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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 30, 2023 |
| Title |
Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
DNA methylation is considered a stable epigenetic mark due to its presumed long-term inheritance through cell divisions. Here, we perform high-throughput bisulfite sequencing on clonally derived cell lines to quantitatively measure mitotic methylation inheritance at the nucleotide level. We find that although DNA methylation is generally faithfully maintained at hypo- and hypermethylated sites, this is not the case at intermediately methylated CpGs. Low fidelity intermediate methylation is interspersed throughout the genome and within genes with no or low transcriptional activity. Moreover, we determine that the probabilistic changes that occur at intermediately methylated sites are due to DNMT1 rather than DNMT3A/3B activity. The observed lack of clonal inheritance at intermediately methylated sites challenges the concept of DNA methylation as a consistently stable epigenetic mark.
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| Overall design |
We devised an experiment to directly assess the fidelity of DNA methylation through cell divisions at the genome-scale, by subcloning populations of cells and performing target DNA capture followed by high-throughput bisulfite sequencing (tcBS-seq) on both the subclones (14 cell lines) and the parent population of cells (2 cell lines). To do so, we established mouse embryonic fibroblasts (MEFs) from two sibling E13.5 mouse embryos and immortalised the cell lines. From these parental lines, we randomly sampled fourteen single cells to establish clonal populations of around 1-2 million cells on which we profiled DNA methylation using tcBS-seq.
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| Contributor(s) |
Hay AD, Kessler NJ, Gebert D, Takahashi N, Tavares H, Teixeira FK, Ferguson-Smith AC |
| Citation(s) |
37660134 |
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| Submission date |
Jun 02, 2023 |
| Last update date |
Sep 15, 2023 |
| Contact name |
Anne Ferguson-Smith |
| E-mail(s) |
afsmith@gen.cam.ac.uk
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| Organization name |
Cambridge University
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| Department |
Genetics
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| Street address |
20 Downing Place
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| City |
Cambridge |
| ZIP/Postal code |
CB2 3EJ |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (16)
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| GSM7441304 |
Immortalised MEF cells, parental population 1 |
| GSM7441305 |
Immortalised MEF cells, subclonal population 1-1 |
| GSM7441306 |
Immortalised MEF cells, subclonal population 1-2 |
| GSM7441307 |
Immortalised MEF cells, subclonal population 1-3 |
| GSM7441308 |
Immortalised MEF cells, subclonal population 1-4 |
| GSM7441309 |
Immortalised MEF cells, subclonal population 1-5 |
| GSM7441310 |
Immortalised MEF cells, subclonal population 1-6 |
| GSM7441311 |
Immortalised MEF cells, subclonal population 1-7 |
| GSM7441312 |
Immortalised MEF cells, parental population 2 |
| GSM7441313 |
Immortalised MEF cells, subclonal population 2-1 |
| GSM7441314 |
Immortalised MEF cells, subclonal population 2-2 |
| GSM7441315 |
Immortalised MEF cells, subclonal population 2-3 |
| GSM7441316 |
Immortalised MEF cells, subclonal population 2-4 |
| GSM7441317 |
Immortalised MEF cells, subclonal population 2-5 |
| GSM7441318 |
Immortalised MEF cells, subclonal population 2-6 |
| GSM7441319 |
Immortalised MEF cells, subclonal population 2-7 |
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| This SubSeries is part of SuperSeries: |
| GSE234695 |
Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance |
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| Relations |
| BioProject |
PRJNA979208 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE234024_all_clonal_MEF_gene_expression_data.tsv.gz |
7.4 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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