Transcription bubble

A transcription bubble is a molecular structure formed during the initialization of DNA transcription, when a limited portion of the DNA double helix is unwound, providing enough space for RNA polymerase (RNAP) to bind to the template strand and begin RNA synthesis. The transcription bubble size is usually 12 to 14 base pairs, which allows the incorporation of complementary RNA nucleotides by the enzyme with ease. The dynamics and structure of the transcription bubble are variable, and play a role in the regulation of gene expression at the transcriptional level. The formation of bubbles depends on the structure of chromatin, the DNA sequence, and transcription factor, including H3K27ac histone acetylation marks, SWI/SNF nucleosome remodeling, and TFIIH and sigma (σ) factors. While the evolutionary history cannot be completely confirmed, scientists have provided various models to explain the most likely progression of bubble evolution, tying it directly to the divergence of archaea, eukaryotes, prokaryotes, and bacteria from the last universal common ancestor (LUCA). Many drugs, including chemotherapeutic and antibiotic compounds, target elements of the transcription bubble to regulate gene transcription.