PXD042368 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Examining the effect of the linker DNA length on protein binding to di-nucleosomes decorated with H3K9me3 and H3K27me3 |
Description | Characteristic features of chromatin states are not limited to particular epigenetic modifications but include other regulatory cues, such as linker DNA length, typically ranging from between 35-55 bp (Valouev et al, 2011; Voong et al., 2016, Cell) to over 200 bp in nucleosome-depleted regions (NDRs) found at active enhancers and promoters (Schones et al, 2008; Hansen He et al, 2010). To investigate whether and how the nucleosome linker DNA affects chromatin recognition by nuclear proteins we performed a set of affinity purifications using di-nucleosomes incorporating different DNA linkers. This dataset contains experiments aimed to probe how the linker DNA length affects protein binding to di-nucleosomes decorated with H3K9me3 or H3K27me3. The following di-nucleosomes were used in affinity pull-down purifications with HeLa nuclear extract followed by label-free MS: 1. unmod. H3, 35 bp linker 2. unmod. H3, 40 bp linker 3. unmod. H3, 45 bp linker 4. unmod. H3, 50 bp linker 5. unmod. H3, 55 bp linker 6. H3K9me3, 35 bp linker 7. H3K9me3, 40 bp linker 8. H3K9me3, 45 bp linker 9. H3K9me3 50 bp linker 10. H3K9me3, 55 bp linker 11. H3K27me3, 35 bp linker 12. H3K27me3, 40 bp linker 13. H3K27me3, 45 bp linker 14. H3K27me3, 50 bp linker 15. H3K27me3, 55 bp linker |
HostingRepository | PRIDE |
AnnounceDate | 2024-04-29 |
AnnouncementXML | Submission_2024-04-29_08:02:28.365.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Andrey Tvardovskiy |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-05-20 12:58:04 | ID requested | |
1 | 2023-12-10 13:06:08 | announced | |
⏵ 2 | 2024-04-29 08:02:29 | announced | 2024-04-29: Updated project metadata. |
Publication List
Lukauskas S, Tvardovskiy A, Nguyen NV, Stadler M, Faull P, Ravnsborg T, Ö, zdemir Aygenli B, Dornauer S, Flynn H, Lindeboom RGH, Barth TK, Brockers K, Hauck SM, Vermeulen M, Snijders AP, M, ü, ller CL, DiMaggio PA, Jensen ON, Schneider R, Bartke T, Decoding chromatin states by proteomic profiling of nucleosome readers. Nature, 627(8004):671-679(2024) [pubmed] |
10.1038/s41586-024-07141-5; |
Keyword List
submitter keyword: nucleosome pull-down, linker DNA, H3K27me3, H3K9me3 |
Contact List
Till Bartke |
contact affiliation | Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany. |
contact email | till.bartke@helmholtz-muenchen.de |
lab head | |
Andrey Tvardovskiy |
contact affiliation | Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany |
contact email | tvardovsky.a@gmail.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD042368
- Label: PRIDE project
- Name: Examining the effect of the linker DNA length on protein binding to di-nucleosomes decorated with H3K9me3 and H3K27me3