AP Syllabus focus:
‘RNA polymerase and transcription factors bind promoter or enhancer DNA sequences, which may lie upstream or downstream, to initiate transcription.’
Gene expression begins when a cell decides to transcribe a gene. This decision depends on specific DNA sequences and proteins that recruit RNA polymerase to the correct start site and set the rate of transcription.
Core Idea: DNA Elements Recruit the Transcription Machinery
Transcription initiation depends on interactions between cis-regulatory DNA sequences (on the same DNA molecule as the gene) and trans-acting proteins (diffusible regulatory proteins).
Promoters
A promoter is the primary “docking site” that positions the transcription machinery at the start of a gene.
This diagram shows a generalized RNA polymerase II promoter with basal transcription factors assembling on promoter DNA before RNA polymerase II binds. It visually emphasizes that promoter recognition and transcription-factor binding are prerequisites for correctly positioning the polymerase at the transcription start region. Source
Promoter: A DNA sequence near a gene where RNA polymerase and associated proteins bind to begin transcription and determine which DNA strand is used as the template.
Key promoter features to know for AP Biology:
Promoters are typically located upstream (5') of the transcription start site, but the key idea is that they are near the gene and define where initiation occurs.
Promoters help determine:
Start point of RNA synthesis
Directionality (which strand is transcribed)
Basal (default) transcription rate in the absence of additional regulatory inputs
Enhancers
An enhancer is a regulatory DNA sequence that can increase transcription by helping assemble or stabilise the transcription machinery at the promoter.
Enhancer: A DNA sequence that binds regulatory proteins to increase transcription, often functioning even when located far from the promoter, either upstream or downstream of the gene.
Important enhancer properties:
Enhancers can be located:
Upstream, downstream, or within noncoding regions associated with a gene
Enhancers work by binding specific regulatory proteins that communicate with the promoter, commonly through DNA looping that brings distant sequences into proximity.
This figure depicts an enhancer bound by activators interacting with promoter-bound transcription machinery through DNA bending/looping. It highlights how mediator and transcription factors help transmit regulatory information from a distant enhancer to RNA polymerase at the promoter, increasing transcription initiation. Source
Proteins That Bind Promoters and Enhancers
Transcription Factors
Transcription factors are proteins that bind specific DNA sequences and influence transcription initiation.
Transcription factor: A regulatory protein that binds DNA (often at a promoter or enhancer) and increases or decreases transcription by affecting RNA polymerase recruitment and activity.
Functional categories commonly discussed:
General transcription factors: required for transcription initiation at many genes; help RNA polymerase bind and start correctly.
Specific transcription factors (activators): bind enhancers (or other regulatory DNA) and raise transcription rates for particular genes in particular cell contexts.
RNA Polymerase at the Start Site
RNA polymerase is the enzyme that synthesizes RNA. Initiation requires correct positioning and assembly with transcription factors at regulatory DNA.
Binding at the promoter helps RNA polymerase locate the correct gene and start site.
Binding of transcription factors at enhancers can increase the probability that RNA polymerase successfully initiates transcription.
How Transcription Initiation Happens (Conceptual Steps)
Transcription initiation is best understood as an ordered set of binding and assembly events.
Building the Initiation Complex
A simplified sequence of events:
Promoter recognition: general transcription factors bind promoter DNA.
RNA polymerase recruitment: RNA polymerase associates with the promoter via protein–DNA and protein–protein interactions.
Enhancer activation (when present):
specific transcription factors bind enhancer DNA
DNA bends/loops so enhancer-bound factors interact with promoter-bound factors
Transcription begins: once assembled and positioned, RNA polymerase starts RNA synthesis at/near the start site.
Why “Upstream or Downstream” Matters
The syllabus emphasises that regulatory sequences may lie upstream or downstream:
Promoters are typically near the start site and set the initiation location.
Enhancers can regulate from variable positions, reflecting that transcription control depends on 3D DNA–protein interactions, not just linear DNA distance.
FAQ
Often, yes: many enhancers are relatively orientation-independent because what matters is transcription factor binding and 3D contact with the promoter.
However, orientation effects can occur for some regulatory elements depending on binding-site arrangement.
A transcription factor regulates genes that contain its compatible DNA binding motif within promoters/enhancers.
Cell type also matters because cofactors and chromatin accessibility influence whether binding leads to initiation.
Common approaches include:
Reporter gene assays (candidate DNA drives a measurable output)
Targeted mutagenesis of binding sites to see changes in transcription
Protein–DNA binding assays to confirm which factors bind the sequence
Differences in the number, location, and combination of enhancer elements can change how strongly activators recruit/stabilise transcription initiation.
Promoter “strength” and competition for limited transcription factors can also contribute.
Genome organisation can restrict enhancer reach through:
Physical separation into regulatory neighbourhoods
Insulator DNA elements that reduce cross-talk
Promoter compatibility, where only certain promoters respond to particular enhancer-bound complexes
Practice Questions
State what binds to (i) promoters and (ii) enhancers to initiate transcription. (2 marks)
(i) RNA polymerase binds at the promoter (1)
(ii) Transcription factors (regulatory proteins/activators) bind at enhancers (1)
Explain how enhancers can increase the rate of transcription initiation even when located downstream of a gene. (5 marks)
Enhancers are DNA sequences that bind specific transcription factors (1)
Enhancers may be upstream or downstream of the gene (1)
DNA can form a loop bringing enhancer-bound proteins near the promoter (1)
Enhancer-bound factors interact with promoter-bound factors and/or RNA polymerase via protein–protein interactions (1)
This increases recruitment/stability/probability of initiation by RNA polymerase, raising transcription rate (1)
