Organization of the 1.9-kb repeat unit RCE1 in the centromeric region of rice chromosomes

Mol Gen Genet. 1999 Feb;261(1):1-10. doi: 10.1007/s004380050935.


This paper presents the first report on the structure of a 14-kb centromere sequence in a cereal genome that includes 1.9-kb direct repeats. The cereal centromeric sequence (CCS1) conserved in some Gramineae species contains a 17-bp motif similar to the CENP-B box, which serves as the binding site for the centromere-specific protein CENP-B in human. To isolate centromeric units from rice (Oryza sativa L.), we performed PCR using the CENP-B box-like sequences (CBLS) as primers. A 264-bp clone was amplified by this method, and called RCS1516. It appeared to be a novel member of the CCS1 family, sharing about 60% identity with the CCS1 sequences of other cereals. Then, a 14-kb genomic clone, lambda RCB11, carrying the RCS1516 sequence was isolated and sequenced. It was found to contain three copies of a 1.9-kb direct repeat, RCE1, separated by 5.1- and 1.7-kb. A 300-bp sequence at the 3' end of RCE1 is highly conserved in all three copies (>90%) and is almost identical to the RCS1516 sequence including the CBLS motif. The copy number of RCE1 was estimated to range from 10(2) to 10(3) in the haploid genome of rice. Cloned RCE1 units were used for fluorescent in situ hybridization (FISH) analysis, and signals were observed on almost every primary constriction of rice chromosomes. Thus it was concluded that RCE1 is a significant component of the rice centromere. The lambda RCB11 clone contained at least four A/T-rich regions, which are candidate for matrix attachment regions (MARs), in the sequences between the RCE1 repeats. Other elements that are homologous to the short centromeric repetitive sequences pSau3A9 and pRG5, detected in both sorghum and rice, were also found in the clone.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Centromere / genetics*
  • Chromosomes / genetics*
  • Conserved Sequence
  • DNA, Plant / chemistry
  • DNA, Plant / genetics
  • In Situ Hybridization, Fluorescence
  • Molecular Sequence Data
  • Nuclear Matrix / genetics
  • Oryza / chemistry
  • Oryza / genetics*
  • Repetitive Sequences, Nucleic Acid / genetics*
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid


  • DNA, Plant

Associated data

  • GENBANK/AB013613
  • GENBANK/AB013614