Comparative analysis of the PDCD2-TBP-PSMB1 region in vertebrates.
Three orthologous genes encoding programmed cell death 2 (PDCD2), TATA-binding protein (TBP), and proteasomal subunit C5 (PSMB1) proteins have been shown previously to be nonrandomly distributed in both mammalian and invertebrate genomes. Here we analyze a conserved synteny of the PDCD2, TBP, and PSMB1 orthologs in four nonmammalian vertebrates. Homologous genes of the chicken, zebrafish, fugu, and Tetraodon nigroviridis were identified. A chicken cosmid harboring the orthologs of these three genes was completely sequenced. The fish genes were analyzed in silico. In all seven vertebrates thus far investigated, the PDCD2 and TBP genes are located tail-to-tail. In six tested species but the zebrafish, the PSMB1 gene mapped head-to-head or in the close vicinity to the TBP, but even in the zebrafish, all three genes were syntenic. In contrast, a three times reused synteny breakpoint in the 5'-region from PDCD2 was detected. A comparative analysis revealed the distribution of putative matrix-attached regions (MARs), which may affect the synteny conservation.
Trachtulec
Zdenek
Z
Center for Integrated Genomics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic. trachtul@biomed.cas.cz
Vlcek
Cestmir
C
Mihola
Ondrej
O
Forejt
Jiri
J
D000818:Animals; D030161:Avian Proteins / Q000235:genetics; D002645:Chickens / Q000235:genetics; D002874:Chromosome Mapping; D003360:Cosmids / Q000235:genetics; D003546:Cysteine Endopeptidases / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D015530:Nuclear Matrix / Q000378:metabolism; D011110:Polymorphism, Genetic; D011506:Proteins / Q000235:genetics*; D018741:Replication Origin / Q000235:genetics; D017422:Sequence Analysis, DNA; D026801:Synteny; D035181:TATA-Box Binding Protein / Q000235:genetics*; D023741:Takifugu / Q000235:genetics; D023721:Tetraodontiformes / Q000235:genetics; D014714:Vertebrates / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics
D030161:Avian Proteins; D011506:Proteins; D035181:TATA-Box Binding Protein; D004247:DNA; D003546:Cysteine Endopeptidases; C096184:proteasome component C5