PXD047582 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: Mass Spectrometry,Human Embryonic Stem Cells, Immunoprecipitation, WNT/beta-CATENIN pathway, TCF7L1 |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD047582
- Label: PRIDE project
- Name: Chromatin immunoprecipitation of ectopic FLAG-tagged TCF7L1 followed by Mass Spectrome-try in H9-TCF7L1 Human Embryonic Stem Cells