•  The genome is shaped by mutation and evolution"

•  Lots of things in genomes - what do we find:"– Genes/pseudogenes"– Telomeres"– Centromeres"– Nucleolar organizer regions"– Origins of replication"– Repeats"

Genome Structure

Pseudogenes •  Genes that have lost their expression or ability to code

protein – become non-functional"•  Occurs through mutation – often a frameshift or stop

codon mutation"•  Frequent: 0.7%

of the human genome consists of pseudogenes, similar to the % of functional genes"

•  63% of the ~900 olfactory genes in humans are pseudogenes!"

Human pseudogenes

Origin of pseudogenes •  Most pseudogenes come from one of two

routes:"•  Duplicated pseudogenes"•  Processed pseudogenes"

Duplicated pseudogenes

Processed pseudogenes

Organisation of the centromere

•  In yeast the organisation is simple, and sequence dependent"

•  Organisation becomes more complex with more organismal complexity"

•  Most organisms have monocentric centromeres, while some, such as C. elegans, have holocentric centromeres"

•  A conserved protein binds to the centromeres in all cases"

Detailed centromere organisation

Fukagawa, 2004. Experimental Cell Research 296:21-27

•  Centromeres in most species are characterised by repeats"

•  Area surrounding centromeres is heterochromatic"

•  Kinetochore is assembled at the central part of the centromere"

•  Telomeres:"– structures at the

end of chromosomes"

– protect the ends of chromosomes from damage and degradation"

–  form the same structure on both ends of all chromosomes"

Telomeres

Telomere structure •  Telomeres consist of three parts: the 3’ overhang; a

stretch of telomeric repeats; and a large stretch of longer, subtelomeric repeats"

•  The 3’ overhang slips into the DNA helix, into another repeat, making a small bubble; the D-loop"

Telomeric cap structure

•  The D-loop protects the 3’ overhang; otherwise it would be sensed as a double-strand break"

•  This whole loop of telomeric DNA is called the “T-loop”"

Nucleolus Organizer Region (NORs)

•  Form secondary constrictions on chromosomes

•  Are the chromosomal regions that nucleoli form around

• Consist of rDNA and flanking regions

rDNA structure

•  A single repeat unit of the rDNA typically contains the 18S, 5.8S, and 28S ribosomal RNA subunits"

•  They have 3 spacers between these genes: internal transcribed spacers 1 and 2 (ITS1 and 2), and the intergenic spacer (IGS) "

•  The genes (and ITS1/2) are all transcribed together from a single promoter, much like a bacterial operon"

Yeast = ~200 copies/1 chromosome"Human = ~500 copies/5 chromosomes"

rDNA Organisation

•  The rDNA is organised into head-to-tail tandem repeats"

•  These can be present on one or more chromosomes"

•  Total rDNA copy number varies dramatically: from around 30 repeats in many fungi, to 10,000 repeats or more in many plants"

Sequence Alignment

Comparative Genomics

Orthology vs Paralogy

•  Conserved synteny: conservation of gene order on chromosomes"

•  Decreases with increasing evolutionary distance"

Conserved Synteny

http://compbio.mit.edu/yeast.html

Conserved Synteny - in blocks

Mouse chromosomes"

Human chromosomes"

Whole Genome Duplication !“The existence of two or more genes encoding proteins with identical or very similar sequences (redundancy) provides the raw material for the evolution of novel functions. Understanding the true nature of redundancy is one of the major challenges in the quest to elucidate the biological role of every gene in the S. cerevisiae genome”!

•  Reason for this high level of redundancy is a duplication of the entire yeast genome in a recent ancestor of S. cerevisiae!!"

•  Found by comparison with Ashbya gossypii, a relative of S. cerevisiae that does not have the whole genome duplication"

Whole Genome Duplication

Dietrich et al., 2004, Science 304: 304-307

Ohnologs •  Whole genome duplications result in most

genes being duplicated"•  This special case of gene duplicates/paralogs

are called “ohnologs”"•  Proposed that ohnologs, freed from the

necessity to perform their primary function, are more able to evolve new functions"

•  Therefore, ohnologs and whole genome duplications are proposed to fuel evolutionary innovation"

Vertebrate ultraconserved elements • Ultraconserved elements are sequences

that show 100% sequence identity between human, rat, & mouse over more than 200bp

•  They are surprising: even the most conserved genes do not show this level of conservation

•  They are non-coding - do not code for proteins

•  Tend to be near developmental genes, and seem to have mostly arisen in the amniotes

•  Act as enhancers of gene expression that stimulate expression by interacting with the promoter"

•  Show tissue-specific patterns of enhancer activity in a mouse assay"

•  Many drive gene expression specifically in the brain"

Enhancer activity of ultraconserved elements

Pennacchio et al, 2006. Nature 444: 499-

•  Codon bias: some codons are preferred over others"

•  Different organisms have different codon biases"

•  Why?"•  One idea is it so

that more common tRNA genes are used"

Codon Bias

Lin et al., 2006, PNAS 103: 14412-14416

Codon Bias

Coghlan & Wolfe, 2000, Yeast 16: 1131-1145

•  Codon bias correlates with gene expression level"