GEO series
Neocentromeres fail to maintain DNA methylation boundaries, driving CENP-A drift, instability, and chromosome missegregation
GSE336584
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
60 samples
Submitted 2026/06/26
Platform GPL16791
Summary
Centromere identity is specified by CENP-A, a histone H3 variant that epigenetically defines centromere position. How CENP-A is maintained at one location in rapidly evolving centromeric DNA is unknown. Using single-cell derived clones of human cell lines, we demonstrate heterogeneity in CENP-A position within cell populations at neocentromeres and a native centromere. CENP-A heterogeneity is accompanied by heterogenous DNA methylation patterns, with DNA methylation shifting according to CENP-A position. We demonstrate centromere epigenetic plasticity over extended proliferation, with native centromeres maintaining stable DNA methylation boundaries, but neocentromeres exhibiting DNA methylation instability, boundary loss and increased missegregation. Finally, we show that neocentromeres are more sensitive to DNA methylation inhibition than native centromeres, and that this inhibition is accompanied by expanded CENP-A-enriched domains and increased missegregation. This study supports a role for DNA methylation boundaries in maintaining centromere position, stability and function and highlights the intrinsic instability of DNA methylation at neocentromeres.
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE336584_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 60 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1231498 and SRA study SRP567869. Searching any of these in the dataset finder brings you back here.
Study design
35 conditions, each sampled once — no replicated groups
IMS13q clone B ×4
IMS13q clone A ×2
IMS13q clone C ×2
Read from the first 40 of 60 sample titles: 35 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9837761 PD-NC4 Parental
- GSM9837762 PD-NC4 clone A1 young
- GSM9837763 PD-NC4 clone C1 young
- GSM9837764 PD-NC4 clone C2 young
- GSM9837765 PD-NC4 clone C3 young
- GSM9837766 PD-NC4 clone C4 young
- GSM9837767 PD-NC4 clone D1 young
- GSM9837768 PD-NC4 clone D2 young
- GSM9837769 PD-NC4 clone E1 young
- GSM9837770 PD-NC4 clone E2 young
- GSM9837771 PD-NC4 clone A1 6mo
- GSM9837772 PD-NC4 clone C1 6mo
- GSM9837773 PD-NC4 clone C2 6mo
- GSM9837774 PD-NC4 clone C3 6mo
- GSM9837775 PD-NC4 clone C4 6mo
- GSM9837776 PD-NC4 clone D1 6mo
- GSM9837777 PD-NC4 clone D2 6mo
- GSM9837778 PD-NC4 clone E1 6mo
- GSM9837779 PD-NC4 clone E2 6mo
- GSM9837780 PD-NC4 clone A1 12mo
- GSM9837781 PD-NC4 clone C1 12mo
- GSM9837782 PD-NC4 clone C2 12mo
- GSM9837783 PD-NC4 clone C3 12mo
- GSM9837784 PD-NC4 clone C4 12mo
- GSM9837785 PD-NC4 clone D1 12mo
- GSM9837786 PD-NC4 clone D2 12mo
- GSM9837787 PD-NC4 clone E1 12mo
- GSM9837788 PD-NC4 clone E2 12mo
- GSM9837789 IMS13q clone Parental
- GSM9837790 IMS13q clone A3
- GSM9837791 IMS13q clone A4
- GSM9837792 IMS13q clone B2
- GSM9837793 IMS13q clone B4
- GSM9837794 IMS13q clone B7
- GSM9837795 IMS13q clone B8
- GSM9837796 IMS13q clone C1
- GSM9837797 IMS13q clone C8
- GSM9837798 IMS13q clone E8
- GSM9837799 BBB Parental
- GSM9837800 BBB clone H2
+ 20 more — browse all 60 samples with per-sample file links →
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