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Dynamics and functional roles of splicing factor autoregulation

Ding, Fangyuan and Su, Christina and Chow, Ke-Huan Kuo and Elowitz, Michael B. (2020) Dynamics and functional roles of splicing factor autoregulation. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20200727-084029052

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Abstract

Non-spliceosomal splicing factors are essential, conserved regulators of alternative splicing. They provide concentration-dependent control of diverse pre-mRNAs. Many splicing factors direct unproductive splicing of their own pre-mRNAs through negative autoregulation. However, the impact of such feedback loops on splicing dynamics at the single cell level remains unclear. We developed a system to dynamically, quantitatively analyze negative autoregulatory splicing by the SF2 splicing factor in response to perturbations in single HEK293 cells. Here, we show that negative autoregulatory splicing provides critical functions for gene regulation, establishing a ceiling of SF2 protein concentration, reducing cell-cell heterogeneity in SF2 levels, and buffering variation in SF2 transcription. Most importantly, it adapts SF2 splicing activity to variations in demand from other pre-mRNA substrates. A minimal mathematical model of autoregulatory splicing explains these experimentally observed features, and provides values for effective biochemical parameters. These results reveal the unique functional roles that splicing negative autoregulation plays in homeostatically regulating transcriptional programs.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.07.22.216887DOIDiscussion Paper
ORCID:
AuthorORCID
Elowitz, Michael B.0000-0002-1221-0967
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Posted July 24, 2020. We thank F. Tan for providing Western blot protocol, N. Nandagopal and Y. Antebi for technical assistance, and Life Sciences Editors (Sabbi Lall) for critical feedback on the manuscript. We also thank S. Sun, A.R. Krainer, D. Sprinzak, D. Baltimore, J.G. Ojalvo, N. Wingreen for discussion and feedback on the project. F.D. was supported by a Fellowship from the Schlumberger Foundation. C.S. is supported by the NIH National Institute of General Medical Sciences training grant GM008042 and by a David Geffen Medical Scholarship. The work was funded by the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative and the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the U.S. Army Research Office, AWS Machine Learning Research Awards, and the Intel Corporation. The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred. M.B.E. is a Howard Hughes Medical Institute Investigator. Data Availability Statement: All original data, python code, DNA constructs, and cell lines are available upon request. Author Contributions: F.D. conceived of the project. F.D. and M.B.E. designed experiments. F.D. and K.C. performed experiments. F.D. analyzed data. C.S. and F.D. did mathematical modeling. F.D., C.S., and M.B.E. wrote the manuscript. The authors declare no competing interests.
Funders:
Funding AgencyGrant Number
Schlumberger FoundationUNSPECIFIED
NIH Predoctoral FellowshipGM008042
David Geffen Medical ScholarshipUNSPECIFIED
Gordon and Betty Moore FoundationGBMF2809
Army Research Office (ARO)W911NF-09-0001
Amazon Web ServicesUNSPECIFIED
IntelUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Record Number:CaltechAUTHORS:20200727-084029052
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200727-084029052
Official Citation:Dynamics and functional roles of splicing factor autoregulation. Fangyuan Ding, Christina Su, Ke-Huan Kuo Chow, Michael B. Elowitz. bioRxiv 2020.07.22.216887; doi: https://doi.org/10.1101/2020.07.22.216887
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:104579
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:28 Jul 2020 16:25
Last Modified:28 Jul 2020 16:25

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