Developmental Genetics

• Developmental Genetics


  The discipline that examines how the genotype is transformed into the phenotype
• Different cell types make different sets of proteins, even though their genomes are identical
• Different cell types use different subsets of these genes
• Levels of regulation of gene expression

  • Differential gene transcription
  • Selective nuclear RNA processing
  • Selective messenger RNA translation
  • Differential protein modification
• Exons


  Regions of DNA coding for a protein
• Introns


  Intervening sequences
• Promoters


  Sites where RNA polymerase binds to the DNA to initiate transcription
• Promoters typically located immediately upstream from the site where the RNA polymerase initiates transcription
• Most promoters contain TATA box, where RNA polymerase will be bound
• Binding of eukaryotic RNA polymerases require additional protein factors to bind efficiently to the promoter
• At least six nuclear proteins called basal transcription factors have been shown to be necessary for the proper initiation of transcription by RNA polymerase II
• Enhancers


  DNA sequences that can activate the utilization of a promoter, controlling the efficiency and rate of transcription from that particular promoter
• Enhancers can activate only cis-linked promoters (i.e., promoters on the same chromosome) but they can do so at great distances (some as great as 50 kilobases away from the promoter)
• Enhancers function by binding specific regulatory proteins called transcription factors
• Different types of genes normally have different enhancers
• Researchers use reporter genes like GFP to investigate whether a particular enhancer is functioning
• Importance of enhancers for differential gene expression

  • Most genes require enhancers for their transcription
  • Enhancers are the major determinant of differential transcription in space (cell type) and time
  • The ability of an enhancer to function while far from the promoter means that there can be multiple signals to determine whether a given gene is transcribed
  • Enhancers can also be used to inhibit transcription
• Transcription factors


  Proteins that bind DNA with precise sequence recognition for specific promoters, enhancers, or silencers
• Most transcription factors can bind to specific DNA sequences
• Transcription factors within such a family share a common framework structure in their DNA-binding sites
• Slight differences in the amino acids at the binding site can alter the sequence of the DNA to which the factor binds
• How transcription factors that bind enhancers can activate a gene

  • Recruiting enzymes (such as histone acetyltransferases) that break up the nucleosomes in the area
  • Stabilizing the transcription initiation
• Three major domains of transcription factors

  • DNA-binding domain
  • Trans-activating domain
  • Protein-protein interaction domain
• Combinatorial association


  Combination of transcription factors to regulate a gene
• The pancreas-specific enhancer of the Pax6 gene has binding sites for the Pbx1 and Meis transcription factors. Both need to be present for the enhancer to activate Pax6 in the pancreas cells
• Silencers


  Sequences that causes a decrease in gene activity
• The fetal mouse liver makes serum albumin, but only after a certain stage of gut development. Contact between the endodermal tube and cardiac mesoderm releases a transcription factor bound to a silencer region in the serum albumin gene
• DNA methylation


  The promoters of inactive genes become methylated at certain cytosine residues
• DNA (cytosine-5)-methyltransferase methylates DNA strands
• Methylcytosine stabilizes nucleosomes and prevents transcription factors from binding
• Conversion can occur only when the cytosine residue is followed by a guanosine
• Cytosine methylation appears to be a major mechanism of transcriptional regulation in vertebrates. However, Drosophila, nematodes, and perhaps most invertebrates do not methylate their DNA
• In vertebrates, the presence of methylated cytosines in the promoter of a gene correlates with the repression of transcription from that gene
• In developing human and chick red blood cells, the DNA of the globin promoters is almost completely unmethylated, whereas the same promoters are highly methylated in cells that do not produce globin
• Genomic imprinting


  The ability to mark a gene as coming either from the father or the mother
• DNA methylation determines whether the gene will be active or inactive
• Methylation pattern changes during development
• In certain mutations of mice and humans, a severe or lethal condition arises if the mutant gene is derived from one parent
• Gene-specific methylation differences can be seen in the chromosomes of embryonic cells which was inherited from both parents
• In mice, the gene for insulin-like growth factor II (Igf-2) on chromosome 7 is active in early embryos only on the chromosome transmitted from the father. The gene (Igf-2r) for a protein that binds this growth factor, located on chromosome 17, is active only in the chromosome transmitted from the mother