We have addressed the possible role of DNA:RNA triple helix formation in regulation of gene expression, particularly in the human beta globin gene locus. There are strict rules for the combinations of bases that can form such structures. We searched for loci that obeyed those rules. Most significantly we have found that an intronic sequence within the adult human beta globin primary transcript can form a triple helix with a target site in the beta globin locus control region (LCR), the major positive compound regulatory element of the beta globin genes. We show that when a full length transcript containing the wild type second beta globin intron is overexpressed it downregulates expression of globin genes by binding to a site in the LCR and displacing transcription factors. A transcript that is identical but with the intronic triplex forming sequence mutated has no effect. This appears to be a feedback system to prevent overexpression of the beta globin genes. We have found another example of this regulation elsewhere in the genome, suggesting that this may a general regulatory mechanism.
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