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On Finding Jewels in the Junk

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In prokaryotes, it only takes a small jazz band to get the music grooving: piano and a rhythm section suffice. The promoter region of a gene is a tiny stage on which RNA polymerase (p) and few transcription factors (dr, b) improvise on a tune, i.e. they initiate or skip transcription. By contrast, it takes a big band in eukaryotes to perform Duke Ellington's 'Caravan'. And since not all the musicians fit to the narrow stage trombones and saxophones are placed elsewhere in the concert hall: transcription factors (tb, sax) bind to sites—enhancer or silencer elements—that are found upstream and downstream of genes and also within introns.

In its typical textbook style, figure 1 oversimplifies the complex interplay of RNA polymerase II with the various transcription factors at a eukaryotic promoter by reducing it to a two-dimensional array, suspiciously omitting downstream located 'gene regulatory sequences'. This flatters our human ability to perceive 2D-maps at a glance but it ain't got that swing. Admittedly, only a 3D-animation could catch the groove of the spatial intricacies that bring enhancer-bound transcription factors into the proximity necessary for the multiple protein-protein interactions that orchestrate eukaryotic transcription initiation. Let alone the possibility that transcription factors bound to one enhancer interact with protein complexes at two or more promoters simultaneously. Please note in figure 1 the stippled grey line tagged 'spacer DNA', we will come to this later.

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