A DNA repair pathway can regulate transcriptional noise to promote cell fate transitions
Abstract
Stochastic fluctuations in gene expression ("noise") are often considered detrimental, but fluctuations can also be exploited for benefit (e.g., dither). We show here that DNA base excision repair amplifies transcriptional noise to facilitate cellular reprogramming. Specifically, the DNA repair protein Apex1, which recognizes both naturally occurring and unnatural base modifications, amplifies expression noise while homeostatically maintaining mean expression levels. This amplified expression noise originates from shorter-duration, higher-intensity transcriptional bursts generated by Apex1-mediated DNA supercoiling. The remodeling of DNA topology first impedes and then accelerates transcription to maintain mean levels. This mechanism, which we refer to as "discordant transcription through repair" ("DiThR," which is pronounced "dither"), potentiates cellular reprogramming and differentiation. Our study reveals a potential functional role for transcriptional fluctuations mediated by DNA base modifications in embryonic development and disease.
Additional Information
© 2021 American Association for the Advancement of Science. This is an article distributed under the terms of the Science Journals Default License. 31 May 2020; accepted 8 July 2021; Published online 22 July 2021. We thank M. Simpson, B. Bruneau, J. Weissman, G. Balazsi, and members of the Weinberger laboratory for thoughtful discussions and suggestions; K. Claiborn for editing; G. Maki for graphics support; N. Raman in the Gladstone Institute Flow Cytometry Facility (NIH S10 RR028962, P30 AI027763, DARPA, and the James B. Pendleton Charitable Trust) for technical assistance; the Gladstone Assay Development and Drug Discovery Core for technical assistance with drug screening; K. Thorn and D. Larson in the UCSF Nikon Imaging Center (NIH S10 1S10OD017993-01A1) for technical assistance with imaging; M. Jost and J. Weissman for CRISPRi reagents; and the Gladstone Institute Genomics Core for technical assistance with single-cell RNA-sequencing. The dual-tagged Sox2 mESCs were a kind donation from B. Bruneau and E. Nora. The Oct4-GFP reprogrammable MEFs (harbor stably integrated OKSM factors) were a kind donation from S. Guo. R.V.D. is supported by an NIH/NICHD F30 fellowship (HD095614-03). R.A.C. acknowledges support from NIH award 1R01GM126045-05. R.H.S. acknowledges support from NIH awards NS083085 and 1R35GM136296. M.M.K.H. acknowledges support from a Dutch Research Council (NWO) ENW-XS award (OCENW.XS3.055). L.S.W. acknowledges support from a Bowes Distinguished Professorship, Alfred P. Sloan Research Fellowship, Pew Scholars in the Biomedical Sciences Program, NIH award R01AI109593, and the NIH Director's New Innovator Award (OD006677) and Pioneer Award (OD17181) programs. Author contributions: R.V.D., M.T., and L.S.W. conceived and designed the study. R.V.D., B.M., and M.T. analyzed the sequencing data. R.V.D., X.C., C.U., S.D., and L.S.W conceived and designed the cellular reprogramming experiments. X.C., D.W.H., W.L., R.H.S., R.A.C., and L.S.W conceived and designed the MS2 imaging experiments. R.V.D., X.C., S.C., D.W.H., W.L., and C.U. performed the experiments. R.V.D., X.C., B.M., M.T., R.A.C., M.M.K.H., and L.S.W. analyzed data. R.V.D., M.M.K.H., B.M., and L.S.W. constructed and analyzed the mathematical models. R.V.D., M.M.K.H., and L.S.W. wrote the manuscript. The authors declare no competing interests. Data and materials availability: The raw and processed sequencing data reported herein have been deposited onto the Gene Expression Omnibus under accession number GSE176044. Custom code for analysis of scRNA-seq data and mathematical modeling are available on GitHub at https://github.com/weinbergerlab-ucsf/Code_Desai_et_al and are archived on Zenodo (79). Reagents, including plasmids and cell lines, are available from the corresponding author upon request.Attached Files
Accepted Version - nihms-1762191.pdf
Supplemental Material - abc6506-Desai-SM-Reproducibility-Checklist.pdf
Supplemental Material - abc6506-Desai-SM-Table-S1.xlsx
Supplemental Material - abc6506-Desai-SM-Table-S2.xlsx
Supplemental Material - abc6506-Desai-SM-Table-S3.xlsx
Supplemental Material - abc6506-Desai-SM-Table-S4.xlsx
Supplemental Material - abc6506-Desai-SM-Table-S5.xlsx
Supplemental Material - abc6506-Desai-SM-Table-S6.xlsx
Supplemental Material - abc6506-Desai-SM-Table-S7.xlsx
Supplemental Material - abc6506-Desai-SM-Table-S8.xlsx
Supplemental Material - abc6506-Desai-SM.pdf
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Additional details
- PMCID
- PMC8667278
- Eprint ID
- 110014
- Resolver ID
- CaltechAUTHORS:20210726-193944737
- NIH Postdoctoral Fellowship
- F30HD095614-03
- NIH
- 1R01GM126045-05
- NIH
- NS083085
- NIH
- 1R35GM136296
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)
- OCENW.XS3.055
- Bowes Distinguished Professorship
- Alfred P. Sloan Foundation
- Pew Charitable Trust
- NIH
- R01AI109593
- NIH
- OD006677
- NIH
- OD17181
- Created
-
2021-07-26Created from EPrint's datestamp field
- Updated
-
2023-07-07Created from EPrint's last_modified field
- Caltech groups
- Division of Biology and Biological Engineering (BBE)