Chromatin Remodeling and Promoter Function

Chromatin Remodeling

• Histone Acetylation: Adds acetyl groups to histones, loosening chromatin structure, enabling transcription.
• DNA Methylation: Adds methyl groups to DNA, inhibiting activator binding, compacting chromatin, thus decreasing transcription. Often occurs in CpG islands (GC-rich regions upstream of promoters).
• Histone Methylation: Influences transcription.
  • Activators: Bind enhancers to histones, increasing transcription.
  • Repressors: Bind silencers to histones, decreasing transcription.
• Mediator Complex: Coordinates interactions between regulatory proteins and RNA polymerase, controlling transcription initiation and elongation.

Promoters

• Promoters: DNA sequences where transcription begins.
• Core Promoter: Contains the TATA box (-25 to -30).
• Proximal Promoter: Located closer to the transcription start site; contains the CCAAT box (-70 to -80) and GC boxes (-110), enhancing transcription efficiency.
• Distal Promoter: Further from the transcription start site, containing enhancers and silencers.

Cis-Acting Elements

• Cis-Acting Elements: DNA sequences regulating nearby genes.
• Enhancers: Up-regulate transcription, increasing it by interacting with activators; can form enchancesomes.
• Silencers: Down-regulate transcription, decreasing it by interacting with repressors.

Trans-Acting Elements

• Trans-Acting Elements: Proteins interacting with cis-elements to control transcription.
• Zinc Finger: Binds specific DNA sequences in the major groove.
• Helix-Turn-Helix: One helix binds DNA; the other provides stability.
• Leucine Zipper: Forms dimers via leucine residues.
• Helix-Loop-Helix: Allows dimerization and DNA regulatory sequence binding.

Post-Transcriptional Regulation

• Alternative Splicing: Different exon combinations yield diverse proteins from a single gene.
• RNA Editing: Changes mRNA nucleotide sequences post-transcription.
• RNA Interference (RNAi): Small RNA molecules affecting mRNA.
  • microRNAs (miRNAs): Endogenous, inhibiting translation through partial complementarity.
  • Small Interfering RNA (siRNA): Exogenous, degrading mRNA via perfect complementarity.

Translational Regulation

• RNA Binding Proteins: Bind to mRNA's 5' UTR to regulate translation efficiency or stability.

Applications

• Glucocorticoid Hormones: Regulate nutrient metabolism, activating multiple genes through hormone response elements (GREs).
• GloFish: Use fluorescent genes (like GFP or RFP) with constitutive promoters for environmental monitoring or decoration.
• Metallothionein IIA Gene (hMTIIA): Encodes a protein that binds heavy metals for protection, regulated by heavy metal response elements (MREs).

Explore the mechanisms of chromatin remodeling and the role of various elements in transcription regulation. This quiz covers histone modifications, DNA methylation, and the importance of promoters in initiating transcription.