upstream downstream

[youknowwho1]

"cis elements upstream of binding site" what does upstream mean?

[blcr11]

Transcription runs 5' (start) to 3' (end). Anything that sits 5' to the start site is outside the transcribed region but lies "upstream" of the start site. A cis-acting element must act on the same segment of "gene" (it usually is DNA, but it can be RNA) to which it is itself a part of, so a cis-acting upstream element is something (a promoter or enhancer, say) that lies 5' to the transcribed gene, and is involved in the regulation of the gene (occasionally genes, plural) immediately in front of it--that at least covers the most common instances of upstream cis-acting elements.

I was assuming this was a question about transcription. If the "binding site" is something other than a promoter or repressor binding site, then whatever process this is, must have some sense of directionality to it. Upstream would be something "before" the site and downstream would be something "after" the site, if that makes any sense.