Examples of cis-acting elements:

Prokaryotic systems:

• Promoter is a DNA sequence where RNA polymerase binds to initiate transcription. There are two promoter sequences in prokaryotic systems known as -10 (Pribnow box or Pribnow-Schaller box) and -35 sequences.
  
  
• Operator is regulatory sequence of DNA located immediately upstream of the structural gene that controls transcription of an operon.
  
  
• Inducers are located upstream of promoter region.
  
  
• Downstream regulatory sequences comprise of GC-rich inverted repeats followed by four adenine (A) residues signal the termination of transcription.

►  Trans-acting elements:

The protein factors which regulate the expression of gene by binding to cis acting DNA sequence are termed as trans-acting elements. Trans-acting molecules generally have two domains: DNA binding domain (which binds to cis elements) and protein binding domain (required for activation or suppression of transcription). Transcription initiation is a tightly regulated process controlled by trans-acting elements both in prokaryotes as well as eukaryotes.

  • DNA – Protein interactions :

Gene regulatory proteins and the transcription factors are capable of binding to the DNA based on the interaction of amino acids of the protein with the nucleotides of the DNA. The regulation is implemented through various interactions between cis-acting elements and trans-acting factors. Examples of some DNA binding proteins are:

• Eukaryotic TATA-binding protein
• σ subunit of bacterial RNA polymerase etc.

There are four types of structures of DNA binding proteins,

• Zinc finger proteins
• Helix loop Helix protein
• Leucine zipper proteins
• Homeodomain proteins