A novel sequence segment and other nncleotide structural features in the long terminal repeat of a BALB/c mouse genomic leukemia virus-related DNA clone

Abstract

A recombinant DNA clone, named AL10, that contains murine leukemia virus (MuLV) related sequences was isolated from BALB/c mouse chromosomal DNA and examined in detail. Restriction endonuclease mapping revealed that the 10.5 kbp EcoRI insert consists of a 3.6 kbp left flanking cellular DNA region and a 6.9 kbp MuLV-related region that has a typical proviral LTR-gag-pol-env structure up to the EcoRI site in the env gene region. Comparison of the AL10 map with ecotropic and xenotropic virus isolates revealed many common restriction sites in the LTR and pol gene regions, but much fewer in the leader and gag regions. A stretch of 1,700 nucleotides containing the cellprovirus junctional region was sequenced and revealed transcriptional consensus signals and other structural features characteristic of MuLV LTRs, as well as two distinctive features: (a) a sequence of approximately 170 bp with direct and inverted terminal repeats not seen in infectious MuLV LTRs was identified in the U3 region between the "enhancer" region and the "CAT" box. This novel segment or its homologous sequences appear to be present in most of the endogenous MuLV-related LTRs and in other chromosomal locations of the mouse (b) The tRNA primer binding site is not complementary to proline tRNA, the primer for all known MuLVs, but is a 17/18 match with rat glutamine tRNA. The integration site of AL10 provirus was in a unique DNA region but contained an "Alu"-like short interdispersed repeat in the 5' adjacent cellular region. The AL10 proviral integration found in BALB/c was also apparent in RFM, AKR and SENCAR mouse cells but not in cells of NFS/N, C3H, HRS/J, SC-1, and a California Lake Casitas wild mouse.

Nucleotide sequence analysis and enhancer function of long terminal repeats associated with an endogenous African green monkey retroviral DNA.

“…It has recently been shown that the retrovirus-like 30S (VL30) mouse genetic element, which is incapable of forming virus particles, uses tRNAGIY as the minus strand primer (26,29). Furthermore, an endogenous murine (27) and an endogenous human (35) 17 nucleotides from the 5' end of the LTR unit was present in 16 copies in the 5' LTR and 12 copies in the 3' LTR. Nucleotide sequence analysis showed similarity between the 8-bp repeats (AAACTTAG) and a repeat unit contained in the decasatellite (AAACTAGGGT) present in AGM cellular DNA as described by Maresca and Singer (22).…”

Characterization of a Molecular Clone of RFM/Un Mouse Chromosomal DNA that Contains a Full-length Endogenous Murine Leukaemia Virus-related Proviral Genome

“…Charon 9 lambda phage was used as the cloning vector (Benton & Davis, 1977;Boone et al, 1983;Ou et al, 1983) except that HindlII-digested DNA fragments from the RFM/Un mouse were used for insertion into the vector and an LTR probe from RFM/Un ecotropic MuLV (Liou et al, 1983;Nikbakht et al, 1985) was used for clone selection. A total of 20 clones were isolated which were subsequently transferred to pBR322.…”

“…Restriction DNA fragments were separated by horizontal electrophoresis using 0.7 or 1 submerged agarose gels and then transferred to nitrocellulose membranes according to the method described by Southern (1975). Methods for hybridization and autoradiography have been described (Yang et al, 1980;Ou et al, 1983). An LTR-specific probe was made by nick translation of an internal PstI/Kpnl fragment isolated from the LTR of a proviral DNA clone of WN1802, the N-tropic MuLV derived from the BALB/c mouse .…”

“…and asterisks (*) respectively represent identical nucleotide bases and identical predicted amino acid residues found in AKV sequences; © © ©, = termination codon. Roblin et al, 1982;Steffen et al, 1982;Liou et al, 1983 ;Ou et al, 1983;Herr, 1984;Nikbakht et al, 1985). These common sites (with their approximate distances in kbp from the 5' terminus of the 5' LTR of pRFM # 6) are:…”

“…Most of these sequences apparently contain long terminal repeats (LTR) as well as gag, pol and env structural genes similar to those found in proviruses of all known infectious MuLVs (Dolberg et al, 1981 ;Rassart & Jolicoeur, 1982), although no extracellular retroviruses directly corresponding to the MuLV-related proviral sequences have been recognized. With the exception of one study (Bacheler, 1984), all molecular clones of mouse chromosomal non-ecotropic and non-xenotropic MuLV-related proviruses thus far reported have been incomplete or contain apparent deletions 0000-7376 Also shown is the 1.5 kbp BgllI/BgllI restriction fragment isolated from clone ALl 0 (Ou et aL, 1983) and used as a gag-specific probe to distinguish 5" LTR-containing fragments from 3" LTR-containing fragments in the initial mapping analysis.…”