GEO series
Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [hESC_H9_d049_ChIP_Seq]
GSE215328
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
135 samples
Submitted 2026/05/04
Platform GPL23227
Summary
CCCTC-binding factor (CTCF) is an evolutionarily conserved transcription factor with diverse regulatory roles. Around stable CTCF binding sites, nucleosomes are highly ordered and DNA methylation is reduced, yet the mechanisms establishing and maintaining this epigenetic environment remain unclear. Utilizing an innovative eBioID method, we identified that virtually all subunits of the nucleosome remodeling and deacetylase (NuRD) complex are associated with CTCF in cells. Further analyses revealed that the NuRD complex is necessary for the chromatin binding of CTCF, and emerges as a novel regulator of the genome architecture. Additionally, we discovered that MBD3-NuRD facilitates the recruitment of TET demethylases to CTCF sites, initiating local DNA demethylation essential for the activation of adjacent gene expression. Embryonic stem cells deficient in the NuRD complex showed impaired lineage commitment. In summary, this study elucidates a mechanism illustrating the interplay between CTCF binding and the epigenome including 3D genome organization and DNA methylation, with the NuRD complex serving as an indispensable mediator.
Published in
Sun W, Wu N, Xia M et al.
· Molecular cell 2026
· PMID 42225060
· doi:10.1016/j.molcel.2026.05.010
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE215328_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 135 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA889778 and SRA study SRP402202. Searching any of these in the dataset finder brings you back here.
Study design
13 conditions, mostly in triplicate
hESC_H9_d0_WT_input ×3
hESC_H9_d0_WT_IP_CTCF ×3
hESC_H9_d0_WT_IP_MBD3 ×3
hESC_H9_d4_WT_input ×3
hESC_H9_d4_WT_IP_CTCF ×3
hESC_H9_d4_WT_IP_MBD3 ×3
hESC_H9_d9_WT_input ×3
hESC_H9_d9_WT_IP_CTCF ×3
+6 more
Supports a between-group comparison across 39 samples.
13 replicated groups read from the first 40 of 135 sample titles; they account for 39 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM6632540 hESC_H9_d0_WT_input_rep1
- GSM6632541 hESC_H9_d0_WT_input_rep2
- GSM6632542 hESC_H9_d0_WT_input_rep3
- GSM6632543 hESC_H9_d0_WT_IP_CTCF_rep1
- GSM6632544 hESC_H9_d0_WT_IP_CTCF_rep2
- GSM6632545 hESC_H9_d0_WT_IP_CTCF_rep3
- GSM6632546 hESC_H9_d0_WT_IP_MBD3_rep1
- GSM6632547 hESC_H9_d0_WT_IP_MBD3_rep2
- GSM6632548 hESC_H9_d0_WT_IP_MBD3_rep3
- GSM6632549 hESC_H9_d4_WT_input_rep1
- GSM6632550 hESC_H9_d4_WT_input_rep2
- GSM6632551 hESC_H9_d4_WT_input_rep3
- GSM6632552 hESC_H9_d4_WT_IP_CTCF_rep1
- GSM6632553 hESC_H9_d4_WT_IP_CTCF_rep2
- GSM6632554 hESC_H9_d4_WT_IP_CTCF_rep3
- GSM6632555 hESC_H9_d4_WT_IP_MBD3_rep1
- GSM6632556 hESC_H9_d4_WT_IP_MBD3_rep2
- GSM6632557 hESC_H9_d4_WT_IP_MBD3_rep3
- GSM6632558 hESC_H9_d9_WT_input_rep1
- GSM6632559 hESC_H9_d9_WT_input_rep2
- GSM6632560 hESC_H9_d9_WT_input_rep3
- GSM6632561 hESC_H9_d9_WT_IP_CTCF_rep1
- GSM6632562 hESC_H9_d9_WT_IP_CTCF_rep2
- GSM6632563 hESC_H9_d9_WT_IP_CTCF_rep3
- GSM6632564 hESC_H9_d9_WT_IP_MBD3_rep1
- GSM6632565 hESC_H9_d9_WT_IP_MBD3_rep2
- GSM6632566 hESC_H9_d9_WT_IP_MBD3_rep3
- GSM6632567 hESC_H9_d0_DMSO_input_rep1
- GSM6632568 hESC_H9_d0_DMSO_input_rep2
- GSM6632569 hESC_H9_d0_DMSO_input_rep3
- GSM6632570 hESC_H9_d0_DMSO_IP_CTCF_rep1
- GSM6632571 hESC_H9_d0_DMSO_IP_CTCF_rep2
- GSM6632572 hESC_H9_d0_DMSO_IP_CTCF_rep3
- GSM6632573 hESC_H9_d0_DMSO_IP_MBD3_rep1
- GSM6632574 hESC_H9_d0_DMSO_IP_MBD3_rep2
- GSM6632575 hESC_H9_d0_DMSO_IP_MBD3_rep3
- GSM6632576 hESC_H9_d0_DMSO_IP_TET1_rep1
- GSM6632577 hESC_H9_d0_DMSO_IP_TET1_rep2
- GSM6632578 hESC_H9_d0_DMSO_IP_TET1_rep3
- GSM6632579 hESC_H9_d0_DMSO_IP_TET2_rep1
+ 95 more — browse all 135 samples with per-sample file links →
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