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\b[Both classes of activator couple sequence recognition to more efficient transcription, but a eukaryotic activator usually acts through a larger chromatin and cofactor system.] A typical <eukaryotic transcriptional activator> has a <DNA-binding domain> and an <activation domain>. The former positions it at a regulatory sequence; the latter recruits or regulates other components. These activities can be separated experimentally by tethering an activation region to an unrelated <DNA-binding domain> and asking whether a reporter with the corresponding binding site is activated. Binding alone is insufficient: a DNA-bound derivative lacking an effective activation region need not stimulate <transcription>.
In <eukaryotes>, the target <DNA> is packaged in <chromatin>. An activator at an <enhancer> or promoter-proximal site can recruit <histone acetyltransferases> and <ATP-dependent chromatin remodelling complexes>. Histone modification and nucleosome repositioning can increase access to regulatory and promoter sequences; acetylated residues can also recruit reader proteins. These are context-dependent routes, not a universal requirement that every activated gene first undergo the same histone change. Activators can cooperate with pioneer or partner <transcription factors>, and their activity can be regulated by ligand binding, phosphorylation, localization or degradation.
Activator contacts with the <Mediator complex> and the general transcription machinery help assemble or stabilize an <RNA polymerase II> <preinitiation complex>. <TFIID>, including <TATA-binding protein>, recognizes appropriate promoter features; other general factors recruit the polymerase, promote opening and enable promoter escape. Regulatory contacts may additionally influence release of paused polymerase and productive elongation. <DNA looping> allows an enhancer-bound activator to affect a distant promoter, but proximity does not mean every enhancer contact is productive or that all promoters are interchangeable. Biochemical reconstitution showed that a mediator fraction was required for activated transcription in vitro, providing evidence that activator–polymerase communication can require an intermediate rather than a direct DNA-to-polymerase contact.<A mediator required for activation of RNA polymerase II transcription in vitro by Peter M. Flanagan and others>[Abstract and pp. 436–438, biochemical requirement for mediator activity]{ref}
The bacterial <catabolite activator protein>, also called <cAMP receptor protein>, is a simpler example of regulated recruitment. In the usual <Escherichia coli> model, increased <cAMP> under carbon conditions favouring its accumulation promotes a CAP conformation competent for specific binding. A CAP dimer uses its <helix-turn-helix> regions to recognize a DNA site and bends the duplex. At a class I CAP-dependent promoter such as the canonical lac arrangement, a site centred near $-61.5$ positions an activating surface to contact the C-terminal domain of the <RNA polymerase> alpha subunit. This stabilizes polymerase recruitment; the CAP–alpha-domain–DNA structure supplies a direct molecular basis for that contact.<Structural basis of transcription activation: the CAP-alpha CTD-DNA complex by Brian Benoff and others>[pp. 1562–1566, CAP–alpha-domain contact and transcription-activation complex]{ref}
CAP is not limited to that single geometry. At class II promoters, a site near $-41.5$ overlaps the promoter region and permits additional contacts with polymerase, affecting more than initial recruitment. Promoter position, orientation and other repressors therefore matter. <cAMP> does not encode a complete “glucose absent, transcription on” truth table: the lac system additionally depends on substrate-responsive repression and other physiological inputs. An activating protein can improve a limiting step without determining the entire expression pattern.
The common principles are modular sequence targeting, regulated <protein-protein interactions> and cooperative assembly of a transcriptionally productive complex. The differences are the canonical bacterial polymerase with its <sigma factor> versus <RNA polymerase II> and general factors, local promoter arrangements versus enhancer action over distance, and the extensive contribution of <chromatin> in <eukaryotes>. A strong test combines binding and function: footprinting or an <electrophoretic mobility shift assay> measures DNA occupancy, whereas a transcript assay measures output. An activation-surface mutant that retains DNA binding but loses transcriptional stimulation separates recruitment from recognition. In a reconstituted system, removing and restoring a required cofactor tests causality; in cells, changes in chromatin or reporter activity alone do not identify the direct protein contact.
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