Yeast rebuild

The setup

• We can now synthesize relatively long stretches of DNA
• This makes it possible to consider (re-)building small chromosomes from scratch. For example, chromosomes I, III and VI in S. cerevisiae are < 350kb long, and are candidates for being rebuilt

This leads to the $64,000 question: If you were to rebuild a yeast chromosome, what changes would you make to it ?

There are (at least) a couple of different overarching goals that can drive how to answer this question:

• The Science goal: Investigate how chromosomes are currently organized, and the importance of various elements of their organization.
• The Engineering goal: Investigate how to build a chromosome with a particular set of capabilities (independent of the actual genes on the chromosome), like a low overall recombination rate.

In either case, a good place to start is to summarize what's known about large-scale chromosome/genome organization in S. cerevisiae so far.

Chromosome/genome organization in S.cerevisiae

• Genome snapshot at SGD

Essential elements of chromosomes

• Centromeres, origins of replication, telomeres
• A length of at least 55kb for mitotic stability and some control of copy number. (Based on a brief skim of the paper; need to re-read this more carefully) (Murray and Szostak, '83)

Gene order and distribution

• Overall: gene order and distribution isn't random. Good overview paper: Pal and Hurst, '04
• Genes involved in the same metabolic pathway (as defined by KEGG) tend to "cluster" on chromosomes, where "cluster" means "large region of chromosome with high concentration of pathway members, although non-members may also be present". 98% of metabolic pathways in S.cerevisiae exhibit this kind of clustering, after controlling for tandem duplicates (Lee and Sonnhammer, '03)
• Genes that are controlled by the same sequence-specific transcription factor tend to be regularly spaced along chromosome arms. Different periods are observed for different chromosome arms. Regularities are consistent with a genome-wide loop model of chromosomes, in which co-regulated genes dynamically co-localize in 3D. (Kepes, '03)
• Adjacent pairs of genes show correlated expression independent of their origin. Correlated triplets, but not quadruplets, were also found more often than expected by chance. Correlation maps also revealed regularly-spaced groups of correlated genes along chromosomes that might be indicative of higher-order chromosome structure. (Cohen et al, '00)
• Statistically significant fraction of genes coding for subunits of stable complexes are located within 10-30kb of each other. This clustering may ensure better coregulation and maintain the right stoichiometry of complexes upon duplication of chromosomal segments (Teichmann and Veitia, '04)
• Gene orientation (ie whether they’re on the plus or minus strand) can be modeled by a first-order Markov model ie the orientation of a gene depends on the orientation of the gene that precedes it. (Note: Transition probabilities for yeast are pretty close to 0.5 ie close to a random coin-flipping model, but the authors claim that the coin-flip model is statistically improbable; I can’t really judge their statistics, but I still don’t put much trust into this model.) (Simons and Morton, '03)
• Essential genes in yeast are clustered, independent of co-expression and tandem duplication. Clusters of essential genes are in regions of low recombination and larger clusters have lower recombination rates. (Pal and Hurst, '03)
• There is negative correlation between chromosome length and G+C content at (silent) third codon positions (GC3s) of ORFS. Chromosome III is abnormal in that it has strong clustering of GC3s; could be because it contains mating-type loci, so there’s selective pressure to keep mating-type switching an intrachromosomal reaction and thus to keep most of the chromosome (between HML and HMR) intact, leading to less structural disruption than other chromosomes (which preserves existing clusters ?) (Bradnam et al, '99)

Recombination frequency

• There are hot- and coldspots of meiotic recombination in S.cerevisiae. Each chromosome has hotspots & coldspots; hotspots tend to cluster around regions with high G+C content whereas coldspots are nonrandomly associated with centromeres and telomeres. Hotspots are also enriched near genes involved in metabolic pathways and ionic homeostasis; coldspots were over-represented near ORFs involved in transport facilitation and intracellular transport. Some types of hotspots require transcription factor binding in order to become active. Hotspots tend to be in intergenic regions. (Gerton et al, '00)

Transcription factor binding sites

• Paper with lots o' data: Harbison et al, '04
• Lots of high-scoring transcription factor binding sites in ORFs, some of which are actually bound to in vivo (but with lower average binding strength than sites in intergenic regions). (My 7.90 class project)