Chromosome Research

, Volume 25, Issue 3–4, pp 299–311 | Cite as

Recurrent establishment of de novo centromeres in the pericentromeric region of maize chromosome 3

  • Hainan Zhao
  • Zixian Zeng
  • Dal-Hoe Koo
  • Bikram S. Gill
  • James A. BirchlerEmail author
  • Jiming JiangEmail author
Original Article


Centromeres can arise de novo from non-centromeric regions, which are often called “neocentromeres.” Neocentromere formation provides the best evidence for the concept that centromere function is not determined by the underlying DNA sequences, but controlled by poorly understood epigenetic mechanisms. Numerous neocentromeres have been reported in several plant and animal species. However, it has been elusive how and why a specific chromosomal region is chosen to be a new centromere during the neocentromere activation events. We report recurrent establishment of neocentromeres in a pericentromeric region of chromosome 3 in maize (Zea mays). This latent region is located in the short arm and is only 2 Mb away from the centromere (Cen3) of chromosome 3. At least three independent neocentromere activation events, which were likely induced by different mechanisms, occurred within this latent region. We mapped the binding domains of CENH3, the centromere-specific H3 histone variant, of the three neocentromeres and analyzed the genomic and epigenomic features associated with Cen3, the de novo centromeres and an inactivated centromere derived from an ancestral chromosome. Our results indicate that lack of genes and transcription and a relatively high level of DNA methylation in this pericentromeric region may provide a favorable chromatin environment for neocentromere activation.


Centromere CENH3 neocentromere centromeric genes centromeric chromatin 



Chromatin immunoprecipitation




Flourescence in situ hybridization


Oat-maize chromosome addition


Single nucleotide polymorphism



We thank Dr. Patrick Schnable for providing the seeds of maize line ax-3 and Drs. Kelly Dawe and Jonathan Gent for valuable comments on the manuscript. This work was supported by the National Science Foundation (NSF) grant 1338897 to B.S.G. and NSF grant IOS-1444514 to J.A.B. and J.J.

Author contributions

H.Z and J.J. designed the research, Z.Z. and D.H.K. performed experiments, H.Z., J.A.B., and J.J. analyzed data, and H.Z., B.S.G., J.A.B., and J.J. wrote the article.

Supplementary material

10577_2017_9564_MOESM1_ESM.pdf (226 kb)
Figure S1 (PDF 225 kb)
10577_2017_9564_MOESM2_ESM.pdf (260 kb)
Figure S2 (PDF 259 kb)
10577_2017_9564_MOESM3_ESM.pdf (124 kb)
Figure S3 (PDF 123 kb)
10577_2017_9564_MOESM4_ESM.pdf (49 kb)
Table S1 (PDF 48 kb)


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Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  1. 1.Department of HorticultureUniversity of Wisconsin-MadisonMadisonUSA
  2. 2.Wheat Genetics Resource Center, Department of Plant PathologyKansas State UniversityManhattanUSA
  3. 3.Division of Biological SciencesUniversity of MissouriColumbiaUSA

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