Genetic individuality of intracisternal A-particles of Mus musculus

Negative and positive effects of an IAP-LTR on nearby Pcdaα gene expression in the central nervous system and neuroblastoma cell lines

Intracisternal A-particles (IAPs) are defective retrovirions encoded by members of a large family of endogenous proviral elements in the murine genome. An intact IAP element was found in the protocadherin alpha (Pcdhalpha) gene cluster of five laboratory mouse strains. However, IAP insertion was not detected in three wild mouse strains we investigated. This IAP insertion caused the disruption of one variable exon of laboratory mouse and down-regulated expression of the Pcdhalpha v8 exon, which is located just downstream of the IAP in the brain following the methylation of 5' regulatory region of Pcdhalpha v8. In contrast, the Pcdhalpha v8 exon was highly expressed in mouse neuroblastoma cell lines. This suggested that the IAP insertion activates the expression of the nearby Pcdhalpha v8 exon in these cell lines. In fact, the Pcdhalpha v8 exon expression was driven by the IAP-long terminal repeat (LTR) following the de-methylation of 5' regulatory region of Pcdhalpha v8. To investigate the promoter activity of the IAP, we constructed an IAP-LTR-ECFP reporter gene and introduced it into neuroblastoma, melanoma, lymphoma, and plasmacytoma cell lines. Interestingly, ECFP-positive cells were observed only in the neuroblastoma cell lines. Moreover, there were no differences in the promoter activities of the IAP-LTR whether it was in the sense or complimentary orientation. Thus, this IAP-LTR has negative and positive regulation on near by gene expression in the brain and neuroblastoma cell lines.

Host-related DNA sequences are localized in the body of schistosome adults

The localization of host (mouse)-related DNA sequences in the adults and cercariae of Schistosoma japonicum and S. mansoni was examined by in situ hybridization using 32P-labelled probes. The hybridization signals to the sequences of the mouse type C and type A retroviruses were clearly observed in the subtegumental layer and inner tissues of S. japonicum adults. In contrast, it was hard to find any signals to these sequences in S. mansoni adults. Distinct signals to the env-specific region of the mouse ecotropic type C retrovirus were observed in the subtegumental layer and inner tissues of S. mansoni adults. No signal to the sequence of the mouse type B retrovirus was found on the sections of either schistosome adult. The signals to the sequence of the genomic clone SmM51 derived from male S. mansoni were found in the tissues of both the schistosome adults. The signals to the sequences of the mouse type A and env-specific region of ecotropic type C retroviruses were not seen in the cercariae of each species, whereas the signals to the sequence of SmM51 were detected in S. mansoni cercariae. These observations suggest that host-related DNA sequences might be incorporated unequally into the schistosome genome during development in the final host.

The expression of intracisternal A particle genes in the preimplantation mouse embryo

Intracisternal A particles (IAP), murine endogenous retrovirus, make up 0.3% of the mouse genome. They are expressed in some normal tissues, certain transformed cell lines, and show stage-specific patterns of expression in early embryos. We have used peptide-specific antisera and the polymerase chain reaction to explore type-specific expression of these IAP during preimplantation development. In this paper we show that the IAP core protein, p73, characteristic of type IIAP, is present throughout preimplantation development while the gag-pol fusion protein p120, characteristic of the variant type I delta 1, is synthesized and expressed only from the 8-cell stage onward. Type IIAP RNA is present at all stages and appearance of p120 at the 8-cell stage could represent new transcription or translation from a preexisting I delta 1 message. The presence of type II IAP RNA varies according to stage, with two sizes of type II transcripts present at all stages except the 2-cell stage at which time only the smaller of the two transcripts can be detected. The reappearance of the larger type II transcript subsequent to the 2-cell stage implies new transcription of this type II subspecies. The presence of type I, II, and p73 in the unfertilized egg strongly suggests maternal inheritance from the oocyte.

