Form and function of topologically associating genomic domains in budding yeast
- Umut Esera,b,1,
- Devon Chandler-Brownc,1,
- Ferhat Ayd,e,
- Aaron F. Straightf,
- Zhijun Duang,h,
- William Stafford Nobled, and
- Jan M. Skotheimc,2
- aDepartment of Applied Physics, Stanford University, Stanford, CA 94305;
- bDepartment of Genetics, Harvard Medical School, Boston, MA 02115;
- cDepartment of Biology, Stanford University, Stanford, CA 94305;
- dDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195;
- eLa Jolla Institute for Allergy and Immunology, La Jolla, CA 92037;
- fDepartment of Biochemistry, Stanford University, Stanford, CA 94305;
- gInstitute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109;
- hDivision of Hematology, University of Washington School of Medicine, Seattle, WA 98195
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Edited by Jasper Rine, University of California, Berkeley, CA, and approved February 22, 2017 (received for review July 26, 2016)
Significance
In metazoans, topological domains are regions in the genome that more frequently associate with themselves than with neighboring regions. These domains are important for regulating transcription and replication. However, topological domains were thought to be absent in budding yeast. Thus, we did not know the degree of conservation of topological organization and its associated functions. Herein, we describe the existence of topologically associating domains in budding yeast and show that these domains regulate replication timing so that origins within a domain fire synchronously. Our work showing conservation in budding yeast sets the stage to use yeast genetics to interrogate the molecular basis of the topological domains defining genome architecture.
Abstract
The genome of metazoan cells is organized into topologically associating domains (TADs) that have similar histone modifications, transcription level, and DNA replication timing. Although similar structures appear to be conserved in fission yeast, computational modeling and analysis of high-throughput chromosome conformation capture (Hi-C) data have been used to argue that the small, highly constrained budding yeast chromosomes could not have these structures. In contrast, herein we analyze Hi-C data for budding yeast and identify 200-kb scale TADs, whose boundaries are enriched for transcriptional activity. Furthermore, these boundaries separate regions of similarly timed replication origins connecting the long-known effect of genomic context on replication timing to genome architecture. To investigate the molecular basis of TAD formation, we performed Hi-C experiments on cells depleted for the Forkhead transcription factors, Fkh1 and Fkh2, previously associated with replication timing. Forkhead factors do not regulate TAD formation, but do promote longer-range genomic interactions and control interactions between origins near the centromere. Thus, our work defines spatial organization within the budding yeast nucleus, demonstrates the conserved role of genome architecture in regulating DNA replication, and identifies a molecular mechanism specifically regulating interactions between pericentric origins.
Footnotes
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↵1U.E. and D.C.-B. contributed equally to this work.
- ↵2To whom correspondence should be addressed. Email: skotheim{at}stanford.edu.
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Author contributions: U.E., D.C.-B., F.A., A.F.S., Z.D., W.S.N., and J.M.S. designed research; U.E., D.C.-B., and J.M.S. performed research; U.E., D.C.-B., and J.M.S. analyzed data; and U.E., D.C.-B., F.A., A.F.S., Z.D., W.S.N., and J.M.S. wrote the paper.
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The authors declare no conflict of interest.
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This article is a PNAS Direct Submission.
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Data deposition: The Hi-C sequences have been deposited in the Sequence Read Archive, https://www.ncbi.nlm.nih.gov/sra (accession no. SRP101770).
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This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1612256114/-/DCSupplemental.
