An auxin response element is a cis-regulatory element involved in auxin-responsive transcription. It is a DNA sequence recognized by regulatory proteins, including auxin response factors. The element, its binding protein and the plant hormone are different participants in the response.[ref]
ARF1, a transcription factor that binds to auxin response elements by T. Ulmasov and others. Abstract, Science 276 (1997), pp. 1865–1868: element recognition and matched binding/response specificity.
A motivating experiment compared the sequence requirements for factor binding in vitro with those associated with a transcriptional response in living cells. Agreement linked molecular recognition to regulation, rather than merely identifying a sequence that happened to lie near an expressed gene.[ref]
ARF1, a transcription factor that binds to auxin response elements by T. Ulmasov and others. Abstract: relationship between DNA-binding specificity and auxin responsiveness.
The synthetic element used in the DR5 auxin response reporter supplies a concrete example. It can drive a measurable reporter gene response, but its output also depends on the regulatory state of the cell. In the original experiments, Aux/IAA proteins could repress reporter expression. Thus a response element is part of a control system: the same regulatory DNA does not guarantee the same output under every cellular condition.[ref]
Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements by T. Ulmasov and others. Abstract, Plant Cell 9 (1997), pp. 1963–1971: synthetic reporter and repression comparisons.
The DR5 auxin response element is a synthetic regulatory DNA arrangement containing repeated auxin response elements. When used to control a reporter gene, it contributes the responsive regulatory part of a DR5 auxin response reporter. The DNA element and the measurable reporter product are different parts of that system.[ref]
Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements by T. Ulmasov and others. Abstract, Plant Cell9 (1997), pp.1963–1971: synthetic tandem-repeat element and reporter comparisons.
The original study compared DR5 with natural regulatory sequences and found strong auxin-responsive expression in the tested plant systems. It also connected binding by auxin response factor 1 with regulatory effects involving Aux/IAA proteins. This made DR5 useful for studying responsive transcription, rather than establishing a direct physical measurement of auxin concentration.[ref]
Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements by T. Ulmasov and others. Abstract: response comparison, factor binding and repression.
An illuminating experimental distinction is between asking whether a protein recognizes this DNA arrangement and asking whether a reporter is expressed in a particular cell. The first concerns molecular binding; the second also depends on the surrounding regulatory system and reporter behavior. A repeated regulatory element can therefore be a sensitive response tool without being a universal hormone-concentration scale.
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