A 4-year-old child, on a well-child- check up, is found to have a large flank mass. A computed tomography (CT) scan demonstrates a large mass arising from the kidney, and a subsequent biopsy reveals a diagnosis of Wilm’s tumor. A pediatric oncologist starts chemotherapy containing the transcription inhibitor Actinomycin D. Which of the following statements is correct regarding transcription?
A. Eukaryotes often produce polycistronic mRNA
B. RNA polymerase requires a primer
C. The RNA chain grows in the 3′-5′ direction
D. Rho factor is critical for the initiation of RNA transcription
E. The TATA box contains a consensus sequence for the binding of RNA polymerase
Answer- The correct answer is E.
RNA polymerase binds to specific sequences on DNA, the promoter regions.
Initiation of transcription involves the binding of the RNA polymerase holoenzyme to the promoter region on the DNA to form a preinitiation complex, or PIC. Characteristic “Consensus” nucleotide sequences of the prokaryotic promoter region are highly conserved.
Structure of bacterial prokaryotic promoter region
- Pribnow box
This is a stretch of 6 nucleotides (5′- TATAAT-3′) centered about 8-10 nucleotides to the left of the transcription start site. (Figure-1)
- -35 Sequence
A second consensus nucleotide sequence (5′- TTGACA-3′), is centered about 35 bases to the left of the transcription start site.
Figure-1- Bacterial promoters share two regions of highly conserved nucleotide sequence. These regions are located 35 and 10 bp upstream (in the 5′ direction of the coding strand) from the start site of transcription, which is indicated as +1. By convention, all nucleotides upstream of the transcription initiation site (at +1) are numbered in a negative sense and are referred to as 5′-flanking sequences. Also by convention, the DNA regulatory sequence elements (TATA box, etc) are described in the 5′ to 3′ direction and as being on the coding strand. These elements function only in double-stranded DNA.
- Eukaryotic promoters are more complex.
- Two types of sequence elements are promoter-proximal and distal regulatory elements.
- There are two elements in promoter proximal ,One of these defines where transcription is to commence along the DNA, and the other contributes to the mechanisms that control how frequently this event is to occur.(Figure-2)
- Most mammalian genes have a TATA box that is usually located 25–30 bp upstream from the transcription start site.
- The consensus sequence for a TATA box is TATAAA, though numerous variations have been characterized.
- Sequences farther upstream from the start site determine how frequently the transcription event occurs.
- Typical of these DNA elements are the GC and CAAT boxes, (Figure-2) so named because of the DNA sequences involved.
- Each of these boxes binds a specific protein.
- Distal regulatory elements enhance or decrease the rate of transcription.
- They include the enhancer/ silencer regions and other regulatory elements
Figure-2- A gene can be divided into its coding and regulatory regions, as defined by the transcription start site (arrow; +1). The coding region contains the DNA sequence that is transcribed into mRNA, which is ultimately translated into protein. The regulatory region consists of two classes of elements. One class is responsible for ensuring basal expression. These elements generally have two components. The proximal component, generally the TATA box or Inr or DPE elements direct RNA polymerase II to the correct site (fidelity). In TATA-less promoters, an initiator (Inr) element that spans the initiation site (+1) may direct the polymerase to this site. Another component, the upstream elements, specifies the frequency of initiation. The distal regulatory elements consist of enhancers and repressors and other regulatory regions .Enhancers and repressors enhance or repress expression and mediate the response to various signals, including hormones, heat shock, heavy metals, and chemicals.
As regards other options
- Prokaryotes often produce polycistronic mRNA, eukaryotic RNAs are mono cistronic.
- RNA polymerase does not require a primer, it can initiate chain synthesis.
- The RNA chain grows in the 5′-3′direction same as DNA chain
- Rho factor is critical for the termination of RNA transcription especially in prokaryotes.
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