VNTR sequence on human chromosome 11p15 that affects transcriptional activity

We found a variable number of tandem repeat (VNTR) sequence with 38-bp repetitive units in the promoter region of a gene of unknown function on human chromosome 11p15. Polymerase chain reaction amplification of this VNTR sequence using genomic DNA from 80 unrelated individuals revealed two common alleles, one with 10 (79% allelic frequency) and the other with 14 (14% allelic frequency) repetitive units, and two rare alleles with 22 (3%) or 30 (3%) repetitive units. We investigated whether differences in the length of this VNTR sequence would affect transcriptional activity of a heterologous promoter by transient transfection to NEC8, embryonal carcinoma cells derived from testis. The activity of the promoter was suppressed significantly when the VNTR region was cloned upstream, in a manner dependent on the number of repeats present in the VNTR sequence. The results implied that this polymorphic VNTR sequence might function as transcriptional regulator in 11p15, with differences in the number of repetitive units influencing efficiency of transcription of the gene lying downstream.