Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere

Huihuang Yan, Hidetaka Ito, Kan Nobuta, Shu Ouyang, Weiwei Jin, Shulan Tian, Cheng Lu, R. C. Venu, Guo Liang Wang, Pamela J. Green, Rod A Wing, C. Robin Buell, Blake C. Meyers, Jiming Jiang

Research output: Contribution to journalArticle

78 Citations (Scopus)

Abstract

The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most multicellular eukaryotes, centromeres are composed of long tracts of satellite repeats that are recalcitrant to sequencing and fine-scale genetic mapping. Here, we report the genomic and genetic characterization of the complete centromere of rice (Oryza sativa) chromosome 3. Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains ∼441 kb of the centromeric satellite repeat CentO. Cen3 includes an ∼1,881-kb domain associated with the centromeric histone CENH3. This CENHS-associated chromatin domain is embedded within a 3113-kb region that lacks genetic recombination. Extensive transcription was detected within the CENH3 binding domain based on comprehensive annotation of protein-coding genes coupled with empirical measurements of mRNA levels using RT-PCR and massively parallel signature sequencing. Genes <10 kb from the CentO satellite array were expressed in several rice tissues and displayed histone modification patterns consistent with euchromatin, suggesting that rice centromeric chromatin accommodates normal gene expression. These results support the hypothesis that centromeres can evolve from gene-containing genomic regions.

Original languageEnglish (US)
Pages (from-to)2123-2133
Number of pages11
JournalPlant Cell
Volume18
Issue number9
DOIs
StatePublished - Sep 2006

Fingerprint

Chromosomes, Human, Pair 3
Centromere
centromeres
Transcription
Chromosomes
transcription (genetics)
Genes
Satellites
chromosomes
genomics
rice
Histones
Chromatin
Fibers
Gene expression
histones
chromatin
Histone Code
Fluorescence
Cells

ASJC Scopus subject areas

  • Plant Science
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Cell Biology

Cite this

Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. / Yan, Huihuang; Ito, Hidetaka; Nobuta, Kan; Ouyang, Shu; Jin, Weiwei; Tian, Shulan; Lu, Cheng; Venu, R. C.; Wang, Guo Liang; Green, Pamela J.; Wing, Rod A; Buell, C. Robin; Meyers, Blake C.; Jiang, Jiming.

In: Plant Cell, Vol. 18, No. 9, 09.2006, p. 2123-2133.

Research output: Contribution to journalArticle

Yan, H, Ito, H, Nobuta, K, Ouyang, S, Jin, W, Tian, S, Lu, C, Venu, RC, Wang, GL, Green, PJ, Wing, RA, Buell, CR, Meyers, BC & Jiang, J 2006, 'Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere', Plant Cell, vol. 18, no. 9, pp. 2123-2133. https://doi.org/10.1105/tpc.106.043794
Yan, Huihuang ; Ito, Hidetaka ; Nobuta, Kan ; Ouyang, Shu ; Jin, Weiwei ; Tian, Shulan ; Lu, Cheng ; Venu, R. C. ; Wang, Guo Liang ; Green, Pamela J. ; Wing, Rod A ; Buell, C. Robin ; Meyers, Blake C. ; Jiang, Jiming. / Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. In: Plant Cell. 2006 ; Vol. 18, No. 9. pp. 2123-2133.
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