Question

When a gene a segment of chromosome is drawn, displaying genes and regulatory regions you will often see an arrow indicating where transcription starts. The arrow faces the direction of transcription. Sometimes these diagrams are also labelled with nucleotide numbers +1 is the first transcribed base, +100 is the hundredth transcribed base, and so on. See Figure 12.9 here for an example. Areas outside of the gene can also be labelled (again, see Figure 12.9 here).

A recent study identified a potential enhancer region at about -44 000 relative to the transcriptional start site of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Is the enhancer region upstream or downstream of the CFTR gene? Hint: look at Figure 12.9 linked above.

Other potential enhancer regions have been identified within the introns of the CFTR gene itself. Would these regulatory regions (the ones in the introns) be upstream or downstream of the transcriptional start site?

Answer 1

Here in the first part it is given that the enhancer region is at -44000th position, it is upstream to the transcription start site. This is because the ' -'  sgn s for the base present before the transcription start site( upstream) nd the '+' sign is for those bases located after the transcription start site (downstream). +1 always will indicate the first transcribed base and -1 for the base just before transcription start site. Thus the -44000th position of enhancer region will be upstream to the transcription start site.

The second regulatory region is insde the intron of CFTR gene itself. Introns are the nucleotide sequences within the transcribed RNA which are removed during RNA splicing. Since the introns are the portions inside the transcribed mRNA, the second regulatory gene will be downstream to the transcription start site.