PXD041835 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Dissecting the effect of a long linker DNA on protein binding to di-nucleosomes decorated with promoter-associated PTMs |
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 around 35-55 bp in most eu- and heterochromatin domains (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. Here, we investigated the effect of a 200 bp di-nucleosome linker DNA represented by scrambled DNA or SV40 promoter DNA sequence on the nuclear protein binding to di-nucleosome decorated with promoter-associated modifications, including H3K4me3K9acK14acK18acK23acK27ac, H4K5acK8acK12acK16acK20me2 and histone variant H2A.Z Below is a description (modifications and linker) of di-nucleosomes used in pull-downs with HeLa nuclear extracts followed by label-free MS: 1. H3K4me3-5ac,H4K20me2-4ac, H2AZ, 50bp linker 2. H3K4me3-5ac,H4K20me2-4ac, H2AZ, 200bp scrambled DNA linker 3. H3K4me3-5ac,H4K20me2-4ac, H2AZ, 200bp SV40 promoter DNA linker 4. Unmod. H3&H4, 50bp linker 5. Unmod. H3&H4, 200bp scrambled DNA linker 6. Unmod. H3&H4, 200bp SV40 promoter DNA linker |
HostingRepository | PRIDE |
AnnounceDate | 2024-04-29 |
AnnouncementXML | Submission_2024-04-29_08:02:10.997.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 | 2023-04-26 15:44:01 | ID requested | |
1 | 2023-12-10 12:45:20 | announced | |
⏵ 2 | 2024-04-29 08:02:12 | 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: NDRs, SV40 promoter,H3K4me3, pull-down, H4ac,H3ac |
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
- PXD041835
- Label: PRIDE project
- Name: Dissecting the effect of a long linker DNA on protein binding to di-nucleosomes decorated with promoter-associated PTMs