Isolation, characterization, and chromosomal location of the tRNA(Met) genes in Atlantic salmon (Salmo salar) and brown trout (Salmo trutta)

Spatial organization of transcription by RNA polymerase III

RNA polymerase III (pol III) transcribes many essential, small, noncoding RNAs, including the 5S rRNAs and tRNAs. While most pol III-transcribed genes are found scattered throughout the linear chromosome maps or in multiple linear clusters, there is increasing evidence that many of these genes prefer to be spatially clustered, often at or near the nucleolus. This association could create an environment that fosters the coregulation of transcription by pol III with transcription of the large ribosomal RNA repeats by RNA polymerase I (pol I) within the nucleolus. Given the high number of pol III-transcribed genes in all eukaryotic genomes, the spatial organization of these genes is likely to affect a large portion of the other genes in a genome. In this Survey and Summary we analyze the reports regarding the spatial organization of pol III genes and address the potential influence of this organization on transcriptional regulation.

A physical map of the genome of Atlantic salmon, Salmo salar

A physical map of the Atlantic salmon (Salmo salar) genome was generated based on HindIII fingerprints of a publicly available BAC (bacterial artificial chromosome) library constructed from DNA isolated from a Norwegian male. Approximately 11.5 haploid genome equivalents (185,938 clones) were successfully fingerprinted. Contigs were first assembled via FPC using high-stringency (1e-16), and then end-to-end joins yielded 4354 contigs and 37,285 singletons. The accuracy of the contig assembly was verified by hybridization and PCR analysis using genetic markers. A subset of the BACs in the library contained few or no HindIII recognition sites in their insert DNA. BglI digestion fragment patterns of these BACs allowed us to identify three classes: (1) BACs containing histone genes, (2) BACs containing rDNA-repeating units, and (3) those that do not have BglI recognition sites. End-sequence analysis of selected BACs representing these three classes confirmed the identification of the first two classes and suggested that the third class contained highly repetitive DNA corresponding to tRNAs and related sequences.

Complete nucleotide sequence of the chum salmon insulin-like growth factor II gene

Insulin-like growth factor II (IGF-II) is thought to play an important role in development and growth of vertebrates. In contrast to mammals, the IGF-II gene is expressed at a high level from the early stages of embryonic development until the adult stage and IGF-II peptide is produced in virtually all organs of bony fish, indicating a physiological importance of IGF-II 'under water'. Therefore, we describe here the complete nucleotide sequence (accession no. X97225) and organization of the chum salmon IGF-II gene. In addition, the phylogenetic relationship of the IGF-II hormones is analysed. Although the chum salmon contains two non-allelic insulin and IGF-I genes, only one IGF-II gene could be identified. The chum salmon IGF-II gene consists of four exons and is comprised of 7992 bp from the putative transcription initiation site to the poly(A) site. Activation of the only promoter of the salmon IGF-II gene gives rise to a single 4 kb transcript. The fish IGF-II gene is much smaller and simpler organized than its known mammalian counterparts that are governed by several tissue-specific and developmental stage-dependent promoters. All known mammalian IGF-II genes to date have been found to form a conserved linkage group with the insulin and tyrosine hydroxylase (TH) genes and are organized as TH-insulin-IGF-II genomic locus. However, in our study we could find no linkage between the insulin and IGF-II genes, or between the insulin, TH and IGF-II genes, at least within approximately 20 kb of the chum salmon IGF-II genomic sequence. In spite of minor differences, the overall organization of the IGF-II genes turned out to be very similar in bony fish. A limited analysis of the phylogenetic relationship between IGF-II prohormones indeed showed a very conservative phylogenesis of IGF-II in bony fish that may indicate the particular significance of IGF-II in these animals.