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Series GSE234024 Query DataSets for GSE234024
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
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.
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.
Contributor(s) Hay AD, Kessler NJ, Gebert D, Takahashi N, Tavares H, Teixeira FK, Ferguson-Smith AC
Citation(s) 37660134
Submission date Jun 02, 2023
Last update date Sep 15, 2023
Contact name Anne Ferguson-Smith
Organization name Cambridge University
Department Genetics
Street address 20 Downing Place
City Cambridge
ZIP/Postal code CB2 3EJ
Country United Kingdom
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (16)
GSM7441304 Immortalised MEF cells, parental population 1
GSM7441305 Immortalised MEF cells, subclonal population 1-1
GSM7441306 Immortalised MEF cells, subclonal population 1-2
This SubSeries is part of SuperSeries:
GSE234695 Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance
BioProject PRJNA979208

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Supplementary file Size Download File type/resource
GSE234024_all_clonal_MEF_gene_expression_data.tsv.gz 7.4 Mb (ftp)(http) TSV
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