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if it's the former, then it could be that we still get expression of different genes on each chromosome due to different ways of packaging (e.g. having heterochromatin at different places). if it's the latter, when one extracts it (using a standard kit) does it come out as one long string or as 46 smaller ones?

thanks for your answer!
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Here is some really good information

http://www.ncbi.nlm.nih.gov/books/NBK26834/

Even though the chromosomes are seperate strands of DNA, there is evidence that a gene on one chromosome can interact with a gene on another chromosome.

http://www.ncbi.nlm.nih.gov/pubmed/18265379

Regulation of gene expression is highly complex and changes dramatically based on cell conditions.  I am not sure if this answers your question completely but hopefully it helps.
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