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When transcription factors attach to the DNA strand - How do they know in which direction they have to initialize the transcription by rna polymerase? Is it always read in the same direction anyway? What about those 'promoters'? Do they influence the transcription direction?

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Do you mean by direction which of the two DNA strands is transcribed? Or do you mean whether the polymerase goes from 5' to 3', or from 3' to 5' on a single strand? –  Mad Scientist Apr 22 at 16:12
@MadScientist Although the first question is also interesting, the second one is the one which I am interested in at the moment. –  Sprechblaseningenieur Apr 22 at 18:45

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Transcription always proceeds in the direction 5' (5-prime) to 3' (3-prime) on the coding strand of DNA. Binding of both transcription factors and RNA polymerase to DNA depends on sequence motifs in the DNA. Transcription always happens in the same direction with respect to the chemical structure of the coding DNA strand, while the transcription direction with respect to the structure of the chromosome depends on which strand the coding sequence is found on (and thus which strand is defined as the coding strand for that gene).

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Just to clarify, RNAP moves relative to the template strand from 3' to 5'. The transcript is polymerized from 5' to 3' and has the same sequence as the coding strand (except U instead of T). –  canadianer Apr 22 at 18:52
Thanks, good point. The whole process is described, with figures, in an NCBI online book here: ncbi.nlm.nih.gov/books/NBK22085 –  jarlemag Apr 22 at 19:10
dudes! thanks! that helped a lot!!! –  Sprechblaseningenieur Apr 22 at 19:50
Glad to hear that. You can also communicate that an answer is useful by clicking the checkmark next to the answer, "accepting" it. –  jarlemag Apr 23 at 0:11
I don't think transcription always goes $5' \rightarrow 3'$ wrt to coding strand. See en.wikipedia.org/wiki/… –  Superbest Jun 20 at 11:49

Transcription always proceeds 5'-3' direction using 3'-5' template strand (antisense/bottom strand). RNAP requires 3'OH on rNTP (purines = A, G, pyrimidines = U, C) to be present to catalyse primer-less RNA polymerisation. RNAP uses 3 aspartate residues in the active site which complex with 2 Mg2+ ions to coordinate rNTP for catalysis by nucleophilic attack of 3'OH on incoming rNTP 5'triphosphate tail (RNA backbone extension) and pyrophosphate binding and release (-ve charged binds to Mg). Bacterial (archeael and eukaryotic) RNAP is now know to have many active sites fit for many purposes, e.g. Trigger loop for extension and GreA for backtracking (5'-3' translocation to remove mismatches/dmged nts).

TFs typically bind to either proximal or distant transcription enhancers (UAS in eukaryotes, via a DNA binding domain). Distant UAS elements can be 1-10 kb away from ORF, inverted and generally orientation free. TF binding creates a DNA loop which brings TF's acidic residues (activation domain) closer to core promoter to stimulate general TF assembly (GTFs) which will recognise core promoter (TFIIH), recruit RNAP to promoter (TFIIB), melt promoter DNA (TFIIH XPB helicase) and initiate transcription. TF binding also acts on mediator complex which is bound to RNAP CTD. Mediator phosphorylates RNAP CTD allowing for transcription initiation to take place after GTFs assembly.

Take home message = TF has 2 domains, DNA binding and Activation which does various stuff

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