PXD022088

PXD022088 is an original dataset announced via ProteomeXchange.

Title	TINC - a method to dissect transcriptional complexes at single locus resolution - reveals novel Nanog regulators in mouse embryonic stem cells
Description	Cellular identity is ultimately dictated by the interaction of transcription factors with regulatory elements (REs) to control gene expression. Advances in genome-wide epigenome profiling techniques have significantly increased our understanding of cell-specific utilization of REs. However, it remains difficult to dissect the majority of factors that interact with these REs due to the lack of appropriate techniques. To address this issue, we developed a novel epigenetic method termed TINC: TALE-mediated Isolation of Nuclear Chromatin. Using TINC we interrogated the protein complex formed at the Nanog promoter in embryonic stem cells (ESCs) and identified many known interactors as well as numerous previously unknown complex members, including RCOR2. Further interrogation of the role of RCOR2 in the ESC network revealed its involvement in the repression of lineage genes and the fine-tuning of pluripotency genes. Consequently, using the Nanog promoter as a paradigm, we demonstrated the power of TINC to provide important insights into the molecular makeup of transcriptional complexes at individual REs as well as into control of cellular identity in general.
HostingRepository	PRIDE
AnnounceDate	2020-12-14
AnnouncementXML	Submission_2020-12-14_00:14:13.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ralf Schittenhelm
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion; QTRAP 6500

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-20 01:15:06	ID requested
⏵ 1	2020-12-14 00:14:14	announced

Knaupp AS, Mohenska M, Larcombe MR, Ford E, Lim SM, Wong K, Chen J, Firas J, Huang C, Liu X, Nguyen T, Sun YBY, Holmes ML, Tripathi P, Pflueger J, Rossello FJ, Schr, ö, der J, Davidson KC, Nefzger CM, Das PP, Haigh JJ, Lister R, Schittenhelm RB, Polo JM, TINC- A Method to Dissect Regulatory Complexes at Single-Locus Resolution- Reveals an Extensive Protein Complex at the Nanog Promoter. Stem Cell Reports, 15(6):1246-1259(2020) [pubmed]

submitter keyword: TINC, stem cells, cellular identity, regulatory elements, Nanog

Jose Polo
contact affiliation	Department of Anatomy and Developmental Biology, Australian Regenerative Medicine Institute, Monash University, Australia
contact email	jose.polo@monash.edu
lab head
Ralf Schittenhelm
contact affiliation	Monash University
contact email	ralf.schittenhelm@monash.edu
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/2020/12/PXD022088

PRIDE project URI

• PRIDE
  1. PXD022088
     1. Label: PRIDE project
     2. Name: TINC - a method to dissect transcriptional complexes at single locus resolution - reveals novel Nanog regulators in mouse embryonic stem cells