Evolutionary Genetics and Speciation

Study Notes

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

Description

This quiz covers the processes of chromosomal rearrangements, gene duplication, and divergence that contribute to the formation of new species. It also explores the role of transposable elements in genetic crossover.