PXD018966

PXD018966 is an original dataset announced via ProteomeXchange.

Title	MARCS: Modification Atlas for Regulation by Chromatin States
Description	Goal of this project was the identification of chromatin interacting proteins whose binding is differentially regulated by various combinatorial chromatin modifications found in different chromatin states such as promoters, enhancers and heterochromatin. To achieve this, recombinant modified nucleosomes representing different chromatin states were assembled from canonical histones, H2A.Z and modified ligated H3/H4 histone proteins and biotinylated nucleosomal DNAs. Assembled nucleosomes were immobilized on streptavidin-coated beads via biotinylated di-nucleosomal 601 DNA and used for nucleosome affinity purifications to identify proteins regulated by chromatin modifications from SILAC-labelled HeLaS3 nuclear extracts (Arg10 and Lys8). SILAC affinity purifications were carried out in "forward" (heavy extract on modified nucleosome and light extract on unmodified nucleosome) and "reverse" (light extract on modified nucleosome and heavy extract on unmodified nucleosome) label-swap experiments and protein abundances were quantified by MaxQuant. Initial trial experiments with biotinylated mono-, di- and tetra- 601 nucleosomes are also deposited along with the data for the di-nucleosome experiments. See also: Bartke et al., 2010. Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 143, 470–484; doi:10.1016/j.cell.2010.10.012. The H4K20me2 samples from this experiment were previously deposited with identifier PXD009281. These were published in: Nakamura et al., 2019. H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nature Cell Biology 21, 311–318; doi: 10.1038/s41556-019-0282-9.
HostingRepository	PRIDE
AnnounceDate	2024-04-29
AnnouncementXML	Submission_2024-04-29_08:01:34.664.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Saulius Lukauskas
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-04 01:26:13	ID requested
1	2023-12-12 16:36:39	announced
⏵ 2	2024-04-29 08:01:35	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: H3K14ac, H3K27me3, H3K27me2, SNAP, H4K20me3, H4K20me2, H3K9me2, H2A.Z, H3K9me3, Chromatin, Nucleosome Affinity Purification, H3K18ac, H4K12ac, H4K5ac, H4K16ac, H4K8ac, H3K4me3, H3K4me1, H3K27ac, H3K23ac, meCpG, H3K9ac, DNA Methylation, SILAC,Epigenetics

Till Bartke
contact affiliation	Institute of Functional Epigenetics, Helmholtz Zentrum Muenchen, Germany
contact email	till.bartke@helmholtz-muenchen.de
lab head
Saulius Lukauskas
contact affiliation	Helmholtz Zentrum Munich
contact email	saulius.lukauskas@helmholtz-muenchen.de
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/PXD018966

PRIDE project URI

• PRIDE
  1. PXD018966
     1. Label: PRIDE project
     2. Name: MARCS: Modification Atlas for Regulation by Chromatin States