Molecular cloning and long terminal repeat sequences of intracisternal A-particle genes in Mus caroli

We isolated DNA clones of intracisternal A-particle (IAP) genes from the genome of an Asian wild mouse, Mus caroli. A typical M. caroli IAP gene was 6.5 kilobase pairs in length and had long terminal repeat (LTR) sequences at both ends. The size of the LTR was 345 base pairs in clone L20, and two LTRs at both ends of this clone were linked to directly repeating cellular sequences of 6 base pairs. Each LTR possessed most of the structural features commonly associated with the retrovirus LTR. The restriction map of the M. caroli IAP gene resembled that of Mus musculus, although the M. caroli IAP gene was 0.4 kilobase pairs shorter than the M. musculus IAP gene in two regions. Sequence homology between the M. caroli and M. musculus IAP LTRs was calculated as about 80%, whereas the LTR sequence of the Syrian hamster IAP gene was about 60% homologous to the M. caroli LTR. The reiteration frequency of the M. caroli IAP genes was estimated as 200 to 400 copies per haploid genome, which is at least 10 times the reported value. These results suggest that the IAP genes observed in the genus Mus are present in multiple copies with structures closely resembling the integrated retrovirus gene.     

Chromosome distribution of intracisternal A-particle sequences in the Syrian hamster and mouse

Metaphase chromosomes of Syrian hamster and BALB/c mice were hybridized in situ with radiolabeled probes derived from cloned intracisternal A-particle (IAP) genes of the corresponding species. The DNAs of these species are known to contain about 900 and 1,000 copies, respectively, of the retrovirus-like IAP sequence elements per haploid genome. Multiple IAP sequences were found on all chromosomes of both hamster and mouse. In the hamster, more than half of the IAP sequences were located in regions of non-centromeric constitutive heterochromatin, at an average concentration per unit chromosome length 5 times greater than in the euchromatic regions. The other dispersed sequences showed marked local variations in concentration along the chromosome lengths; both discrete foci and large grain clusters were observed as well as regions apparently lacking IAP sequences. Within the resolution of the techniques, IAP sequences appeared to be more evenly distributed over the mouse chromosomes; however, some prominent variations in concentration were seen. The number of potentially active IAP genes in the Syrian hamster, and by extension in the mouse, may be restricted by the preferential location of IAP sequences in genetically inert regions of the genome.     

Nucleotide sequence of the Syrian hamster intracisternal A-particle gene: close evolutionary relationship of type A particle gene to types B and D oncovirus genes.

We determined the complete nucleotide sequence of the intracisternal A-particle gene, IAP-H18, cloned from the normal Syrian hamster liver DNA. IAP-H18 was 7,951 base pairs in length with two identical long terminal repeats of 376 base pairs at both ends. On the coding strand, imperfect open reading frames corresponding to gag and pol of the retrovirus genome were observed, whereas many stop codons were present in the region corresponding to env. The putative H18 gag gene (809 amino acids) had a sequence homologous to the N-terminal half of the mouse mammary tumor virus gag gene and locally to the Rous sarcoma virus gag gene. The putative H18 pol gene (900 residues) was homologous to the Rous sarcoma virus pol gene almost throughout the entire region. Two conserved regions among the retrovirus pol genes have been reported. One presumably corresponds to the DNA polymerase and the RNase H domain, and the other corresponds to the DNA endonuclease domain of the multifunctional protein pol. By the comparison of the deduced amino acid sequences of the putative endonuclease domain of six representative oncovirus genomes, a phylogenetic tree of the oncovirus genomes was constructed, and the intracisternal A-particle (type A) genome was found to be more closely related to the mouse mammary tumor virus (type B) and squirrel monkey retrovirus (type D) genomes.     

A short repeat in the genome of the DNA sequences flanking bovine growth hormone genes

The phage clones containing a gene coding for bovine growth hormone were isolated from a bovine genomic library. Comparison of the 5' and 3' regions flanking the bovine growth hormone gene by Southern blot hybridization revealed that they share homology. Screening the bovine genomic library by nick-translated DNA fragment from 5' flanking region leads to conclusion that this sequence is present in 0.1% of clones. Each analysed clone carrying the sequence contains some copies of it.     

Molecular cloning of retrovirus-like genes present in multiple copies in the Syrian hamster genome.

Endogenous retrovirus-like sequences homologous to intracisternal type-A particle (IAP) genes, which are present in the inbred mouse (Mus musculus) genome, were cloned from a Syrian hamster gene library. A typical hamster IAP gene was 7 kb long and segments homologous to long terminal repeat (IAP) sequences present in Mus musculus IAP genes were located at both ends of the gene. Contrary to the pattern found in the Mus musculus IAP genes, the organization of the cloned hamster IAP genes was not markedly polymorphic and deletion was not observed among these cloned genes. A sequence about 0.8 kb long and located close to the 3' end of the hamster IAP gene was well conserved in both IAP gene families, although they showed less overall homology with one another. The reiteration frequency of the hamster IAP genes was calculated to be 950 copies per haploid genome. Since such IAP genes with the above properties were not found in the genome of the Chinese hamster, whose progenitors diverged from those of the Syrian hamster about 7.5 Myr ago, the integration of a huge number of Syrian hamster IAP genes must have occurred subsequent to such divergence.     

A microcomputer program for the identification of tRNA genes

A microcomputer program which locates tRNA genes within longDNA sequences is described. The search is performed either byidentifying tRNA-like secondary structures or by locating eukaryoticRNA polymerase III promoter consensus sequences. The programis also useful in finding inverted repeats allowing the formationof stem-loop secondary structures in tRNA. The program has beendeveloped in BASIC and 6502 Assembler and runs on the AppleII plus and He microcomputers. The execution is quite fast;all the operations are carried out in 1–90 s, dependingon the required task and on the sequence length. Received on March 1, 1985; accepted on April 25, 1985     

Structure of the Syrian hamster ribosomal DNA repeat and identification of homologous and nonhomologous regions shared by human and hamster ribosomal DNAs

We have cloned and partially characterized Bam HI fragments of Syrian hamster DNA containing most of the ribosomal RNA-coding region. Several restriction site polymorphisms within the transcribed portions of the hamster rDNA repeats have been noted. Approximately three-fifths of the repeats contain a Bam HI site upstream of the 18 S coding sequences. Approximately four-fifths of the repeats contain a Bam HI site very close to the 5' end of the 28 S coding sequences. This microheterogeneity has been maintained in the DNA of baby hamster kidney (BHK)-21 cells, a cell line established nearly 20 years ago. R-loop analysis with homologous hamster rRNAs has established the size of the coding regions and the internal transcribed spacer. Heterologous R-loop analyses with cloned hamster rDNAs and human rRNAs reveal several well-defined regions within the 28 S gene where the homology between human and hamster RNAs is greatly reduced. These regions are not detectable in heteroduplexes of hamster and human rDNAs. Sequences encoding the 18 S gene do not exhibit such reduced homology.