IMPLICON: a high-resolution method to uncover DNA methylation at imprinted regions
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ABSTRACT:
PROVIDER: PRJNA609357 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11207800_1.fastq.gz | Fastqsanger.gz | |||
| SRR11207800_2.fastq.gz | Fastqsanger.gz | |||
| SRR11207801_1.fastq.gz | Fastqsanger.gz | |||
| SRR11207801_2.fastq.gz | Fastqsanger.gz | |||
| SRR11207802_1.fastq.gz | Fastqsanger.gz |
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Project description:Genomic imprinting is an epigenetic phenomenon leading to parental allele specific expression. Dosage of imprinted genes is crucial for normal development and its dysregulation accounts for a number of human disorders. Imprinted expression is dictated by differences in DNA methylation between parental alleles at specific regulatory elements known as imprinting control regions (ICRs). Although a number of approaches can be used for methylation inspection at ICRs, we lack an easy and cost-effective method to simultaneously measure DNA methylation at multiple imprinted regions. Here, we present IMPLICON, a new high-throughput method measuring DNA methylation levels at imprinted regions with base-pair resolution and over 1000-fold genomic coverage. We initially designed this method to look at ICRs in adult tissues of inbred mice. Then, we validated in hybrid mice from reciprocal crosses for which we could discriminate methylation profiles in the two parental alleles. Lastly, we developed a human version of IMPLICON and detected imprinting errors in naïve human embryonic and induced pluripotent stem cells. We also provide rules and guidelines in which this method can be adapted to investigate the DNA methylation landscape of any set of genomic regions. In summary, IMPLICON is a rapid, cost-effective and scalable method, which could become the gold standard in both imprinting research and diagnostics.
2020-06-22 | GSE146129 | GEO
Project description:Genomic imprinting is an epigenetic phenomenon leading to parental allele-specific expression. Dosage of imprinted genes is crucial for normal development and its dysregulation accounts for several human disorders. This unusual expression pattern is mostly dictated by differences in DNA methylation between parental alleles at specific regulatory elements known as imprinting control regions (ICRs). Although several approaches can be used for methylation inspection, we lack an easy and cost-effective method to simultaneously measure DNA methylation at multiple imprinted regions. Here, we present IMPLICON, a high-throughput method measuring DNA methylation levels at imprinted regions with base-pair resolution and over 1000-fold coverage. We adapted amplicon bisulfite-sequencing protocols to design IMPLICON for ICRs in adult tissues of inbred mice, validating it in hybrid mice from reciprocal crosses for which we could discriminate methylation profiles in the two parental alleles. Lastly, we developed a human version of IMPLICON and detected imprinting errors in embryonic and induced pluripotent stem cells. We also provide rules and guidelines to adapt this method for investigating the DNA methylation landscape of any set of genomic regions. In summary, IMPLICON is a rapid, cost-effective and scalable method, which could become the gold standard in both imprinting research and diagnostics.
| S-EPMC7498334 | biostudies-literature
Project description:Imprinted genes are critical for normal human growth and neurodevelopment. We developed a strategy to identify new DNA differentially methylated regions (DMRs), a hallmark of imprinted genes. Using genome-wide methylation profiling, candidate DMRs were selected by identifying CpGs with putative allelic differential methylation in normal biparental tissues. In parallel, we looked for parent of origin-specific DNA methylation patterns in paternally derived human androgenetic complete hydatidiform mole (AnCHM), and maternally derived mature cystic ovarian teratoma (MCT). Using this approach, we found known DMRs associated with imprinted genomic regions as well as new DMRs for known imprinted genes, NAP1L5 and ZNF597. Most importantly, novel candidate imprinted genes were identified. The paternally methylated DMR for one candidate, AXL, a receptor tyrosine kinase, was validated by methylation analyses in humans. Further validation in mouse embryos showed that Axl was expressed preferentially from the maternal allele in a DNA methylation–dependent manner. We have analyzed 3 androgenetic complete hydatidiform mole (AnCHM), 16 white blood cell (WBC), 1 mature cystic ovarian teratoma (MCT), 5 placenta, and 1 lymphoblastoid cell line paternal UPD4 sample
2011-01-26 | E-GEOD-22091 | biostudies-arrayexpress
Project description:Imprinted genes are critical for normal human growth and neurodevelopment. We developed a strategy to identify new DNA differentially methylated regions (DMRs), a hallmark of imprinted genes. Using genome-wide methylation profiling, candidate DMRs were selected by identifying CpGs with putative allelic differential methylation in normal biparental tissues. In parallel, we looked for parent of origin-specific DNA methylation patterns in paternally derived human androgenetic complete hydatidiform mole (AnCHM), and maternally derived mature cystic ovarian teratoma (MCT). Using this approach, we found known DMRs associated with imprinted genomic regions as well as new DMRs for known imprinted genes, NAP1L5 and ZNF597. Most importantly, novel candidate imprinted genes were identified. The paternally methylated DMR for one candidate, AXL, a receptor tyrosine kinase, was validated by methylation analyses in humans. Further validation in mouse embryos showed that Axl was expressed preferentially from the maternal allele in a DNA methylation–dependent manner.
