A 38 nt region and its flanking sequences within gag of Friend murine leukemia virus are crucial for splicing at the correct 5′ and 3′ splice sites

Authors

  • Akihito Machinaga,

    1. Department of Bioinformatics, Faculty of Engineering, Hachioji, Tokyo, Japan
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  • Sayaka Takase-Yoden

    Corresponding author
    1. Department of Bioinformatics, Faculty of Engineering, Hachioji, Tokyo, Japan
    • Correspondence

      Sayaka Takase-Yoden, Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236, Tangi-machi, Hachioji, Tokyo 192-8577, Japan. Tel: +81 42 691 2375; fax: +81 42 691 2375; email: takase@soka.ac.jp

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ABSTRACT

The genome of the Friend murine leukemia virus (Fr-MLV) contains a 5′ splice site (5′ss) located at 205 nt and a 3′ss located at 5489 nt. In our previous studies, it was shown that if the HindIII–BglII (879–1904 bp) fragment within gag is deleted from the proA8m1 vector, which carries the entire Fr-MLV sequence, then cryptic splicing of env-mRNA occurs. Here, attempts were made to identify the genomic segment(s) in this region that is/are essential to correct splicing. First, vectors with a serially truncated HindIII–BglII fragment were constructed. The vector, in which a 38 bp fragment (1612–1649 bp) is deleted or reversed in proA8m1, only produced splice variants. It was found that a 38 nt region within gag contains important elements that positively regulate splicing at the correct splice sites. Further analyses of a series of vectors carrying the 38 bp fragment and its flanking sequences showed that a region (1183–1611 nt) upstream of the 38 nt fragment also contains sequences that positively or negatively influence splicing at the correct splice sites. The SphI–NdeI (5140–5400 bp) fragment just upstream of the 3′ss was deleted from vectors that carried the 38 bp fragment and its flanking sequences, which yielded correctly spliced mRNA; interestingly, these deleted vectors showed cryptic splicing. These findings suggest that the 5140–5400 nt region located just upstream of the 3′ss is required for the splicing function of the 38 nt fragment and its flanking sequences.

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