LIT1, an imprinted antisense RNA in the human KvLQT1 locus identified by screening for differentially expressed transcripts using monochromosomal hybrids

Mammalian imprinted genes are frequently arranged in clusters on particular chromosomes. The imprinting cluster on human chromosome 11p15 is associate d with Beckwith-Wiedemann syndrome (BWS) and a variety of human cancers. To clarify the genomic organization of the imprinted cluster, an extensive sc reen for differentially expressed transcripts in the 11p15 region was perfo rmed using monochromosomal hybrids with a paternal or maternal human chromo some 11. Here we describe an imprinted antisense transcript identified with in the KvLQT1 locus, which is associated with multiple balanced chromosomal rearrangements in BWS and an additional breakpoint in embryonal rhabdoid t umors. The transcript, called LIT1 (long QT intronic transcript 1), was exp ressed preferentially from the paternal allele and produced in most human t issues. Methylation analysis revealed that an intronic CpG island was speci fically methylated on the silent maternal allele and that four of 13 BWS pa tients showed complete loss of maternal methylation at the CPG island, sugg esting that antisense regulation is involved in the development of human di sease. In addition, we found that eight of eight Wilms' tumors exhibited no rmal imprinting of LIT1 and five of five tumors displayed normal differenti al methylation at the intronic CpG island, This contrasts with five of six tumors showing loss of imprinting of IGF2. We conclude that the imprinted g ene domain at the KvLQT1 locus is discordantly regulated in cancer from the imprinted domain at the IGF2 locus. Thus, this positional approach using h uman monochromosomal hybrids could contribute to the efficient identificati on of imprinted loci in humans.