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Suppose you are working with an operon in a diploid organism.

I'm looking for either a biochemical or genetic explanation.

What I'm having trouble with mainly is understanding how something would only be able to regulate a gene on one chromosome but not the other. I was thinking cis would be favored because the gene is close by, but everything is just floating around randomly in the cell so it should favor cis either way and level out if you waited long enough.

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  • $\begingroup$ Aside from "just floating around randomly", molecules also change the conformation of DNA and can move along the DNA. Such effects will propagate along the DNA and thus act in cis but not trans. $\endgroup$
    – Armand
    Aug 11 '21 at 5:01
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I was thinking cis would be favored because the gene is close by

Your intuition is correct. Cis-regulatory elements like enhancers are more efficient at enhancing transcription of genes in cis than genes in trans, but trans interactions of cis-regulatory elements do occur. Take a look at figure 2B of this paper and the accompanying text:

... quantitative RT-PCR showed that relative levels of GFP transcripts from constructs inserted at 37B were similar to those from transgenes at 53F, with 1.7% [95% C.I., 1.6–1.8%] of total GFP transcript in eye discs where GMR acts in trans relative to those where activation is in cis ...

The interaction of alleles between homologous chromosomes is called transvection, and this can be realized as binding of the enhancer associated with one allele to the promoter of the other allele. Figure 9 of this paper is a good explanatory graphic.

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