Evolutionary Genetics and Speciation

Gene Targeting and Silencing

• Gene targeting: deletion of a gene by gene targeting can be done in some organisms, such as yeast, mice, and moss
• Gene silencing: discovery of gene silencing using double-stranded RNA, also known as RNA interference (RNAi), and development of gene knockdown using Morpholino oligos

Epigenomics

• Epigenomics: study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome
• Epigenome: record of chemical changes to DNA and histone proteins of an organism that can be passed down to an organism's offspring via transgenerational epigenetic inheritance
• Epigenetic modifications: DNA methylation and histone modifications form the epigenetic code

DNA Methylation Profiling

• Restriction enzyme-based methods: use one or more enzymes that will restrict DNA only if it is unmethylated (e.g. HpaII or NotI) or methylated (e.g. McrBC)
• Bisulfite-conversion based approaches: unmethylated cytosines are converted to uracil, offering single CpG resolution; the gold standard for DNA methylation analysis
• Immunoprecipitation-based methods: use 5-methylcytosine-specific antibodies (MeDIP) or methyl-binding domain proteins to enrich for the methylated (or unmethylated) fraction of the genome

Genome Evolution

• Genome size: varies in size, number of genes, and gene density among organisms
• Sequencing: ~4,300 genomes completely sequenced, with over 9,600 genomes and 370 metagenomes in progress
• Gene density: not correlated with genome size, and varies among domains (bacteria, archaea, eukarya)

Gene Duplication and Divergence

• Gene duplication: contributes to genome evolution, and can lead to the evolution of new gene functions
• Exon duplication and exon shuffling: mechanisms that contribute to genome evolution
• Lysozyme gene duplication: example of gene duplication and divergence, resulting in the evolution of a new gene function (α-lactalbumin)

Comparative Genomics

• Comparative genomics: comparing genome sequences provides clues to evolution and development
• Cladogram or phylogenetic tree: demonstrates the relationships among species
• Human and chimpanzee genomes: differ by 1.2% at single base-pairs and 2.7% because of insertions and deletions
• FOXP2 gene: product turns on genes involved in vocalization, and differs between humans and chimpanzees

Antisense RNA Technology

• Antisense technology: involves the production of complementary nucleic acid molecules against the mRNA molecule to stop the translation into protein
• Antisense oligonucleotides (AON): short length of either RNA or DNA that is complementary to mRNA
• Mechanisms of action: blocking RNA splicing, accelerating degradation of RNA, preventing migration of mRNA from nucleolus to cytoplasm, and stopping translation of diseased protein

MicroRNA (miRNA)

• miRNA: small RNA molecules that regulate gene expression
• miRNA genes: hundreds identified among 73 eukaryotic organisms and 15 viruses
• miRNA gene transcription: most miRNA genes are transcribed by RNA Pol II
• miRNA expression: differential expression among cell types, and contributes to cell proliferation, differentiation, fate determination, and differentiated cell function