A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae reveals novel insights into factors that stabilize chromatin structure on newly replicated DNA
- PMID: 38407959
- PMCID: PMC10990430
- DOI: 10.1093/genetics/iyae016
A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae reveals novel insights into factors that stabilize chromatin structure on newly replicated DNA
Abstract
The disruption of chromatin structure can result in transcription initiation from cryptic promoters within gene bodies. While the passage of RNA polymerase II is a well-characterized chromatin-disrupting force, numerous factors, including histone chaperones, normally stabilize chromatin on transcribed genes, thereby repressing cryptic transcription. DNA replication, which employs a partially overlapping set of histone chaperones, is also inherently disruptive to chromatin, but a role for DNA replication in cryptic transcription has never been examined. In this study, we tested the hypothesis that, in the absence of chromatin-stabilizing factors, DNA replication can promote cryptic transcription in Saccharomyces cerevisiae. Using a novel fluorescent reporter assay, we show that multiple factors, including Asf1, CAF-1, Rtt106, Spt6, and FACT, block transcription from a cryptic promoter, but are entirely or partially dispensable in G1-arrested cells, suggesting a requirement for DNA replication in chromatin disruption. Collectively, these results demonstrate that transcription fidelity is dependent on numerous factors that function to assemble chromatin on nascent DNA.
Keywords: DNA replication; chromatin; cryptic transcription.
© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Conflict of interest statement
Conflicts of interest The author(s) declare no conflict of interest.
Similar articles
-
The Rtt106 histone chaperone is functionally linked to transcription elongation and is involved in the regulation of spurious transcription from cryptic promoters in yeast.J Biol Chem. 2008 Oct 10;283(41):27350-27354. doi: 10.1074/jbc.C800147200. Epub 2008 Aug 15. J Biol Chem. 2008. PMID: 18708354
-
Core promoter activity contributes to chromatin-based regulation of internal cryptic promoters.Nucleic Acids Res. 2021 Aug 20;49(14):8097-8109. doi: 10.1093/nar/gkab639. Nucleic Acids Res. 2021. PMID: 34320189 Free PMC article.
-
A link between Sas2-mediated H4 K16 acetylation, chromatin assembly in S-phase by CAF-I and Asf1, and nucleosome assembly by Spt6 during transcription.FEMS Yeast Res. 2015 Nov;15(7):fov073. doi: 10.1093/femsyr/fov073. Epub 2015 Aug 9. FEMS Yeast Res. 2015. PMID: 26260510
-
The replication-independent histone H3-H4 chaperones HIR, ASF1, and RTT106 co-operate to maintain promoter fidelity.J Biol Chem. 2012 Jan 13;287(3):1709-18. doi: 10.1074/jbc.M111.316489. Epub 2011 Nov 29. J Biol Chem. 2012. PMID: 22128187 Free PMC article.
-
Insights into Spt6: a histone chaperone that functions in transcription, DNA replication, and genome stability.Trends Genet. 2023 Nov;39(11):858-872. doi: 10.1016/j.tig.2023.06.008. Epub 2023 Jul 20. Trends Genet. 2023. PMID: 37481442 Review.
References
-
- Abe T, Sugimura K, Hosono Y, Takami Y, Akita M, Yoshimura A, Tada S, Nakayama T, Murofushi H, Okumura K, et al. . 2011. The histone chaperone facilitates chromatin transcription (FACT) protein maintains normal replication fork rates. J Biol Chem. 286(35):30504–30512. doi:10.1074/jbc.M111.264721. - DOI - PMC - PubMed
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources