Regulation sequences and Molecules

Regulation of transcription, the initial step in all gene expression, is controlled by regulatory sequences of DNA that are usually embedded in the noncoding regions of the genome. The interaction between these DNA sequences and regulatory molecules, such as transcription factors, can induce or repress the transcriptional machinery, influencing the kinds and amounts of products that are produced.

The regulatory DNA sequences are called cis-acting because they influence expression of genes on the same chromosome as the regulatory sequence . The regulatory molecules are called trans-acting because they can diffuse (transit) through the cell from their site of synthesis to their DNA-binding sites (Fig. 1). For example, a protein transcription factor (a trans-acting molecule) that regulates a gene on chromosome 6 might itself have been produced from a gene on chromosome 11. The binding of proteins to DNA is through structural motifs such as the zinc finger (Fig. 2), leucine zipper, or helix-turn-helix in the protein.

Figure 1: Cis-acting elements and trans-acting factors. mRNA = messenger RNA; Pol II = RNA polymerase II.

Figure 2:  Zinc (Zn) finger is a common motif in proteins that bind DNA. Cys = cysteine; His = histidine.