title: Evidence for an evolutionary force that prevents epigenetic silencing between tail-to-tail rice genes with a short spacer.
abstract: During the course of evolution, the genome should have toned down various types of genomic noise, such as those that cause the unstable expression or gene silencing observed in transgenic organisms. We found a rice genomic segment where two genes, encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPs) and ribosomal protein small subunit 20 (rps20), are located in a tail-to-tail orientation and separated by only 300 bp of spacer. It is possible that this kind of structure would give rise to unstable expression due to antisense RNA derived from the neighboring gene. We examined this possibility using Northern blot, reverse transcription-polymerase chain reaction (RT-PCR), and 3' RACE analyses, but obtained no evidence for instability or antisense RNAs of these housekeeping genes. Comparison of the sequences in the corresponding regions among related rice species revealed a lower level of genetic divergence of both the 3'-untranslated region (3'-UTRs) than of the other noncoding regions; in particular both of the boundaries between the 3'-UTRs and the spacer were markedly conserved. The conservation of both the terminal regions is most likely the result of purifying selection, implying a functional role for the strict termination of the transcription of these genes to prevent gene-silencing-related events.
authors.affiliation: Laboratory of Plant Breeding, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: So
authors.initials: S
authors.lastname: Kobayashi
authors.forename: Yuji
authors.initials: Y
authors.lastname: Noro
authors.forename: Hironori
authors.initials: H
authors.lastname: Nagano
authors.forename: Kaoru T
authors.initials: KT
authors.lastname: Yoshida
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Takano-Shimizu
authors.forename: Yuji
authors.initials: Y
authors.lastname: Kishima
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Sano
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D015152:Blotting, Northern; D017931:DNA Primers; D018076:DNA, Complementary; D044127:Epigenesis, Genetic; D019143:Evolution, Molecular; D020868:Gene Silencing; D017343:Genes, Plant; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D017386:Sequence Homology, Amino Acid
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary