PXD047582

PXD047582 is an original dataset announced via ProteomeXchange.

Title	Chromatin immunoprecipitation of ectopic FLAG-tagged TCF7L1 followed by Mass Spectrome-try in H9-TCF7L1 Human Embryonic Stem Cells
Description	TCF7L1 is a member of the T cell factor/Lymphoid enhancer factor (TCF/LEF) family of tran-scription factors that are part of the WNT/beta-CATENIN signaling pathway. TCF7L1 modulates transcription by interacting with other regulators on chromatin. TCF7L1 has been shown to be one of the key factors in maintaining pluripotency in human embryonic stem cells (ESCs). We previously demonstrated that the absence of TCF71 causes H9 hESCs to differentiate sponta-neously (Sierra et al., 2018 Development 145(4).pii:dev161075). Mechanistically, how TCF7L1 inhibits differentiation and keeps cells in the pluripotent state is not clear. Identifying transcrip-tional regulators on chromatin is a critical step to elucidating one of several molecular mecha-nisms controlled by TCF7L1. We previously developed a FLAG tagged TCF7L1 transgene that is controlled by a doxycycline-inducible TET-ON system and generated the H9-TCF7L1 line (Sier-ra et al., 2018 Development 145(4).pii:dev161075). Here we used the H9-TCF7L1 line and em-ployed the method called rapid immunoprecipitation (IP) mass spectrometry of endogenous pro-tein (RIME) (Mohammed et al., 2016 Nat Protoc 11(2):316-26) to identify TCF7L1-associated proteins on chromatin. Coupling of these two methods (the FLAG tagged TETON inducible sys-tem and RIME) allowed us to control the level of TCF7L1 expression in hESCs, immunopreci-pate TCF7L1 using an anti-FLAG antibody and capture TCF7L1-bound associated complexes on chromatin. Our MS analysis identified some known proteins that have been shown to associate with the WNT/beta-CATENIN/TCF/LEF pathway, as well as novel complexes that have not been linked with TCF7L1. Gene Ontology analysis suggest these proteins function in chromatin modi-fication, splicing, and RNA processing. Our data could create new ideas for in-depth studies of TCF7L1 controlling pluripotency in human ESCs and for understanding how TCF7L1 may act in other cell types.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:45:49.425.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Linh Vuong
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Fusion; nanoACQUITY UPLC

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-06 15:11:16	ID requested
1	2024-06-16 01:38:09	announced
⏵ 2	2024-10-22 06:45:51	announced	2024-10-22: Updated project metadata.

10.1002/pmic.202300641;

Vuong LM, Pan S, Sierra RA, Waterman ML, Gershon PD, Donovan PJ, Characterization of a chromatin-associated TCF7L1 complex in human embryonic stem cells. Proteomics, 24(20):e2300641(2024) [pubmed]

submitter keyword: Mass Spectrometry,Human Embryonic Stem Cells, Immunoprecipitation, WNT/beta-CATENIN pathway, TCF7L1

Peter J. Donovan
contact affiliation	Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.
contact email	pdonovan@uci.edu
lab head
Linh Vuong
contact affiliation	UCI
contact email	linhmv@uci.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/2024/06/PXD047582

PRIDE project URI

• PRIDE
  1. PXD047582
     1. Label: PRIDE project
     2. Name: Chromatin immunoprecipitation of ectopic FLAG-tagged TCF7L1 followed by Mass Spectrome-try in H9-TCF7L1 Human Embryonic Stem Cells