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Anatomy and evolution of a DNA replication origin

Abstract

DNA amplification occurs at the DNA puff II/9A locus in the fungus fly Sciara coprophila. As a foundation to study the molecular mechanism for the initiating events of II/9A DNA re-replication, we have sequenced 14 kb spanning a DNase hypersensitive site (DHS) upstream of the 1 kb amplification origin and through transcription units II/9–1 and II/9–2 downstream of the origin. These elements are annotated as well as the ORC binding site at the origin and the transition point (TP) between continuous and discontinuous DNA syntheses that marks the origin of bidirectional replication at the nucleotide level. A 9 bp motif found at the TP is repeated near the other end of the 1 kb ORI and may identify a putative second TP. The steroid hormone ecdysone induces DNA amplification as well as transcription and puffing at locus II/9A. Within the 14 kb, several matches to the ecdysone response element (EcRE) consensus sequence were identified, including some in the amplification origin region. EcRE O-P is at a central axis of a remarkable symmetry, equidistant to the TPs that are themselves equidistant to EcRE O-1 and EcRE O-2. DNA sequence alterations have occurred throughout the II/9A region in a newly discovered polymorphism (#2). Polymorphism #2 is not specific to developmental stage, sex, or tissue, and it does not impair DNA amplification. The DHS, both 9 bp TP sequences, and EcREs O-1, O-P, and O-2 are conserved between the polymorphism #1 and #2 sequences, suggesting their functional importance and retention during evolutionary selection. Moreover, a 72 bp sequence in the Sciara DHS at DNA puff II/9A is conserved in DNA puff C-3 of Rhynchosciara americana. Comparisons are discussed between the Sciara II/9A amplicon and the chorion locus amplicon on the third chromosome of Drosophila.

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Data Availability

The 14 kb sequence from DNA puff II/9A polymorphism #1 has been submitted to GenBank (NCBI/NIH, Bethesda, MD) with the following accession number: BankIt2352620 Sciara MT582500. The 10 kb sequence from DNA puff II/9A polymorphism #2 has been submitted to GenBank (NCBI/NIH, Bethesda, MD) with the following accession number: BankIt2352636 Sciara MT582501.

Code availability

Not applicable.

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Acknowledgements

We are grateful to Miiko Sokka for his help with some of the statistical analyses. We thank Jacob Bliss for maintenance of the Sciara fly stocks.

Funding

We received funding from NIH-GM121455 (currently) and NIH-GM35929 (previously).

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YY sequenced and analyzed 14 kb of the Sciara II/9A origin region, prepared the figures, and compiled the data and methods. EAG analyzed polymorphism #2 by PCR and sequencing 4 kb from the Sciara II/9A origin region; he also helped to prepare figures of the polymorphism results. MSF did the experiment with the Sciara 91S stock; he also did some initial work for Supplemental Table 1. HSS maintained the Sciara fly stocks and helped to select for the HoLo strain which has just polymorphism #1. SAG oversaw the project and wrote this paper.

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Correspondence to Susan A. Gerbi.

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Yamamoto, Y., Gustafson, E.A., Foulk, M.S. et al. Anatomy and evolution of a DNA replication origin. Chromosoma 130, 199–214 (2021). https://doi.org/10.1007/s00412-021-00756-x

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Keywords

  • DNA replication origin
  • Sciara DNA puff II/9A
  • Ecdysone response element
  • DNA re-replication and amplification
  • Genomic polymorphism