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How are bidirectional promoters expressed ? (Won't RNA Pol have to go in 3'-5' direction?) Why are they more commonly found in eukaryotes than prokaryotes?

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up vote 4 down vote accepted

Genes controlled by bidirectionl promoters are in head-to-head configurations, meaning that their 5' ends are facing one-another. Remember that DNA is double stranded, so this means one gene is on the 'top' strand and one gene is on the 'bottom' strand. Check out the diagram below, genes are in capitals, bidirectional promoter in parenthesis. Both genes are transcribed 5'->3'

                                         --> Gene 1
 5'-atgcagtcatga(ctgactaagt...tcagtcatga)CTGACTGACTAGTCAT-3'
    |||||||||||| ||||||||||||||||||||||| ||||||||||||||||
 3'-TACGTCAGTACT(gactgattca...agtcagtact)gactgactgatcagta-5'
      Gene 2 <--

As for why they are more commonly found in eukaryotes, those questions are definitely hard to answer. It has been shown that genes on bidirectional promoters are expressed together more often than two genes that are next to each other on different promoters. That means this might be a eukaryotic strategy similar to prokaryote's usage of polycistronic mRNA, an easy way to have similar expression patterns of genes that should often be expressed in similar amounts.

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Do you think one of the reason it is more often found in eukaryotes is because they have longer genes and use of bidirectional promoter would decrease the chances of mistake in expressing downstream genes ? –  biogirl Aug 16 '13 at 7:22
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