RNA transcription is the process of copying genetic information from DNA to RNA. It's a crucial step in gene expression, allowing cells to produce proteins and regulate their functions.

The transcription process involves three main stages: initiation, elongation, and termination. Each stage requires specific enzymes and factors, working together to ensure accurate and efficient RNA production from the DNA template.

Transcription Process

Role of RNA polymerase in transcription

• RNA polymerase is the key enzyme that synthesizes RNA from a DNA template consists of multiple subunits working together to perform transcription (core enzyme and sigma factor in prokaryotes, multiple subunits in eukaryotes)
• During initiation, RNA polymerase binds to the promoter region of the gene, separates the double-stranded DNA to expose the template strand, and positions itself at the transcription start site
• In elongation, RNA polymerase moves along the template strand in the 3' to 5' direction, catalyzes the formation of phosphodiester bonds between ribonucleotides, and synthesizes the RNA strand complementary to the template DNA strand
• Upon termination, RNA polymerase encounters a termination signal, releases the newly synthesized RNA strand, and dissociates from the DNA template

Transcription initiation: prokaryotes vs eukaryotes

• Prokaryotic transcription initiation involves RNA polymerase directly binding to the promoter region containing conserved sequences like -10 (Pribnow box) and -35 elements, with the sigma factor ($\sigma$) aiding in promoter recognition and binding without the need for extensive transcription factor assembly
• Eukaryotic transcription initiation requires the assembly of general transcription factors (GTFs) like TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH at the promoter in a specific order, with TFIID recognizing and binding to the TATA box, followed by the recruitment of other GTFs and RNA polymerase II to form the preinitiation complex (PIC), and additional regulatory transcription factors can modulate gene expression

Promoters and transcription factors

• Promoter regions are located upstream of the transcription start site, contain specific DNA sequences recognized by transcription factors and RNA polymerase, act as binding sites for the transcriptional machinery, and regulate the initiation of transcription and gene expression
• Transcription factors are proteins that bind to specific DNA sequences in the promoter or enhancer regions, can act as activators or repressors of gene expression, with activators promoting the recruitment and assembly of the transcriptional machinery and repressors preventing or reducing the binding of RNA polymerase or activators, and modulate gene expression in response to cellular signals (hormones) or developmental cues (embryonic patterning)

Steps of transcription elongation and termination

1. Elongation:

   • RNA polymerase escapes the promoter and enters the elongation phase
   • Nucleoside triphosphates (NTPs) are added to the growing RNA strand
   • RNA polymerase maintains a transcription bubble, separating the DNA strands
   • The nascent RNA strand forms a short DNA-RNA hybrid with the template strand
   • RNA polymerase moves along the template strand, synthesizing RNA in the 5' to 3' direction

2. Termination:

   • Occurs when RNA polymerase encounters a termination signal
   • In prokaryotes:
     • Rho-dependent termination involves the Rho protein binding to the nascent RNA and causing dissociation
     • Rho-independent termination occurs at specific sequences that form a stem-loop structure, causing RNA polymerase to stall and dissociate
   • In eukaryotes:
     • Termination is coupled with polyadenylation of the 3' end of the RNA
     • Cleavage and polyadenylation specificity factor (CPSF) and cleavage stimulation factor (CstF) recognize specific sequences and cleave the RNA
     • Poly(A) polymerase adds a poly(A) tail to the 3' end of the cleaved RNA