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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 22, 2020 |
| Title |
IMPLICON: a high-resolution method to uncover DNA methylation at imprinted regions |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
[IMPLICON] Amplicon bisulfite libraries targetting imprinted control regions for mouse and human
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| Contributor(s) |
Klobučar T, Kreibich E, Krueger F, Arez M, Pólvora-Brandão D, von Meyenn F, Reik W, Teixeira da Rocha S, Eckersley-Maslin M |
| Citation(s) |
32621604 |
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| Submission date |
Feb 28, 2020 |
| Last update date |
Oct 02, 2020 |
| Contact name |
Felix Krueger |
| E-mail(s) |
fkrueger@altoslabs.com
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| Organization name |
Altos Labs
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| Department |
Bioinformatics
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| Street address |
Granta Park
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| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
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| Platforms (2) |
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| Samples (30)
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| Relations |
| BioProject |
PRJNA609357 |
| SRA |
SRP251099 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE146129_RAW.tar |
610.0 Kb |
(http)(custom) |
TAR (of COV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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