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?
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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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