Chromosoma

, Volume 126, Issue 4, pp 465–471 | Cite as

A replication-time-controlling sequence element in Schizosaccharomyces pombe

Original Article

Abstract

Eukaryotic replication origins are highly variable in their activity and replication timing. The nature and role of cis-acting regulatory sequences that control chromosomal replication timing is not well defined. In the fission yeast, Schizosaccharomyces pombe, a 200-bp late-replication-enforcing element (LRE), has been shown to enforce late replication of ARS elements in plasmids. Here, we show that a short (133-bp) fragment of the LRE (shLRE) is required for causing late replication of adjoining origins in its native as well as in an ectopic early-replicating chromosomal location. Active from both sides of an early-replicating origin, the shLRE is a bona fide cis-acting regulatory element that imposes late replication timing in the chromosome.

Keywords

ARS elements Replication origins Replication timing 2D gel analysis Fission yeast 

Notes

Acknowledgments

We are grateful to Mitradas M. Panicker, K. VijayRaghavan, Joel A. Huberman, and Rajiva Raman for extending laboratory facilities for conducting part of the work and to JAH for critical reading of the manuscript and valuable suggestions. This work was supported by the Council of Scientific and Industrial Research (CSIR), India, Research Grant # 38(1233)/09/EMRII to DDD. VPT was a recipient of a Senior Research Fellowship from the Indian Council of Medical Research (ICMR), India.

Authors’ contributions

DDD conceived and coordinated the study. DDD and VPT designed and performed the experiments. DDD and VPT wrote the paper.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

412_2016_606_MOESM1_ESM.docx (14 kb)
Supplemental Table 1 (DOCX 14 kb)
412_2016_606_Fig5_ESM.gif (2.8 mb)
Supplemental Fig. 1

Diagram showing the strategy for confirmation of the new S. pombe strains by PCR. [Cont. = Chromosomal context; LF1 = Left flanking 1; Ura4 = Selectable marker; LF2 = Left flanking 2; ARS = ars2004/ars727; RF1 = Right flanking 1]. Amplification by the two pairs of primers, (i) context F-ura4R and (ii) ura4F-ARSF/R, confirms the new strains. (GIF 2881 kb)

412_2016_606_MOESM2_ESM.tif (2.8 mb)
High Resolution Image (TIFF 2881 kb)
412_2016_606_Fig6_ESM.gif (18.6 mb)
Supplemental Fig. 2

FACS profiles of different cell types at different sampling time points. (GIF 19079 kb)

412_2016_606_MOESM3_ESM.tif (18.6 mb)
High Resolution Image (TIFF 19079 kb)

