A new gypsy-type retrotransposon, RIRE7: preferential insertion into the tandem repeat sequence TrsD in pericentromeric heterochromatin regions of rice chromosomes.

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-amplified fragments that made up all parts of the RIRE7 sequence showed that RIRE7 is a gypsy-type retrotransposon with partial homology in the pol region to the rice gypsy-type retrotransposons RIRE2 and RIRE3 identified 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 flanking 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 identified 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 confirmed by the identification 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 findings strongly suggest that RIRE7 and TrsD are components of the pericentromeric heterochromatin of rice chromosomes.