PXD015251

PXD015251 is an original dataset announced via ProteomeXchange.

Title	Analysis of factors bound to native metaphase ESC chromosomes following purification by flow cytometry
Description	Stem cells are able to self-renew and also generate differentiated progeny. How gene expression patterns are transmitted through mitosis remains unresolved. Conventional studies have relied upon rigorous cell-cycle-stage synchronisation to find factors in mitotic lysates that could ‘bookmark’ the genome. Here we use an alternative approach, purifying native-unfixed mitotic chromosomes from different cell types using flow cytometry and directly identifying chromosome-bound proteins by LC-MS/MS. This revealed a rich profile of pluripotency- and lineage-specific transcription factors that remained bound to mitotic chromosomes in pluripotent ESCs and lymphocytes, as well as factors implicated in chromosome condensation, architecture and gene silencing. Removal of DNA methylation, PRC2 activity, or in situ cleavage of cohesin, each resulted in the reduced compaction of mitotic chromosomes. These data provide a comprehensive catalogue of bookmarking factors in pluripotent versus lineage-restricted cells and demonstrate an expected duality of function by candidates in regulating both gene expression and mitotic chromosome structure.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:07:13.982.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Holger Kramer
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-30 08:19:21	ID requested
1	2020-06-15 03:10:27	announced
2	2020-09-11 03:32:48	announced	2020-09-11: Updated publication reference for PubMed record(s): 32807789.
⏵ 3	2024-10-22 05:07:14	announced	2024-10-22: Updated project metadata.

10.1038/s41467-020-17823-z;

Djeghloul D, Patel B, Kramer H, Dimond A, Whilding C, Brown K, Kohler AC, Feytout A, Veland N, Elliott J, Bharat TAM, Tarafder AK, L, ö, we J, Ng BL, Guo Y, Guy J, Huseyin MK, Klose RJ, Merkenschlager M, Fisher AG, Identifying proteins bound to native mitotic ESC chromosomes reveals chromatin repressors are important for compaction. Nat Commun, 11(1):4118(2020) [pubmed]

submitter keyword: Mitosis, stem cells, chromosomes, chromatin

Amanda G. Fisher
contact affiliation	Lymphocyte Development Group MRC London Institute of Medical Sciences Imperial College School of Medicine Hammersmith Hospital Campus Du Cane Road London, W12 0NN United Kingdom
contact email	amanda.fisher@lms.mrc.ac.uk
lab head
Holger Kramer
contact affiliation	MRC London Institute of Medical Sciences
contact email	h.kramer@lms.mrc.ac.uk
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/2020/06/PXD015251

PRIDE project URI

• PRIDE
  1. PXD015251
     1. Label: PRIDE project
     2. Name: Analysis of factors bound to native metaphase ESC chromosomes following purification by flow cytometry