Nucleotide sequence of a complete mouse intracisternal A-particle genome: relationship to known aspects of particle assembly and function

The 7,095-nucleotide sequence of a mouse genomic intracisternal A-particle (IAP) element, MIA14, is reported. MIA14 is known to be colinear with IAP 35S RNA and to contain functional long terminal repeats. Its internal genetic organization was determined by comparisons with a homologous Syrian hamster element and the related retroviruses simian retrovirus 1 (simian type D) and Rous sarcoma virus (avian type C). MIA14 contains a gag-protease open reading frame of 827 codons and a pol region of 867 codons entered by a frame shift of -1. The env region of 1,100 base pairs has multiple stop codons in all reading frames, consistent with the failure thus far to detect IAP-related glycosylated envelope components. RNA transcribed in vitro from a cDNA clone containing a closely homologous gag-protease open reading frame was translated in a cell-free system. The main product was a 73-kilodalton polypeptide immunoprecipitable with antiserum against the authentic IAP gag-related structural protein p73. Rather than ending at the gag-protease boundary, p73 appears to contain 7 to 8 kilodaltons of peptide encoded by the protease domain, a peculiarity possibly related to the observed impairment of normal protein processing in IAPs. The N-terminal 217 codons of gag are unique to murine IAPs and may have been contributed by recombination with a cellular gene. The mouse-specific region of gag encodes a hydrophobic signal peptide with an atypical cleavage site. Delayed cleavage of this peptide could result in anchoring of newly synthesized p73 to the endoplasmic reticulum membrane and restriction of particle assembly to this site.

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.

Amounts, synthesis, and some properties of intracisternal A particle-related RNA in early mouse embryos

Early mouse embryos express two morphological subtypes of intracisternal A-type particles, one resembling those occurring in mouse tumors (referred to as IAP) and the other apparently specific for early embryos [referred to as IAP(epsilon)]. Using cloned fragments of IAP genes as labeled probes in dot-hybridization experiments, we detected IAP-related RNA sequences in mouse oocytes and preimplantation embryos. IAP RNA is relatively abundant in ovarian oocytes, is reduced in amount to approximately equal to 1/10th in the ovulated egg, and increases approximately equal to 100 times (from approximately equal to 1.3 X 10(3) to approximately equal to 1.5 X 10(5) molecules per embryo) between the one-cell stage and late blastocyst stage. Most of the IAP RNA consists of a single size class of about 5.4 kilobases, and a major fraction of this RNA is polyadenylylated. Quantitative considerations suggest that only a few percent of the IAP RNA in embryos are associated with particles. In two-cell embryos, the number of IAP RNA molecules is less than 1/10th the number of IAP(epsilon) particles, suggesting that IAP(epsilon) is genetically distinct from IAP and presumably represents a family of as yet unidentified retrovirus-like elements.

Long terminal repeat sequences of intracisternal A particle genes in the Syrian hamster genome: identification of tRNAPhe as a putative primer tRNA

We have determined the nucleotide sequences of long terminal repeat (LTR) regions of Syrian hamster intracisternal A particle (IAP) genes. The size of the LTRs was 350 base-pairs (bp) and 376 bp in two clones, H10 and H18, respectively. Two LTRs at both ends of the IAP gene were linked to directly repeating 6 bp hamster sequences. Many structural features common to the integrated retroviral LTRs such as "CAT" box, "TATAA" box, polyadenylation signal, and terminal inverted repeat (3 bp), were present on each LTR. The estimated length of R region (about 60 bp) was similar to that of the murine leukemia-sarcoma virus. In contrast, the calculated U5 region of 54 bp was the shortest among those of the retroviruses so far studied. Furthermore, from the analysis of primer binding sites, phenylalanine tRNA was for the first time identified as a presumed primer tRNA for reverse transcription. These results clearly distinguish Syrian hamster IAP LTRs from other retroviral ones. Based on the comparison of the sequences between Syrian hamster and laboratory mouse LTRs, the structural features peculiar to the IAP LTRs and the origin of the IAP genes are discussed.

