The tutorial is intended for a rather general interdisciplinary audience. The tutorial will outline the basic events of transcriptional initiation on polymerase II promoters like binding of activating factors, assembly of a preinitiation complex, and formation of a fully competent initiation complex. The major elements of transcription control sequences and their basic functional features will be introduced. This includes transcription factor binding sites that are most important among these elements. They consist of about 10 to 30 nucleotides, not all of which are equally important for protein binding.
Direct repeats are quite common within regulatory DNA regions.
The consist either of short sequences which are repeated two or more times within a short region or they can be complex repeats where a pattern of two or more elements is repeated. Repeat structures are often associated with enhancers. The last category is represented by three-dimensional structures, which are hard to assess computationally at the time and cannot be discussed in too much detail for that reason. Computational methods used to describe the first three elements of transcription control regions will be demonstrated and briefly discussed. However, in most cases it is not possible to collect sufficient data to perform a rigorous correlation analysis.