Gene Regulation Flashcards
Transcriptional regulatory proteins (Transcription factors)
Bind DNA at regulatory sequences (enhancers) and stimulate (activator) or block (Repressor) transcription by RNA polymerase by recruiting RNA polymerase or enzymes that modify chromatin structure and chemistry
TFs are modular (has DNA binding domain and activation or repression domain)
DNA binding site composed of two half-sites
Often gene-specific and almost always organism-specific
Use different motifs that usually contain a recognition alpha helix that inserts in the major groove of DNA and makes multiple contacts, amino acids recognize at edges of DNA so don’t need to open up helix
Mutations in TFs (p53 tumor suppressor protein, leads to cancer)
Gene regulation
Process of turning on and off the expression of genes in response to developmental, environmental and hormonal signals
Important for differentiation, specialized proteins for each cell’s distinctive properties
Controlled at several different steps but most is at transcription
Control of transcription in bacteria
Genes are often clustered in operons
mRNAs are polycistronic (multiple proteins from single mRNA, not different isoforms)
Repressors proteins bind operators
Tryptophan expression is constitutive (always present at low levels), if levels high, repressor binds trp, which then binds operator and blocks binding of RNA polymerase
Activation of lac operon by activator binding and recruiting RNA polymerase to begin transcription
TFs bind enhancers and stimulate RNA polymerase II
Activators work via large mediator complex
Enhancer sequences can be located upstream or downstream, can be great distance because forms loop
If translocation, enhancers can be juxtaposed with wrong gene to drive expression
TFs can also recruit chromatin modifiers
Chromatin needs to decondense for RNA polymerase
1) covalent history modifications (acetylation, de-acetylation, methylation, phosphorylation on H3 and H4 tails)
- histone acetyltransferases (HACs) activate
- histone deacetylases (HDACs) repress
2) ATP-dependent nucleosome remodeling (move, slide, exchange) from promoters so transcription initiation complex can assemble
Synthesis and activity of transcription factors themselves are regulated.
Covalent modification (phosphorylation), intracellular trafficking, selective degradation
Controlled by extra cellular signals
Most TFs bind and regulate multiple genes, cause of side effects in drugs
Defects in transcription regulators
Can block differentiation and contribute to cancer development
Cell stays in immature state and continues to divide
Transcriptional profiling
Gene expression profiling (transcriptional profiling) measure abundance of mRNAs in cells or tissues
DNA microarray measures relative mRNA levels
RNA-seq which is a whole genome sequencing method that can measure relative abundance of all RNAs made in the cell
Transcriptional regulation in hemoglobin
Beta-globin gene only expressed in adult erythroid cells found in bone marrow
One upstream and one downstream enhancer
Complex array of gene regulatory proteins control expression of gene
Concentrations of these are thought to change with development or type of cells
Beta globin cluster contain multiple genes that are developmentally regulated, subject to shared controlled region that controls chromatin structure (locus of control region LCR)
Cluster is tightly packed in cells where globin genes are not expressed (brain or skin cells)
If LCR is deleted, cluster is silences, no beta globin production (B thalassemia)
Cell memory is often transmitted through transcriptional mechanisms
Cells have same DNA yet must remember which genes to express and which to keep silent
1) auto regulation: TF required for own transcription
2) epigenetic inheritance via modification of
A) chromatin: inheritance of active or repressed chromatin state (acetylation, methylation)
B) DNA: “imprinting” results in gene silencing, methylated CpG islands attract histone modifiers, leads do condensed chromatin and transcription repression
