GEO series
Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_IAA72h_ChIP_Seq]
GSE215326
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
30 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 GSE215326_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 30 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA889769 and SRA study SRP402179. Searching any of these in the dataset finder brings you back here.
Study design
10 conditions, mostly in triplicate
HEK293T_IAA_minus_72h_input ×3
HEK293T_IAA_minus_72h_IP_CTCF ×3
HEK293T_IAA_minus_72h_IP_MBD3 ×3
HEK293T_IAA_minus_72h_IP_TET1 ×3
HEK293T_IAA_minus_72h_IP_TET2 ×3
HEK293T_IAA_plus_72h_input ×3
HEK293T_IAA_plus_72h_IP_CTCF ×3
HEK293T_IAA_plus_72h_IP_MBD3 ×3
+2 more
Supports a between-group comparison across 30 samples.
10 replicated groups read from 30 sample titles; they account for 30 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM6632509 HEK293T_IAA_minus_72h_input_rep1
- GSM6632510 HEK293T_IAA_minus_72h_input_rep2
- GSM6632511 HEK293T_IAA_minus_72h_input_rep3
- GSM6632512 HEK293T_IAA_minus_72h_IP_CTCF_rep1
- GSM6632513 HEK293T_IAA_minus_72h_IP_CTCF_rep2
- GSM6632514 HEK293T_IAA_minus_72h_IP_CTCF_rep3
- GSM6632515 HEK293T_IAA_minus_72h_IP_MBD3_rep1
- GSM6632516 HEK293T_IAA_minus_72h_IP_MBD3_rep2
- GSM6632517 HEK293T_IAA_minus_72h_IP_MBD3_rep3
- GSM6632518 HEK293T_IAA_minus_72h_IP_TET1_rep1
- GSM6632519 HEK293T_IAA_minus_72h_IP_TET1_rep2
- GSM6632520 HEK293T_IAA_minus_72h_IP_TET1_rep3
- GSM6632521 HEK293T_IAA_minus_72h_IP_TET2_rep1
- GSM6632522 HEK293T_IAA_minus_72h_IP_TET2_rep2
- GSM6632523 HEK293T_IAA_minus_72h_IP_TET2_rep3
- GSM6632524 HEK293T_IAA_plus_72h_input_rep1
- GSM6632525 HEK293T_IAA_plus_72h_input_rep2
- GSM6632526 HEK293T_IAA_plus_72h_input_rep3
- GSM6632527 HEK293T_IAA_plus_72h_IP_CTCF_rep1
- GSM6632528 HEK293T_IAA_plus_72h_IP_CTCF_rep2
- GSM6632529 HEK293T_IAA_plus_72h_IP_CTCF_rep3
- GSM6632530 HEK293T_IAA_plus_72h_IP_MBD3_rep1
- GSM6632531 HEK293T_IAA_plus_72h_IP_MBD3_rep2
- GSM6632532 HEK293T_IAA_plus_72h_IP_MBD3_rep3
- GSM6632533 HEK293T_IAA_plus_72h_IP_TET1_rep1
- GSM6632534 HEK293T_IAA_plus_72h_IP_TET1_rep2
- GSM6632535 HEK293T_IAA_plus_72h_IP_TET1_rep3
- GSM6632536 HEK293T_IAA_plus_72h_IP_TET2_rep1
- GSM6632537 HEK293T_IAA_plus_72h_IP_TET2_rep2
- GSM6632538 HEK293T_IAA_plus_72h_IP_TET2_rep3
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