| Property |
Value |
| Working Groups |
RG Oudelaar, 
RG Papantonis |
| Subproject |
P02, P03 |
| Open Access |
Yes |
| Publication Type |
Journal Article |
| Peer Reviewed |
Yes |
| PMID |
40360814 |
| DOI |
10.1038/s41594-025-01555-z |
| Publication Year |
2025 |
| Title |
CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation |
| Journal |
Nature Structural & Molecular Biology |
| ISSN |
1545-9993 |
| eISSN |
1545-9985 |
| URL |
https://doi.org/10.1038/s41594-025-01555-z |
| Journal Abbreviation |
Nat Struct Mol Biol |
| Authors |
Karpinska MA, Zhu Y, Fakhraei Ghazvini Z, Ramasamy S, Barbieri M, Cao TBN, Varahram N, Aljahani A, Lidschreiber M, Papantonis A, Oudelaar AM |
| First Author |
Karpinska MA |
| Last Author |
Oudelaar AM |
External Resources
nature.c...-z.pdfhttps://www.nature.com/articles/s41594-025-01555-z.pdf Article fulltext
E-MTAB-9010https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9010 EMBL ArrayExpress identifier (E-MTAB-9010, reused)
gro-2/149402http://resolver.sub.uni-goettingen.de/purl?gro-2/149402 GRO.publications identifier
GSE263641https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE263641 NCBI GEO Dataset (GSE263641)
GSE131620https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131620 NCBI GEO Dataset (GSE131620, reused)
GSE140528https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140528 NCBI GEO Dataset (GSE140528, reused)
GSE256663https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE256663 NCBI GEO Dataset (GSE256663, reused)
GSE257528https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE257528 NCBI GEO Dataset (GSE257528, reused)
GSE259000https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE259000 NCBI GEO Dataset (GSE259000, reused)
GSE257306https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE257306 NCBI GEO Dataset (GSE257306, reused)
9606https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606 NCBI taxonomy (human, Homo sapiens)
0000-0002-1516-2083https://orcid.org/0000-0002-1516-2083 ORCID identifier (Magdalena A. Karpinska)
0000-0002-3246-6484https://orcid.org/0000-0002-3246-6484 ORCID identifier (Zahra Fakhraei Ghazvini)
0009-0008-3909-1321https://orcid.org/0009-0008-3909-1321 ORCID identifier (Yi Zhu)
0000-0003-0617-694Xhttps://orcid.org/0000-0003-0617-694X ORCID identifier (Shyam Ramasamy)
0000-0002-9080-631Xhttps://orcid.org/0000-0002-9080-631X ORCID identifier (Mariano Barbieri)
0000-0002-5612-2774https://orcid.org/0000-0002-5612-2774 ORCID identifier (Tran Bich Ngoc Cao)
0000-0001-6640-2641https://orcid.org/0000-0001-6640-2641 ORCID identifier (Abrar Aljahani)
0000-0002-6740-2755https://orcid.org/0000-0002-6740-2755 ORCID identifier (Michael Lidschreiber)
0000-0001-7551-1073https://orcid.org/0000-0001-7551-1073 ORCID identifier (Argyris Papantonis)
0000-0002-3425-0476https://orcid.org/0000-0002-3425-0476 ORCID identifier (A. Marieke Oudelaar)
66https://rdp.sfb1565.uni-goettingen.de/literature/publications/66 Published Data Registry entry (CRC 1565, preprint)
4/26https://rdp.sfb1565.uni-goettingen.de/archive/4/26 Research Data Archive (supplemental material)
03av75f26https://ror.org/03av75f26 ROR identifier (03av75f26, Max Planck Institute for Multidisciplinary Sciences)
021ft0n22https://ror.org/021ft0n22 ROR identifier (021ft0n22, University Medical Center Göttingen)
SCR_016368https://scicrunch.org/resolver/SCR_016368 SciCrunch identifier (RRID:SCR_016368, Bowtie 2)
SCR_026118https://scicrunch.org/resolver/SCR_026118 SciCrunch identifier (RRID:SCR_026118, cooltools)
SCR_016366https://scicrunch.org/resolver/SCR_016366 SciCrunch identifier (RRID:SCR_016366, Deeptools)
SCR_015687https://scicrunch.org/resolver/SCR_015687 SciCrunch identifier (RRID:SCR_015687, DESeq2)
SCR_008520https://scicrunch.org/resolver/SCR_008520 SciCrunch identifier (RRID:SCR_008520, FlowJo)
SCR_016381https://scicrunch.org/resolver/SCR_016381 SciCrunch identifier (RRID:SCR_016381, Illumina NextSeq 550 System)
SCR_013291https://scicrunch.org/resolver/SCR_013291 SciCrunch identifier (RRID:SCR_013291, MACS)
SCR_001905https://scicrunch.org/resolver/SCR_001905 SciCrunch identifier (RRID:SCR_001905, R Project for Statistical Computing)
SCR_015899https://scicrunch.org/resolver/SCR_015899 SciCrunch identifier (RRID:SCR_015899, STAR)
goeseek.gwdguser.de/studies/248https://goeseek.gwdguser.de/studies/248 Supplemental material (goeseek study)
static-c...SM.pdfhttps://static-content.springer.com/esm/art%3A10.1038%2Fs41594-025-01555-z/MediaObjects/41594_2025_1555_MOESM2_ESM.pdf Supplemental material (peer review)
static-c...SM.pdfhttps://static-content.springer.com/esm/art%3A10.1038%2Fs41594-025-01555-z/MediaObjects/41594_2025_1555_MOESM1_ESM.pdf Supplemental material (reporting summary)
static-c...M.xlsxhttps://static-content.springer.com/esm/art%3A10.1038%2Fs41594-025-01555-z/MediaObjects/41594_2025_1555_MOESM4_ESM.xlsx Supplemental material (source data)
static-c...M.xlsxhttps://static-content.springer.com/esm/art%3A10.1038%2Fs41594-025-01555-z/MediaObjects/41594_2025_1555_MOESM3_ESM.xlsx Supplemental material (table)
10.5281/zenodo.14932098https://doi.org/10.5281/zenodo.14932098 Zenodo identifier (10.5281/zenodo.14932098)
Linked Antibodies
| PID |
AG |
Type |
Antigen symbol |
Antibody Registry ID |
Name |
| primary-0169 |
|
primary |
H2Av |
AB_2737370 |
Spike-in Antibody |
| primary-0170 |
|
primary |
|
AB_469272 |
Fc Receptor Binding Inhibitor Polyclonal Antibody, Functional Grade, eBioscience™ |
| primary-0171 |
|
primary |
|
AB_400384 |
APC-Cy™7 Mouse Anti-Human CD19 |
| primary-0172 |
|
primary |
CTCF |
AB_2753160 |
CTCF Antibody |
| primary-0173 |
|
primary |
SMC1A |
AB_307121 |
Anti-SMC1A antibody |
| primary-0174 |
|
primary |
CRSP7 |
AB_1907253 |
Rabbit anti-CRSP7 Antibody Affinity Purified |