Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription

Chong, Shasha and Graham, Thomas G. W. and Dugast-Darzacq, Claire and Dailey, Gina M. and Darzacq, Xavier and Tjian, Robert (2022) Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription. Molecular Cell, 82 (11). pp. 2084-2097. ISSN 1097-2765. doi:10.1016/j.molcel.2022.04.007. https://resolver.caltech.edu/CaltechAUTHORS:20210821-004311309

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Abstract

Gene activation by mammalian transcription factors (TFs) requires multivalent interactions of their low-complexity domains (LCDs), but how such interactions regulate transcription remains unclear. It has been proposed that extensive LCD-LCD interactions culminating in liquid-liquid phase separation (LLPS) of TFs is the dominant mechanism underlying transactivation. Here, we investigated how tuning the amount and localization of LCD-LCD interactions in vivo affects transcription of endogenous human genes. Quantitative single-cell and single-molecule imaging reveals that the oncogenic TF EWS::FLI1 requires a narrow optimum of LCD-LCD interactions to activate its target genes associated with GGAA microsatellites. Increasing LCD-LCD interactions toward putative LLPS represses transcription of these genes in patient-derived cells. Likewise, ectopically creating LCD-LCD interactions to sequester EWS::FLI1 into a well-documented LLPS compartment, the nucleolus, inhibits EWS::FLI1-driven transcription and oncogenic transformation. Our findings show how altering the balance of LCD-LCD interactions can influence transcriptional regulation and suggest a potential therapeutic strategy for targeting disease-causing TFs.

Item Type:

Article

Related URLs:

URL	URL Type	Description
https://doi.org/10.1016/j.molcel.2022.04.007	DOI	Article
https://doi.org/10.1101/2021.08.16.456551	DOI	Discussion Paper
https://gitlab.com/tjian-darzacq-lab/nucleolar-spt-analysis	Related Item	Code

ORCID:

Author	ORCID
Chong, Shasha	0000-0002-5372-311X
Graham, Thomas G. W.	0000-0001-5189-4313
Dugast-Darzacq, Claire	0000-0001-8602-3534
Dailey, Gina M.	0000-0002-8988-963X
Darzacq, Xavier	0000-0003-2537-8395
Tjian, Robert	0000-0003-0539-8217

Additional Information:

© 2022 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Received 16 September 2021, Revised 14 February 2022, Accepted 1 April 2022, Available online 27 April 2022. We thank L. Lavis for providing fluorescent HaloTag ligands; Q. Zhu for help with molecular cloning; K. Adiga for help optimizing conditions of doxycycline induction; S. Irgen-Gioro for help performing flow cytometry; the CRL Flow Cytometry Facility and Molecular Imaging Center; the Caltech Flow Cytometry Facility and Biological Imaging Center; and A. Hansen, S. Teves, Q. Han, and members of the Tjian/Darzacq labs for critical reading of the manuscript. This work was supported by the John D. Baldeschwieler and Marlene R. Konnar Foundation (to S.C.), the Jane Coffin Childs Memorial Fund for Medical Research (to T.G.W.G.), California Institute of Regenerative Medicine grant LA1-08013 (to X.D.), NIH grants UO1-EB021236 and U54-DK107980 (to X.D.), and the Howard Hughes Medical Institute (to R.T.). Author contributions: Conceptualization, R.T. and S.C.; funding acquisition, R.T., X.D., C.D.-D., S.C., and T.G.W.G.; investigation, S.C., T.G.W.G., C.D.-D., G.M.D., and R.T.; software: S.C. and T.G.W.G.; visualization, S.C., T.G.W.G., and C.D.-D.; project administration, R.T. and S.C.; writing – original draft, S.C., R.T., T.G.W.G., and C.D.-D.; writing – review & editing, S.C., R.T., T.G.W.G., C.D.-D., and X.D.; supervision, R.T. Declaration of interests: R. Tjian and X. Darzacq are co-founders of Eikon Therapeutics. Data and code availability: Original microscopy data has been deposited at Zenodo and Mendeley Data and is publicly available as of the date of publication. DOIs are listed in the key resources table. All codes for spaSPT data analyses have been submitted to GitLab and are publicly available (https://gitlab.com/tjian-darzacq-lab/nucleolar-spt-analysis). Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Funders:

Funding Agency	Grant Number
John D. Baldeschwieler and Marlene R. Konnar Foundation	UNSPECIFIED
Jane Coffin Childs Memorial Fund for Medical Research	UNSPECIFIED
California Institute of Regenerative Medicine	LA1-08013
NIH	UO1-EB021236
NIH	U54-DK107980
Howard Hughes Medical Institute (HHMI)	UNSPECIFIED

Subject Keywords:

transcriptional control; low-complexity domains; multivalent interactions; liquid-liquid phase separation; Ewing sarcoma; EWS::FLI1; nucleolus; single-cell and single-molecule imaging; intrinsically disordered regions; transcription factor

Issue or Number:

DOI:

10.1016/j.molcel.2022.04.007

Record Number:

CaltechAUTHORS:20210821-004311309

Persistent URL:

https://resolver.caltech.edu/CaltechAUTHORS:20210821-004311309

Official Citation:

Shasha Chong, Thomas G.W. Graham, Claire Dugast-Darzacq, Gina M. Dailey, Xavier Darzacq, Robert Tjian, Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription, Molecular Cell, Volume 82, Issue 11, 2022, Pages 2084-2097.e5, ISSN 1097-2765, https://doi.org/10.1016/j.molcel.2022.04.007.

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ID Code:

110343

Collection:

CaltechAUTHORS

Deposited By:

Tony Diaz

Deposited On:

21 Aug 2021 17:30

Last Modified:

28 Jun 2022 18:54

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