Sequence signals in eukaryotic upstream regions

In eukaryotes, as in prokaryotes, evidence is accumulating showing that transcription factors recognize and bind to certain promoter elements. Sequence and chromatin structure perturbation specify the transcription initiation site and govern its efficiency. Two oligomers have been implicated in these processes: the TATAAATA and CCAAT. In the present work, all mammalian, non-mammalian vertebrate and invertebrate sequences accumulated in the database have been aligned by their mRNA start positions and scanned for recurrences of the 32 complementary triplets. The more significant signals are summarized here. In particular, TAT/ATA recurs very frequently further upstream, at -275, in addition to the 'classical' -40 position. Downstream their level is very low. The CAAT box complementary triplet components are not among the more striking signals. Closer examination of the -275 region indicates that to a large extent the signal is due to both the ATAT and the TATA quartets. Comparison of the frequencies of these quartets at -275 with the CAAT quartet at -80 suggests that the former signal is twice the strength of the latter. The oligomers' distribution charts support notions that several components are involved in recognition, making the regulatory regions more robust and less sensitive to mutations.