PXD041835

PXD041835 is an original dataset announced via ProteomeXchange.

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

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.

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;

submitter keyword: NDRs, SV40 promoter,H3K4me3, pull-down, H4ac,H3ac

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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD041835

PRIDE project URI

• PRIDE
  1. PXD041835
     1. Label: PRIDE project
     2. Name: Dissecting the effect of a long linker DNA on protein binding to di-nucleosomes decorated with promoter-associated PTMs