Identification of a cis-acting element which assists in the recruitment of alternative transcription start sites/promoters

The transcription start sites (TSSs) of the human plasma prekallikrein gene (KLKB1) determined in RNA from kidney are mostly localized within intron 1 and exon 2, suggesting that the region encompassing exon 1, intron 1, and exon 2 comprises an alternative promoter. Reporter gene analyses in HepG2 and immortalized human kidney epithelial cells confirmed a significant transcriptional activity of this putative promoter region. However, when the TSSs recruited for transcription of the reporter gene were determined, only a few transcripts starting within the insert were detected, whereas the majority of TSSs were located in the vector backbone up to about 2000 bp upstream of the insert. Further reporter gene studies with deletion mutants of the fragment exon 1-intron 1-exon 2 revealed that the 3′-terminal 13-bp segment of intron 1 is sufficient to promote transcriptional activity and induce upstream displacement of the TSS. We conclude that the 13-bp segment represents a cis-acting element which can displace TSSs by provoking the recruitment of alternative promoters and/or by masking intergenic transcription terminating signals.