PXD027238-1

PXD027238 is an original dataset announced via ProteomeXchange.

Title	Identifying Specific Protein Interactors of Nucleosomes Carrying Methylated Histones using Quantitative Mass Spectrometry
Description	Chemical modification of histone proteins by methylation plays a central role in chromatin regulation by recruiting epigenetic ‘readers’ via specialized binding domains. Depending on the degree of methylation, the exact modified amino acid, and the associated reader proteins histone methylations are involved in the regulation of all DNA-based processes, such as transcription, DNA replication, and DNA repair. We have previously established a method that allows the unbiased identification of nuclear proteins which binding to nucleosomes is regulated by the presence of specific histone modifications (1,2). The method is based on an in-vitro reconstitution of semi-synthetic nucleosomes bearing a predefined set of histone modifications which are subsequently used as baits for affinity purification pull-down experiments with nuclear extracts followed by identification and quantification of nucleosome-interacting proteins using LC-MS/MS. Here we provide a representative set of label-free MS results for nucleosome pull-down affinity purification experiments performed using unmodified as well as H3K4me3- and H3K9me3-modified di-nucleosomes and nuclear extract obtained from HeLa S3 cells. 1. Bartke T, Vermeulen M, Xhemalce B, Robson SC, Mann M, Kouzarides T (2010) Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 143:470-484 2. Makowski MM, Gräwe C, Foster BM, Nguyen NV, Bartke T, Vermeulen M (2018) Global profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry. Nat Commun 9:1653
HostingRepository	PRIDE
AnnounceDate	2022-08-11
AnnouncementXML	Submission_2022-08-11_12:51:57.445.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	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-12 01:43:08	ID requested
⏵ 1	2022-08-11 12:51:57	announced
2	2023-11-14 08:52:11	announced	2023-11-14: Updated project metadata.

10.1007/978-1-0716-2481-4_16;

submitter keyword: histone PTMs, H3K4me3, H3K9me3, nucleosome pull-down affinity purification

Till Bartke
contact affiliation	Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
contact email	till.bartke@helmholtz-muenchen.de
lab head
Andrey Tvardovskiy
contact affiliation	Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
contact email	andrey.tvardovskiy@helmholtz-muenchen.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD027238
     1. Label: PRIDE project
     2. Name: Identifying Specific Protein Interactors of Nucleosomes Carrying Methylated Histones using Quantitative Mass Spectrometry