Genetics Review Article

I'm writing a review article (for a student journal at the University of Pittsburgh) about how comparisons of the genomes of species, alone, is not necessarily a good indicator of how similar the organisms are (it is good for constructing phylogenies, though).The idea is that portions of the genomes which are different can affect how the similar portions are used. So for instance, we know that chimpanzees and humans share approximately 98.8% of our DNA. Well the 1.2% we don't share may affect the portions we do share in substantial ways. For instance, they may cause alternative-splicing of the primary mRNA transcript from the similar portions.This is also consistent with our new discoveries about genetics, which show that increased complexity does not necessarily mean an increased number of genes.So basically I'm looking for mechanisms which may cause similar portions of genomes to perform different functions in different species.So far, my list includes:1. alternative splicing
2. transcriptional initiation
3. transciptional regulation patternsI would also like to include the following:1. DNA rearrangement
2. post-translational modificationsFirst off, I really don't know what DNA rearrangement is. I've only seen it referred to briefly. Just guessing, I think it is when parts of genes are switched and swapped to produce variation (like how various antibodies are produced). Is this correct?Second, I would like to know if anyone knows of any post-translational modifications that may be species-specific. Even if it may not be species-specific, I would like to know if there are any research articles. I've only found one which is from 1981, which is way too old.Also, any thoughts on the subject or other ideas are welcome.Thanks

Thanks for the response, I always enjoy your posts.

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Perhaps I am just naively confused with the transition from your first to second paragraphs but if genome comparisons are good at reconstructing species phylogenies then are they not good indicators of how similar the component organisms are ipso facto.

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The transition is a bit awkward. I'm supposed to discuss the naive position that "if species share 98.8% of their DNA then the species are 98.8% similar."While DNA similarity is a good indication of how closely related species are, the DNA similarity alone is not a good indicator how similar the species are (so the argument goes). The reason why is that the differing portions of the genome can effect the similar portions.In other words, just because we share 98.8% of our DNA with chimpanzees doesn't mean our gene products or the physiological effects caused by those genes are 98.8% the same. There are alot of papers which show that species diversification can result from species-specific alternative splicing of very similar DNA portions. So, while the nucleotide sequence of an open reading frame may be the same for two species, it does not mean that the products are the same.Similarly, even if we share a lot of the same gene products with a chimpanzee, these gene products can be coordinated through transcriptional regulation to produce a myriad of physiological affects. So in one species they may be coordinated differently than in another species. (maybe coordinated isn't the right word, i'm referring to simultaneous transcripton of particular genes). There is evidence that the increased complexity we see in vertebrates compared to invertebrates is the result of the complex coordination of our genes, and not necessarily an increase in gene products (we do have about double their genes, but most seem to be duplications).Does this make sense?