What does "downstream" refer to in molecular biology?

In molecular biology, "downstream" generally refers to the direction toward the 3' end of a DNA or RNA strand. This terminology is often used to describe the position of genes or regulatory elements in relation to a particular point of reference, such as a transcription start site.

When considering gene expression, the transcription process initiates at the promoter region, located upstream of the gene. As transcription progresses, the RNA polymerase moves along the template DNA strand in the direction of the 3' end, synthesizing RNA in the 5' to 3' direction. Therefore, anything located in the direction that RNA polymerase is heading—toward the 3' end—is considered downstream.

This understanding is crucial when examining gene structure, the arrangement of exons and introns, and the various regulatory elements that can influence gene expression, such as enhancers or silencers, which are often described in terms of their positions relative to the transcription start site.