2011-01-26 | GSE22091 | GEO
Project description:Imprinted macro ncRNAs such as Airn play an important role in silencing protein-coding genes in cis, macro ncRNAs could be a common feature in all imprinted gene clusters. By applying the RNA Expression on Tiling Array (RETA) technique, macro ncRNAs were found to be abundant in 26 known mouse genomic regions containing imprinted genes were detected. All well-known imprinted macro ncRNAs were up-regulated upon depletion of DNA methylation.
2017-02-25 | GSE26718 | GEO
Project description:Genomic imprinting is a important biological process, which leads to parental specific gene expressions. Improper gene imprinting results in several developmental abnormalities, cancer and other diseases. Studies in mice indicated genomic imprinting establishment relied on parental allele-specific DNA methylation during gametogenesis. Despite the fact that genomic imprinting is highly conserved in mammalian, the species specific pattern exists. Until now, except that of in mouse, informations about imprinting patterns is little, especially in primates. Through generation genome-wide 5mC and 5hmC profiles for two types of haploid genomes from rhesus monkeys, including parthenogenetic haploid ESCs ( PG ha ESCs) (derived from rhesus monkey parthenogenetic embryos) and sperms. We clearly characterized and distinguished methylome (5mC) from hydroxymethylome (5hmC)(which can not discriminate from methylome in traditional bisulfite (BS) sequencing) in haploid genomes. Based on these information, we determined distribution patterns of 5mC and 5hmC in ha ESCs and sperms. Interestingly, both 5hmC levels and distribution patterns were similar in ha ESCs and sperms, and 5hmC which is enriched in the regions with low 5mC frequency. Meanwhile through comparing DNA methylation and hydroxymethylation status between sperms and ha ESCs, we first provided a fundamental information of monkey imprinted differentially methylated regions (DMRs) distribution in monkey chromosomes. Second, we observed that DMRs did not overlap with hydroxymethylated regions (DMR or DhMR), suggesting that establishment of imprinted regions was not interfered by 5hmC. Our results demonstrate DNA methylation profiling of PG ha ESCs and sperms can be uesed as a powerful and effective method to map and characterize imprinted regions in non-human primates genome.
2016-12-08 | GSE75817 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE15746: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 1 GSE15747: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 2 Refer to individual Series
2010-05-19 | E-GEOD-15801 | biostudies-arrayexpress
Project description:Large-scale transcriptome and methylome data analyses obtained by high-throughput technologies have been enabling the identification of novel imprinted genes. We investigated genome-wide DNA methylation patterns in multiple human tissues, using a high-resolution microarray to uncover hemimethylated CpGs located in promoters overlapping CpG islands, aiming to identify novel candidate imprinted genes. Using our approach, we recovered ~30% of the known human imprinted genes, further 168 candidates were identified, 61 of which with at least three hemimethylated CpGs shared by more than two tissue types. Thirty-four of these candidate genes are members of the protocadherins cluster on 5q31.3; in mice, protocadherin genes have non-imprinted monoallelic randomic expression, which might be the case in humans. Among the remaining 27 genes, ZNF331 was recently validated as an imprinted gene, and six of them have been reported as candidates, supporting our prediction. Five candidates (CCDC166, ARC, PLEC, TONSL and VPS28) map to 8q24.3, and might constitute a novel imprinted cluster. Additionally, we performed a comprehensive compilation of known human and mice imprinted genes from literature and databases, and a comparison among high-throughput imprinting studies in humans. The screening for hemimethylated CpGs shared by multiple human tissues, together with the extensive review, appears as a useful approach to reveal candidate imprinted genes.
2017-09-26 | GSE103413 | GEO
Project description:Epigenetic profiling of DNA methylation, histone H3 lysine 4 trimethylation and histone H3 lysine 9 trimethylation at imprinted gene clusters in the mouse. Imprinted control regions were identified by comparing DNA and histone methylation patterns between sperm, heart and cerebellum.
2010-05-18 | E-GEOD-16588 | biostudies-arrayexpress
Project description:Inborn defects in DNA repairare associated with complex developmental disorders whose causal mechanisms are poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the nucleotide excision repair (NER) structure-specific endonuclease ERCC1-XPF complex interacts with the insulator binding protein CTCF, the cohesin subunits SMC1A and SMC3 and with MBD2; the factors co-localize with ATRX at the promoters and control regions (ICRs) of imprinted genes during postnatal hepatic development. Loss of Ercc1or exposure to mitomycin C triggers the localization of CTCF to heterochromatin, the dissociation of the CTCF-cohesin complex and ATRXfrom promoters and ICRs,altered histone marks and the aberrant developmental expression of imprinted genes without altering DNA methylation. We propose that ERCC1-XPF cooperates with CTCF and the cohesinto facilitatet he developmental silencing of imprinted genes and that persistent DNA damage triggers chromatin changes that affect gene expression programs associated with NER disorders.
2017-04-04 | PXD005897 | Pride