imprinted loci on chromosome 16 that would not be evident in array-based assays and could contribute to the birth defects observed in association with UPD(16)mat and in ACDMPV.
2019-04-16 | GSE125589 | GEO
Project description:BackgroundCongenital malformations associated with maternal uniparental disomy of chromosome 16, upd(16)mat, resemble those observed in newborns with the lethal developmental lung disease, alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV). Interestingly, ACDMPV-causative deletions, involving FOXF1 or its lung-specific upstream enhancer at 16q24.1, arise almost exclusively on the maternally inherited chromosome 16. Given the phenotypic similarities between upd(16)mat and ACDMPV, together with parental allelic bias in ACDMPV, we hypothesized that there may be unknown imprinted loci mapping to chromosome 16 that become functionally unmasked by chromosomal structural variants.ResultsTo identify parent-of-origin biased DNA methylation, we performed high-resolution bisulfite sequencing of chromosome 16 on peripheral blood and cultured skin fibroblasts from individuals with maternal or paternal upd(16) as well as lung tissue from patients with ACDMPV-causative 16q24.1 deletions and a normal control. We identified 22 differentially methylated regions (DMRs) with ≥ 5 consecutive CpG methylation sites and varying tissue-specificity, including the known DMRs associated with the established imprinted gene ZNF597 and DMRs supporting maternal methylation of PRR25, thought to be paternally expressed in lymphoblastoid cells. Lastly, we found evidence of paternal methylation on 16q24.1 near LINC01082 mapping to the FOXF1 enhancer.ConclusionsUsing high-resolution bisulfite sequencing to evaluate DNA methylation across chromosome 16, we found evidence for novel candidate imprinted loci on chromosome 16 that would not be evident in array-based assays and could contribute to the birth defects observed in patients with upd(16)mat or in ACDMPV.
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Project description:RNA was extracted from adult male and adult female Drosophila melanogaster with reversed sex-chromosome parent-of-origin (e.g. maternal-X/paternal-Y vs. paternal-X/maternal-Y)
2013-11-01 | GSE51942 | GEO
Project description:RNA was extracted from adult male and adult female Drosophila melanogaster with reversed sex-chromosome parent-of-origin (e.g. maternal-X/paternal-Y vs. paternal-X/maternal-Y) Parent-of-origin effects were assayed in X/Y males, XY/Y males, and XY/X females. Direct comparisons were made between individuals with the same karyotype (e.g. X/Y males or XY/Y males) incorporating dye-swaps.
2013-11-01 | E-GEOD-51942 | biostudies-arrayexpress
Project description:We looked for parent of origin effects on genome-wide gene expression in a reciprocal cross between C57BL/6J x B6(C)-H2bm12/KhEgJ mice (the latter strain is a knockout of H2-ab1 on a C57BL/6J background). The aim is to find genes whose expression is altered in trans depending on whether the mother or father carried a knockout allele for H2-ab1. In this experiment differential expression of a gene is inferred from a difference in its overall expression levels. We sequenced RNA from 30 F1 mice from the H2-ab1 heterozygous cross. Both heterozygous and wild type F1 animals were sequenced in order to find both parental and parent of origin effects. We measured expression in the lungs (average 6.2 million reads per sample) and hippocampus (6.6 million reads).
2013-11-01 | E-MTAB-1998 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE20005: Parent-of-origin effects in seeds of Arabidopsis thaliana: Affymetrix GSE20006: Parent-of-origin effects in seeds of Arabidopsis thaliana: Agilent Refer to individual Series
2010-08-26 | E-GEOD-20007 | biostudies-arrayexpress
Project description:We report the identification of parent-of-origin specific gene expression in Arabidopsis seeds. F1 hybrid seeds were generated by reciprocally crossing Arabidopsis accessions Col-0 and Bur-0. Seeds were harvested at 4 DAP and total RNA was isolated and analyzed by deep sequencing. Overall identification of parent-of-origin-allelic expression by analysis of SNP distribution
2011-04-30 | E-GEOD-27292 | biostudies-arrayexpress
Project description:Multiple regulatory layers influence allele-specific expression (ASE), particularly through sequence-dependent and parent-of-origin-dependent mechanisms at the transcriptional level. However, little is known about allele-specific gene regulation at the post-transcriptional level. Here, we conduct transcriptome-wide analysis of allele-specific m6A in mice. Using early postnatal cerebellum and cerebrum samples from reciprocal crosses of two divergent mouse strains, we employed quantitative m6A assays to measure allelic differences in m6A at single-base resolution. Our study reveals widespread sequence-dependent allelic imbalance in m6A methylation, identifying thousands of allele-specific m6A (ASm6A) sites with statistically significant and reproducible allelic methylation differences across diverse samples. We find evidence of potential cis-regulatory variants within 50-nt flanking regions of these ASm6A sites, with the highest enrichment at the motif positions. Intriguingly, we detect parental effects on allelic methylation across m6A sites exhibiting parent-of-origin-dependent ASE. For both sequence- and parent-of-origin-dependent allelic m6A methylation, we observe opposing allelic preferences between methylation and expression, suggesting a potential role of ASm6A in regulating ASE through negative effects on gene expression. Overall, our findings reveal that both cis-acting and parent-of-origin effects influence ASm6A, offering new insights into post-transcriptional mechanisms of ASE regulation.
2024-04-26 | GSE265978 | GEO
Project description:Imprinted genes are expressed from one parental allele in a parent-of-origin manner. This monoallelic behavior is regulated by allele-specific DNA methylation that is confined to differentially methylated regions (DMRs). To date there are over 80 known human imprinted genes of which only three are known to have paternally methylated DMRs. In mice there exists an additional paternally methylated DMR associated with Rasgrf1. The Rasgrf1 gene forms part of the MAPK signaling pathway and plays a role in long-term memory formation and growth control. A RASGRF1-associated parent-of-origin specific DMR in humans and its methylation status in sperm DNA have not been explored. The primary aim of this study was to determine whether the human RASGRF1 gene contains a DMR and whether this DMR is paternally methylated and shows roughly 50% methylation in somatic tissue. Computational assessments were done to identify putative CTCF binding sites, CpG islands (CGIs) that could serve as potential RASGRF1 DMRs and tandem repeats within or adjacent to these CGIs. The methylation status of three putative CGIs was assessed using quantitative pyrosequencing technology. None of the putative CTCF binding sites was found to occur in the predicted CGIs. The three putative CGIs linked to RASGRF1 did not display allele-specific methylation. While one of the three CGIs was found to be hypomethylated in both blood DNA and sperm DNA, the other two were found to be hypermethylated. The CGIs evaluated in this study did not fit the criteria of being a allele-specific DMR. Unlike the mouse Rasgrf1 locus, the human RASGRF1-associated CpG rich regions do not exhibit differential methylation in a parent-of-origin manner.
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