GEO series
Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_siNURD_CTCF_ChIP_Seq]
GSE253694
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
36 samples
Submitted 2026/05/04
Platform GPL30209
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 GSE253694_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 36 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1066782 and SRA study SRP484819. Searching any of these in the dataset finder brings you back here.
Study design
12 conditions, mostly in triplicate
HEK293T_siCHD3_IP_CTCF ×3
HEK293T_siCHD3_input ×3
HEK293T_siCHD4_IP_CTCF ×3
HEK293T_siCHD4_input ×3
HEK293T_siCHD5_IP_CTCF ×3
HEK293T_siCHD5_input ×3
HEK293T_siMBD2_IP_CTCF ×3
HEK293T_siMBD2_input ×3
+4 more
Supports a between-group comparison across 36 samples.
12 replicated groups read from 36 sample titles; they account for 36 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8026497 HEK293T_siCHD3_IP_CTCF_rep1
- GSM8026498 HEK293T_siCHD3_IP_CTCF_rep2
- GSM8026499 HEK293T_siCHD3_IP_CTCF_rep3
- GSM8026500 HEK293T_siCHD3_input_rep1
- GSM8026501 HEK293T_siCHD3_input_rep2
- GSM8026502 HEK293T_siCHD3_input_rep3
- GSM8026503 HEK293T_siCHD4_IP_CTCF_rep1
- GSM8026504 HEK293T_siCHD4_IP_CTCF_rep2
- GSM8026505 HEK293T_siCHD4_IP_CTCF_rep3
- GSM8026506 HEK293T_siCHD4_input_rep1
- GSM8026507 HEK293T_siCHD4_input_rep2
- GSM8026508 HEK293T_siCHD4_input_rep3
- GSM8026509 HEK293T_siCHD5_IP_CTCF_rep1
- GSM8026510 HEK293T_siCHD5_IP_CTCF_rep2
- GSM8026511 HEK293T_siCHD5_IP_CTCF_rep3
- GSM8026512 HEK293T_siCHD5_input_rep1
- GSM8026513 HEK293T_siCHD5_input_rep2
- GSM8026514 HEK293T_siCHD5_input_rep3
- GSM8026515 HEK293T_siMBD2_IP_CTCF_rep1
- GSM8026516 HEK293T_siMBD2_IP_CTCF_rep2
- GSM8026517 HEK293T_siMBD2_IP_CTCF_rep3
- GSM8026518 HEK293T_siMBD2_input_rep1
- GSM8026519 HEK293T_siMBD2_input_rep2
- GSM8026520 HEK293T_siMBD2_input_rep3
- GSM8026521 HEK293T_siMBD3_IP_CTCF_rep1
- GSM8026522 HEK293T_siMBD3_IP_CTCF_rep2
- GSM8026523 HEK293T_siMBD3_IP_CTCF_rep3
- GSM8026524 HEK293T_siMBD3_input_rep1
- GSM8026525 HEK293T_siMBD3_input_rep2
- GSM8026526 HEK293T_siMBD3_input_rep3
- GSM8026527 HEK293T_siNC_IP_CTCF_rep1
- GSM8026528 HEK293T_siNC_IP_CTCF_rep2
- GSM8026529 HEK293T_siNC_IP_CTCF_rep3
- GSM8026530 HEK293T_siNC_input_rep1
- GSM8026531 HEK293T_siNC_input_rep2
- GSM8026532 HEK293T_siNC_input_rep3
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