Methods of Gene Regulation

1. DNA Methylation:
2. Histone Acetylation
3. Homeotic Genes: master genes that control the pattern of body formation during early embryonic development

• Ex: in flies genes control formation of body structures like body segments and antenna
  • Mutant homeotic genes produce body parts in wrong places
• Homeobox is a specific nucleotide sequence that codes for protein
• Hox genes contain homeobox and direct development of specific body part
  • Products of genes act as transcription factors
  • Appear in clusters and order on DNA controls order of expression and timing of body part development

1. X inactivation:
2. Transcription Initiation:
3. Coactivators & Mediators: additional proteins that contribute to the binding of transcription complex components
4. RNA processing/Alternative Splicing:
5. RNA interference (RNAi): gene silencing caused by short noncoding RNA that bind to complementary sequences of mRNAs & block expression

• Short Interfering RNAs (siRNAs): short double-stranded RNA, one strand is degraded → allows remaining strand to complement and inactivate a sequence of mRNA
• Long noncoding RNA: some condense chromosome
• PiRNA: reestablishes methylation patterns during gamete formation and block expression of some transposons → induce the formation of heterochromatin → block transcription
• Dicer: Enzyme that trims small double-stranded RNAs into molecules that can block translation.                                         
• MicroRNAs (miRNAs): Functions in RNA silencing and post-transcriptional regulation of gene expression.
  • Degrades mRNA if bases are completely complementary, If the match is less than complete, then translation is blocked

1. MRNA degradation: occurs bcuz of RNAi and bcuz mRNA are unstable molecules

• Poly-A-Tail and 5’ cap maintain mRNA stability but degradation slowly occurs as mRNA ages & degrading enzymes target tail and cap + untranslated UTR regions
• Amount of protein made depends on rate of mRNA degradation

1. Protein Degradation: final stage of proteins; as proteins age, they lose functionality as 3D shape changes → nonfunctional proteins marked for destruction with protein ubiquitin
2. Protein Processing: protein chemical modification can activate/inactivate protein by adding/removing phosphate
3. Translation Initiation: translation can be blocked by regulatory proteins that bind to untranslated sequence (UTR) at 5’ or 3’ end → prevents ribosomal attachment

Epigenetic (above the genes) Changes

• Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence

• Do not alter DNA sequence,

• Can affect gene expression through reversible modifications such as…
  • Histone acetylation, DNA methylation, genomic imprinting, X-inactivation

Regulation of Chromatin Structures

• Histone modification: change in the organization of histone proteins with DNA.                                 
• Access to DNA for transcription can be affected by..
• Acetylation: enzymes add acetyl to histones → histones loosen grip on DNA → DNA uncoils → activated transcription
• Methylation: enzymes attach methyl groups (-CH3) to histone proteins → histones tighten grip on DNA → preventing DNA from uncoiling and being expressed → repressed transcription
  • Protects against restriction fragments; DNA methylation inactivates genes (long-term)

Regulation of Transcription Initiation

• After chromatin modification, transcription is next point of regulation
• Transcription Initiation Complex: group of proteins associated with RNA pol II and inhibit/promote activity → make region of DNA more/less able to bind to transcription machinery
  • Proteins assemble on promoter sequence upstream (towards 5’ end) & adjacent to gene to be transcribed
  • Gene expression can be inhibited or activated by binding of repressors or activators to enhancers
• General transcription factors: proteins required by all transcription events to initiate transcription
  • Some target the TATA box sequence associated with promoter
• Specific transcription factors: other proteins associated with regulating specific transcription activities–specific to cell type, genes, or timing of transcription.
  • 2 kinds which bind to enhancers
    • Activators
    • Repressors: stop transcription & translation
  • Control Elements: segments of noncoding DNA that serve as binding sites for protein transcription factors to regulate transcription
    • DNA sequences located near (proximal) or far (distal) from the promoter, upstream
  • Enhancers: Distal control elements grouped together
  • Particular combination of control elements in an enhancer associated with a gene
    • Diff combination → diff regulation of transcription

Transcription Factors

Structure

• Usually have DNA binding domains and binding domains for other transcription factors

Transcription factors as repressors:

1. Bind to enhancers and block activators
2. Silencing: bind to chromatin structure and remove acetyl

The Steps of Regulation of Transcription & Transcription Initiation Complex

1. Enhancers bind to activator                                                                                                                           
2. Since enhancer can be far from gene, a DNA-bending protein enables activators to bind to mediator proteins and general transcription factors at the promoter
3. A transcription initiation complex is formed → initiate transcription