47. Regulation of the gene expression at the level of the process of transcription. Regulation of RNA polymerase II in eukaryotes through phosphorylation and suppressor proteins. Regulatory sites in the promoter regions in eukaryotes. Transcription factors (TF) and transcription complexes. Epigenetic modifications – DNA methylation and covalent modification of histones – role in the processes of replication and transcription.

Overview

Gene expression is regulated mainly at the level of transcription, through promoter and enhancer elements, transcription factors, the state of RNA polymerase II and the chromatin environment. This topic covers these mechanisms in prokaryotes and eukaryotes, including epigenetic modification of DNA and histones.

Transcription and RNA polymerases

Transcription is the process by which RNA is synthesized using a DNA segment as a template.

• DNA stores genetic information.
• Genes are expressed via transcription into RNA.
• RNA is synthesized from the 5' to 3' direction.
• RNA and DNA strands are antiparallel and complementary.
• Specific promoter and terminator sequences define start and end.

DNA-dependent RNA Polymerase:

• Separates DNA strands temporarily.
• Uses one DNA strand as a template.
• Catalyzes phosphodiester bond formation.
• Involved in gene regulation.

Structure: Complex quaternary protein.

• Ribonucleotides (ATP, UTP, GTP, CTP) provide energy.
• Energy released from phosphate bond cleavage.
• Pyrophosphate hydrolyzed by pyrophosphatase, pushing reaction forward.

1. Initiation

• Transcription factors bind TATA box (promoter).
• RNA Polymerase forms the transcription initiation complex.
• DNA unwinds, and phosphodiester bonds begin forming.

2. Elongation

• RNA Polymerase adds complementary nucleotides to the 3' end of RNA.
• DNA helix reforms after polymerase passes.
• Topoisomerases relieve supercoiling.

3. Termination

• RNA Polymerase halts at terminator sequence.
• Transcript is released.

Consists of:

• Promoter
• RNA Coding Region
• Terminator

• RNA Polymerase has 5 subunits (α, α, β, β’, σ).
• Holoenzyme initiates transcription; core enzyme continues elongation.

Termination Types:

• Rho-independent: GC-rich hairpin + U-rich tail.
• Rho-dependent: Rho protein disrupts transcription complex.

• RNA Polymerase I: rRNA (45S precursor → 18S, 5.8S, 28S)
• RNA Polymerase II: mRNA, snRNA (targeted by α-amanitin)
• RNA Polymerase III: tRNA, 5S rRNA, other small RNAs

• Toxin α-amanitin inhibits RNA Polymerase II.
• Halts mRNA synthesis → cell death.

1. **Transcription Steps**: I Eat Tacos → Initiation, Elongation, Termination
2. **Prokaryotic RNA Polymerase Subunits**: ααββ’σ = 'All Big Boys Shine'
3. **Eukaryotic RNA Polymerases**:

• I = rRNA (I make Ribosomes)
• II = mRNA (I make Messages)
• III = tRNA (I make Tiny RNAs)