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

Abstract

The genome of Mus musculus contains multiple copies (500-1000) of DNA sequences related to the 35S RNA of intracisternal type A particles (LAPs). 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 (1,2). These sequences were contained in polyadenylylated RNA molecules of several discrete sizes ranging from 29S to 35S (3). All of the RNA species contain related sequences as judged by hybridization studies (2), and both the 35S RNA from neuroblastoma A particles and the predominant 29S species from myeloma particles have been shown to direct the cell-free synthesis of the major (73,000-dalton) A-particle structural protein (3). There are no close sequence homologies between the genomic RNA of IAPs and those of representative type B and type C viruses of M. musculus (1, 2, 4, 5). However,-IAPs do share partial sequence homology (6) with a distinctive class of.retrovirus endogenous to the Asian murine species M. cervicolor and M. caroli (7,8).Hybridization kinetics have indicated that DNA sequences homologous to IAP RNAs are reiterated to the extent of 500 or more copies per haploid genome of both somatic and germ cells of M. musculus (6, 9). On the other hand, only'20-25 copies of the related genes were found in the DNAs of M. cervicolor and M. caroli (6-8, 10), from whose progenitors M. musculus diverged about 5 million years ago (7, 11). Thus, the evolution of The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C. §1734 solely to indicate this fact. 3571M. musculus appears to have been accompanied by a striking amplification of IAP-related genetic information, which now makes up about 0.3% of the total cellular DNA.In situ hybridization studies show that these sequences are distributed among many, perhaps all, of the mouse chromosomes (9). Beyond this, there has been no information about the internal structure of the TAP genes, their arrangement within the mouse genome, and the degree of variation among individual members of this extensive genetic family. This report describes results of studies addressed to these questions.MATERIALS AND METHODS Blot Hybridization. High molecular weight DNA was prepared (9) from BALB/c mouse myeloma MOPC-104E, a neuroblastoma tissue culture line N4 of A/Jax origin, livers of NIH Swiss mice, and the F9 teratoma cell line derived from a tumor in strain 129 mice (12). DNAs were digested to completion with restriction endonucleases (New England BioLabs) and the digests were electrophoresed in agarose gels. DNA fragments were recovered from the gels by binding on glass microbeads (13) or were transferred to cellulose nitrate sheets by a modification (14) of the Southern blot technique (15). For use a...

Intracisternal A-particle gene expression in normal mouse thymus tissue: gene products and strain-related variability.

“…Such transcripts may be derived from members of a recognized class of type I IAP genes that contain 1.8-kb deletions in this region (40), as recently suggested by Wujcik et al (J. Virol 52: [29][30][31][32][33][34][35]1985).…”

“…1. The immobilized RNAs were hybridized with a radioactive probe prepared from cloned IAP DNA (29), and the assay was calibrated with authentic IAP poly(A) RNA extracted from gradient-banded myeloma particles (30). IAP sequence levels were first calculated as a proportion of the total poly(A) RNA and then converted to absolute tissue concentrations ( Table 1).…”

“…Preparation of radioactive probe. We used a recombinant plasmid, pMIA1, containing 5.2 kb of internal sequence from a genomic IAP gene copy (29 ,uCi/ml in methionine-free DMEM containing 10% dialyzed fetal calf serum. Individual thymuses were placed in 60-mm culture dishes and teased to single-cell suspensions in methionine-free DMEM.…”

Identification and classification of feline endogenous retroviruses in the cat genome using degenerate PCR and in silico data analysis

“…One of the earliest approaches was to stimulate the induction of virus release from normal cells after treatment with ionizing radiation, chemical mutagens, or carcinogens (Weiss et al, 1971). ERVs were also detected based on their homology to synthetic primer binding site probes (Kröger & Horak, 1987) as well as DNA hybridization and sequencing (Dunwiddie et al, 1986;Lueders & Kuff, 1980;Ono et al, 1985). Recently, sufficient data for phylogenetic analyses were successfully obtained by using PCR to directly amplify ERV sequences from the host genomic DNA of pigs (Klymiuk et al, 2002;Patience et al, 2001), sheep (Klymiuk et al, 2003), cattle (Garcia-Etxebarria & Jugo, 2010;Xiao et al, 2008b), dog (Jo et al, 2012) and other vertebrates (Herniou et al, 1998) Several endogenous retroviruses have been detected in the genome of domestic cats (Felis catus); these viruses include endogenous feline leukaemia virus (enFeLV) (Soe et al, 1983), RD-114, a C-type retrovirus (McAllister et al, 1972), MAC-1 primate retrovirus-related virus (Bonner & Todaro, 1979), ECE1 (Beyer et al, 1987), FcEV (van der Kuyl et al, 1999), FERVmlu1 and FERVmlu2 (Yuhki et al, 2008), and ERV-DC (Anai et al, 2012).…”

Transposition of two different intracisternal A particle elements into an immunoglobulin kappa-chain gene.

“…However, unlike retroviruses, IAPs have no known extracellular phase (12,36). Approximately 1,000 DNA sequences homologous to IAP RNA (IAP elements) are scattered throughout the mouse genome (28,29). Like many of the repeated sequences in lower eucaryotes (41,42), mouse IAP elements have a gross structural organization similar to that of the proviral forms of vertebrate retroviruses (10,26,54).…”