A new gypsy -type retrotransposon, RIRE7 : preferential insertion into the tandem repeat sequence TrsD in pericentromeri
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O R I GI N A L P A P E R
N. Kumekawa á N. Ohmido á K. Fukui á E. Ohtsubo H. Ohtsubo
A new gypsy -type retrotransposon, RIRE7 : preferential insertion into the tandem repeat sequence TrsD in pericentromeric heterochromatin regions of rice chromosomes Received: 28 September 2000 / Accepted: 5 December 2000 / Published online: 24 February 2001 Ó Springer-Verlag 2001
Abstract A portion of an insertion sequence present in a member of the RIRE3 family of retrotransposons in Oryza sativa L. cv. IR36 was found to have an LTR sequence followed by a PBS sequence complementary to the 3¢-end region of tRNAMet, indicative of another rice retrotransposon (named RIRE7). Cloning and sequencing of PCR-ampli®ed fragments that made up all parts of the RIRE7 sequence showed that RIRE7 is a gypsytype retrotransposon with partial homology in the pol region to the rice gypsy-type retrotransposons RIRE2 and RIRE3 identi®ed in rice previously. Interestingly, various portions of the RIRE7 sequence were homologous to several DNA segments present in the centromere regions of cereal chromosomes. Further cloning and nucleotide sequencing of fragments ¯anking RIRE7 copies showed that RIRE7 was inserted into a site within a tandem repeat sequence that has a unit length of 155 bp. The tandem repeat sequence, named TrsD, was homologous to tandem repeat sequences RCS2 and CentC, previously identi®ed in the centromeric regions of rice and maize chromosomes. Fluorescence in situ hybridization (FISH) analysis of the metaphase chromosomes of O. sativa cv. Nipponbare showed that both RIRE7 and TrsD sequences were present in the centromere regions of the chromosomes. The presence of RIRE7 and the TrsD sequences in the centromere regions of several chromosomes was con®rmed by the Communicated by R. Hagemann N. Kumekawa á E. Ohtsubo á H. Ohtsubo (&) Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan E-mail: [email protected] Tel.: +81-3-5841-7854 Fax: +81-3-5841-8484 N. Ohmido Hokuriku National Agricultural Experiment Station, Joetsu 943-0193, Japan K. Fukui Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
identi®cation of several YAC clones whose chromosomal locations are known. Further FISH analysis of rice pachytene chromosomes showed that the TrsD sequences were located in a pericentromeric heterochromatin region. These ®ndings strongly suggest that RIRE7 and TrsD are components of the pericentromeric heterochromatin of rice chromosomes. Key words Oryza sativa á Retrotransposon á Gypsy á Pericentromeric heterochromatin region á Tandem repeat
Introduction Genome sizes dier greatly in plants due to the presence of dierent amounts of interspersed or tandem repeat DNA sequences (Graham 1995; Bennetzen 1996). Interspersed DNA sequences include retrotransposons with LTRs (long terminal repeats) like those in proviruses, the integrated forms of retroviruses (for reviews, see Bingham and Zachar 1989; Varmus and Brown 1989). The internal region ¯anked by LTRs has gag and po
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