TRANSCRIPTS FROM A NOVEL HUMAN KRAB ZINC-FINGER GENE CONTAIN SPLICED ALU AND ENDOGENOUS RETROVIRAL SEGMENTS

During the course of an investigation into the potential effects of en dogenous retroviruses on adjacent gene expression, we isolated two cDN A clones containing a small sequence segment belonging to the human en dogenous retrovirus family, HERV-H, Characterization of the clones rev ealed that they represent transcripts from a novel KRAB zinc finger ge ne termed ZNF177, The two cDNA clones differ at their 5' termini and i n the presence of a 559-bp internal exon, The clone containing this in ternal exon has six imperfect zinc finger motifs followed by seven per fect copies of the C2H2 type but has a frame shift between the KRAB do main and the downstream zinc finger region. The smaller clone lacks th e six imperfect motifs and has an intact ORF. The 5' putative untransl ated regions of both cDNAs contain an 86-bp HERV-H env segment and a s egment of an Alu repeat, both in the antisense orientation, that have been incorporated by splicing. RT-PCR experiments show evidence of alt ernative splicing but the majority of transcripts appear to contain th e Alu and env segments. Genomic PCR and hybridization experiments sugg est that a partial HERV-H element is integrated within the ZNF177 locu s, which Southern analysis has shown to be a single-copy gene. Norther n and RT-PCR analyses suggest that ZNF177 is transcribed at a low leve l in a variety of cell types. (C) 1996 Academic Press, Inc.