References

  1. Brewer BJ, Fangman WL (1987) The localization of replication origin on ARS plasmids in Saccharomyces cerevisiae. Cell 51:463–471CrossRefPubMedGoogle Scholar
  2. Cotobal C, Segurado M, Antequera F (2010) Structural diversity and dynamics of genomic replication origins in Schizosaccharomyces pombe. EMBO J 29:934–942CrossRefPubMedPubMedCentralGoogle Scholar
  3. Dimitrova DS, Gilbert DM (1999) The spatial position and replication timing of chromosomal domains are both established in early G1 phase. Mol Cell 4:983–993CrossRefPubMedGoogle Scholar
  4. Dubey DD, Srivastava VK, Pratihar AS, Yadava MP (2010) High density of weak replication origins in a 75-kb region of chromosome 2 of fission yeast. Genes Cells 15:1–12CrossRefPubMedGoogle Scholar
  5. Ferguson BM, Fangman WL (1992) A position effect on the time of replication origin activation in yeast. Cell 68:333–339CrossRefPubMedGoogle Scholar
  6. Friedman KL, Diller JD, Ferguson BF, Nyland SVM, Brewer BJ, Fangman WL (1996) Multiple determinants controlling activation of yeast replication origins late in S phase. Genes Dev 10:1595–1607CrossRefPubMedGoogle Scholar
  7. Hayano M, Kanoh Y, Matsumoto S, Renard-Guillet C, Shirahige K, Masai H (2012) Rif1 is a global regulator of timing of replication origin firing in fission yeast. Genes Dev 26:137–150CrossRefPubMedPubMedCentralGoogle Scholar
  8. Hayashi MT, Katou Y, Itoh T, Tazumi M, Yamada Y, Takahashi TS, Nakagawa T, Shirahige K, Masukata H (2007) Genome-wide localization of pre-RC sites and identification of replication origins in fission yeast. EMBO J 26:1327–1339CrossRefPubMedPubMedCentralGoogle Scholar
  9. Hayashi MT, Takahashi TS, Nakagawa T, Nakayama J, Masukata H (2009) The heterochromatin protein Swi6/HP1 activates replication origins at the pericentromeric region and silent mating-type locus. Nat Cell Biol 11:357–362CrossRefPubMedGoogle Scholar
  10. Hiratani I, Gilbert DM (2009) Replication timing as an epigenetic mark. Epigenetics 4(2):93–97CrossRefPubMedPubMedCentralGoogle Scholar
  11. Huberman JA, Spotila LD, Nawotka KA, El-Assouli SM, Davis LR (1987) The in vivo replication origin of the yeast 2 microns plasmid. Cell 51(3):473–481CrossRefPubMedGoogle Scholar
  12. Kanoh Y, Matsumoto S, Fukatsu R, Kakusho N, Kono N, Renard-Guillet C, Masuda K, Iida K, Nagasawa K, Shirahige K, Masai H (2015) Rif1 binds to G quadruplexes and suppresses replication over long distances. Nat Struct Mol Biol 22(11):889–897PubMedGoogle Scholar
  13. Kim SM, Huberman JA (2001) Regulation of replication timing in fission yeast. EMBO J 20:6115–6126CrossRefPubMedPubMedCentralGoogle Scholar
  14. Kim SM, Zhang DY, Huberman JA (2001) Multiple redundant sequence elements within the fission yeast ura4 replication origin enhancer. BMC Mol Biol 2:e1CrossRefGoogle Scholar
  15. Kim SM, Dubey DD, Huberman JA (2003) Early-replicating heterochromatin. Genes Dev 17:330–335CrossRefPubMedPubMedCentralGoogle Scholar
  16. Knott SR, Peace JM, Ostrow AZ, Gan Y, Rex AE, Viggiani CJ, Tavare S, Aparicio OM (2012) Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell 148:99–111CrossRefPubMedPubMedCentralGoogle Scholar
  17. Lõoke M, Kristjuhan K, Värv S, Kristjuhan A (2013) Chromatin-dependent and -independent regulation of DNA replication origin activation in budding yeast. EMBO Rep 14:191–198CrossRefPubMedGoogle Scholar
  18. MacAlpine DM, Rodriguez HK, Bell SP (2004) Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 18:3094–3105CrossRefPubMedPubMedCentralGoogle Scholar
  19. Okuno Y, Satos H, Sekiguchi M, Masukata H (1999) Clustered adenine/thymine stretches are essential for function of a fission yeast replication origin. Mol Cell Biol 19:6699–6709CrossRefPubMedPubMedCentralGoogle Scholar
  20. Pratihar AS, Tripathi VP, Yadav MP, Dubey DD (2015) Chromosomal context and replication properties of ARS plasmids in Schizosaccharomyces pombe. J Biosci 40(5):845–853CrossRefPubMedGoogle Scholar
  21. Rothstein RJ (1983) One-step gene disruption in yeast. Methods Enzymol 101:202–211CrossRefPubMedGoogle Scholar
  22. Tazumi A, Fukuura M, Nakato R, Kishimoto A, Takenaka T, Ogawa S, Song JH, Takahashi TS, Nakagawa T, Shirahige K, et al. (2012) Telomere-binding protein Taz1 controls global replication timing through its localization near late replication origins in fission yeast. Genes Dev 26:2050–2062CrossRefPubMedPubMedCentralGoogle Scholar
  23. Vogelauer M, Rubbi L, Lucas I, Brewer BJ, Grunstein M (2002) Histone acetylation regulates the time of replication origin firing. Mol Cell 10:1223–1233CrossRefPubMedGoogle Scholar
  24. Yamazaki S, Hayano M, Masai H (2013) Replication timing regulation of eukaryotic replicons: Rif1 as a global regulator of replication timing. Trends Genet 29(8):449–460CrossRefPubMedGoogle Scholar
  25. Yompakdee C, Huberman JA (2004) Enforcement of late replication origin firing by clusters of short G-rich DNA sequences. J Biol Chem 279:42337–42344CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Department of BiotechnologyVeer Bahadur Singh Purvanchal UniversityJaunpurIndia

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