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| Status |
Public on Jun 21, 2023 |
| Title |
Engineering Pluripotent DNA Methylation by CpG Island Methylation Response (CIMR) to Synthetic CpG-free ssDNA Insertion |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
|
| Summary |
Integration of synthetic CpG Free DNA induces de novo DNAme in the flanking CpG island.
Cellular differentiation requires global changes to DNA methylation (DNAme), where it functions to regulate transcription factor and chromatin remodeling activity, and genome interpretation. Here, we describe a simple DNAme engineering approach in pluripotent stem cells (PSCs), extending across large stretches of CpG dense “islands (CGIs).” Integration of synthetic CpG free single-stranded DNA (ssDNA) induces a target CpG Island Methylation Response (CIMR) in multiple PSC lines, Nt2d1 embryonal carcinoma cells, and mouse PSCs, but not in highly methylated CpG Island Methylator Phenotype (CIMP) positive cancer lines. CIMR DNAme at MLH1 spans the CGI, is robustly maintained throughout cellular differentiation, suppresses target gene activity, and sensitizes derived cardiomyocytes and thymic epithelial cells to the chemotherapy cisplatin. Additional CIMR DNAme is reported on at TP53 and ONECUT1 CGIs. Collectively, this new resource enables total CpG Island DNAme engineering in pluripotency and the genesis of novel epigenetic models of development and disease
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| Overall design |
H1 pluripotent stem cells with and without integration of a CpG free insert which encodes for antibiotic resistance. Cells are selected, sorted for individual clones and assessed for induction of DNA methylation by Infinium DNA methylation arrays (850k). Initial comparisons have been made to larger CpG free plasmid repair template.
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| |
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| Contributor(s) |
Tompkins JD |
| Citation(s) |
37323577 |
| |
| Submission date |
Aug 07, 2022 |
| Last update date |
Jun 23, 2023 |
| Contact name |
wei chen |
| E-mail(s) |
weichen2@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Cancer Biology-BRI
|
| Street address |
1500 E Duarte Rd
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL23976 |
Illumina Infinium HumanMethylation850 BeadChip |
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| Samples (47)
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| Relations |
| BioProject |
PRJNA867009 |
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