PXD054375
PXD054375 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | 3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes |
| Description | Studying the dynamics of three-dimensional (3D) chromatin structure is essential to the understanding of biological processes in the nucleus. Integrative analysis of multi-omics data in recent publications have provided comprehensive and multilevel insight into 3D genome organization emphasizing its role for transcriptional regulation. While enhancers are regulatory elements that play a central role in the spatiotemporal control of gene expression, chromatin looping has been broadly accepted as a means for enhancer-promoter interactions yieldingcell-type-specific gene expression signatures. On the other hand, G-quadruplexes (G4s) are non-canonical DNA secondary structures that are enriched at promoters and related to increased gene expression, both. A role for G4s in promoter-distal regulatory elements, such as super-enhancers (SE), as well as in 3D genome organization and chromatin looping mediating long-range enhancer-promoter interactions has, however, remained elusive. Here we show that mature microRNA 9 (miR-9) is enriched at promoters and SE of genes that are inducible by tissue growth factor beta 1 (TGFB1) signaling. Further, we find that nuclear miR-9 is required for chromatin features related to increased transcriptional activity, such as broad domains of the euchromatin histone mark H3K4me3 (histone 3 tri-methylated lysine 4) and G4s. Moreover, we show that nuclear miR-9 is required for promoter-super-enhancer looping. Our study places a nuclear microRNA in the same structural and functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a critical regulator of proliferation programs in cancer and fibrosis. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-12-21 |
| AnnouncementXML | Submission_2024-12-21_11:24:35.470.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Witold Szymanski |
| SpeciesList | scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090; |
| ModificationList | CarbamidomethylDTT |
| Instrument | timsTOF Ultra |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-07-30 02:13:51 | ID requested | |
| ⏵ 1 | 2024-12-21 11:24:35 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: TimsTof, sp3, mouse, interactome |
Contact List
| Guillermo Barreto | |
|---|---|
| contact affiliation | Universite de Lorraine, CNRS, Laboratoire IMoPA, Nancy |
| contact email | Guillermo.Barreto@univ-lorraine.fr |
| lab head | |
| Witold Szymanski | |
| contact affiliation | Philipps-University Marburg Biochemical/Pharmacological Center Department of Medicine |
| contact email | witold.szymanski@uni-marburg.de |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive.ucsd.edu/v08/MSV000095480/ |
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