mice in research
I hope this kind of helps. I work with mice and human cells right now. The reason that mice work as such good models for humans is because their genetics is so close to ours and they are cheap and easy to maintain(compared to other species that may be more closely related), they reproduce quickly and and with many offspring, inbred strains have been maintained for so many years that you can be pretty certain genetic homogeneity within a strain, they have a lifespan that is short enough to see results in a reasonable amount of time, and they lack many of the ethical issues associated with working with apes.
There is also a lot of history with mice being used as models, so there is already lots of information making it more useful than trying to research on an animal with very little prior information.
Many of our genes are similar to Drosophila or even baker's yeast, some homologous in function as well as sequence. Yet the complexity in these systems is far less than in mammals. For example, Drosophila have one set of genes called the Hox genes while all mammals have four sets of these genes. This occurred because sometime during the evolution of mammals, the genome duplicated twice. I am pretty sure all mammals have four copies of these genes, at least all the ones being studied.
Another reason to use mice is because they can get similar diseases as us. They can get tumors or diabetes which is really helpful in studying disease.
Since our genome is very similar to mice we can create many of the same proteins. There are basic functions that are going to always be the same whether you are a mouse or a human, the cell cycle, respiration, cellular structures, so these are going to act similar if not identically between species. Also our body plans are very similar to mice (as compared to say a nematode, another popular model organism) which means that the genes that help create these body plans are going to be very similar. The major differences are going to be when and where these genes get turned on and off and how much is being expressed and turned into protein. These are the type of things that can be found in a mouse model but always need to be double checked in the human.
I can give you an example. There is a mouse gene called Rb1 or RB1 in humans. It is a cell cycle gene and homologues can be found in many multicellular organisms. It regulates G1/S transition. In humans, there is a hereditary mutation that causes retinoblastoma in babies. I won't go into the details of the genetics but the main point is that it causes cancer in the retina and in the bones later in life. In mice, when you knock out one copy of this gene you don't get in cancer in the eye but rather in the pituitary and the thyroid. SO here is the same gene, the same protein product, (they have virtually identical sequences) but when it is mutated in human it has a different effect than in mice. This is most likely due to the different development of the organs and the different times when this protein is needed. Yet the loss of the protein creates the same effect, excessive proliferation because of an inability to control the cell cycle.
So I hope this gives you a vague idea of why knowing the mouse genome is useful. It is not going to be the answer though because we don't use our genes in the same way, otherwise we'd be mice. Also, I am not sure for what strains of mouse they've sequenced because inbred mice all have little quirks and mutations.
About genes that are expressed or not, well there have been computer programs that search the genomes and find possible open reading frames and lots of these genes are listed as unknowns. You can guess at their function from amino acid sequences but you can never know. Also you can never know if they are being expressed unless you go and check to see if their is mRNA in the cells. Then you don't know if it is becoming protein unlesss you check to see if their is protein in the cell. With multicellular organisms, this means it could be in our liver and nowhere else so looking just in brain cells will tell you nothing. Unfortunately, there is no quick way of knowing which genes are truly coding or not although many large scale studies in yeast have been done just seeing if open reading frames lead to expression. When it comes down to actually saying yes or no, you still have to do it one at a time because even if the protein has the same structure as another it may be phosphorylated in humans and not mice and therefore have a different function.
Alot of the DNA we don't turn into protein has other funtions too. First there are the RNAs, ribosomal, t-RNA, miRNAs. THe first two are for translating proteins while the last seem to be small pieces of RNA that actually regulate genes. Also a lot of DNA contains regulatory regions where proteins can bind and control gene expression. Therefore its still of importance even though its not protein.
Here is a link to all you could possibly want to know about mice genetics. Also this site has links to all different types of organisms used to study genetics.
http://public.ornl.gov/hgmis/external/organism.cfm?organism=Mouse
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