Intracisternal A particles: RNA expression and DNA methylation in murine teratocarcinoma cell lines

Two main intracisternal-A-particle-specific RNA species (29 to 30S and 35 to 36S) are variably expressed in particle-producing and particle-nonproducing murine teratocarcinoma cell lines. An analysis of DNA methylation patterns after hybridization with an intracisternal-A-particle-specific probe showed an apparent direct correlation between DNA methylation and RNA expression. However, when the methylation assay was performed on the excised intracisternal A particle genes in one of the particle-rich cell lines (PCC6), some undermethylated sequences were detectable. These results are consistent with the concept that only few of the genes are transcriptionally active.

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.

Sequences homologous to retrovirus-like genes of the mouse are present in multiple copies in the Syrian hamster genome

The genome of M. musculus contains many copies of DNA sequences homologous to the 35S RNA of intracisternal type-A particles (IAP) (1,2). A major class of IAP genes has been identified and isolated from a mouse library in Charon 4A (3). Cloned mouse IAP genes were used as probes to study homologous sequences in the DNA of other species. Sequences related to mouse IAP genes were detected in the DNAs from a variety of animal cells. DNAs from rat, gerbil, and hamster cells all gave strong reactions which could be localized to discrete restriction fragments on genomic blots. The reaction of Syrian hamster DNA was particularly strong. Fragments derived from different parts of the IAP gene all reacted with Syrian hamster DNA, and the reactive restriction fragments in the Syrian hamster DNA could be ordered with reference to the known restriction map of the IAP genes. The data suggest that sequences related to mouse IAP genes make up a 7 Kb unit in the Syrian hamster genome. Since the majority of the hamster sequences are quite divergent from those in the mouse, the ease with which they are detected suggests that they must be reiterated in the hamster genome.

Terminally redundant sequences in cellular intracisternal A-particle genes

The sequences coding for intracisternal A-particle RNA form a family of related but not identical genetic elements which are present in 650 to 1,000 copies within the mouse genome. We showed that different intracisternal A-particle genes had a terminally redundant sequence of about 400 base pairs, one-half of which arose from the 3' end of the intracisternal A-particle RNA. A second portion of the redundant region did not contain 3-related sequences and was probably derived from the 5' end of intracisternal A-particle RNA. Thus, there were endogenous intracisternal A-particle genes in the cellular DNA-3'-5'--3'-5'-cellular DNA configuration identified for type B and C retroviruses. This indicated that the initial integration of intracisternal A-particle genes into the Mus musculus genome occurred by the same mechanism as the integration of other retroviruses. Two types of heterogeneity were identified among the 5' sequences of the two genes.

Intracisternal A-particle genes: identification in the genome of Mus musculus and comparison of multiple isolates from a mouse gene library

The genome of Mus musculus contains multiple copies (500 -1000) of DNA sequences related to the 35S RNA of intracisternal type A particles (IAPs). Using labeled IAP RNA as a probe in blot-hybridization experiments, we have identified a characteristic electrophoretic pattern of reactive fragments generated by restriction endonuclease cleavage of mouse DNA. From the genomic blots, we deduced a composite restriction map for a 6.5- to 7-kilobase (kb) DNA region containing sequences homologous to the IAP RNA. Units of this type appeared to be interspersed without obvious regularity in nonhomologous flanking regions. A 5.2-kb segment of this unit was inserted directly into plasmid pBR322 from HindIII/EcoRI digest of mouse DNA. The fragment was cloned and then labeled by nick-translation and used to scan a mouse embryo gene library (average 16-kb inserts in lambda Charon 4A); 1% of the library samples hybridized, confirming the extensive reiteration of IAP genetic units. Among six different library isolates containing 6.5- to 7-kb IAP units, some restriction sites were highly conserved whereas others varied in both occurrence and position. Despite this variation, heteroduplexes between the individual isolates showed continuous IAP homology regions of 7 kb. No flanking region homologies were seen in this limited sample. Some evidence suggests that mouse DNA may contain other dispersed sequence elements related to but smaller than the genetic unit defined above.

Immunological relationship between the structural proteins of intracisternal A-particles of Mus musculus and the M432 retrovirus of Mus cervicolor

A specific immunological relationship has been demonstrated between the main structural protein (p73) of intracisternal A-particles and a major internal protein (p24) of the M432 retrovirus.