Transcription from DNA to RNA
Bacteria, archaea, and eukaryotes must all transcribe genes from their genomes. While the cellular location may be different (eukaryotes perform transcription in the nucleus; bacteria and archaea perform transcription in the cytoplasm), the mechanisms by which organisms from each of these clades carry out this process are
A short overview of transcription
Listing some basic requirements for transcription
Let us first consider the tasks at hand by using some of our foundational knowledge and imagining what might need to happen during transcription if the goal is to make an RNA copy of a piece of one strand of a double-stranded DNA molecule. We'll see that using some basic logic allows us to infer many of the important questions and things that we need to know
Let us imagine that we want to design a
• Where should the machine start? Along the millions to billions of base pairs, where should the machine
• Where should the machine stop?
• If we have start and stop sites, we will need ways of encoding that information so that our machine
• How many RNA copies of the DNA will we need to make?
• How fast do the RNA copies need to
• How accurately do the copies need to
• How much energy will the process take and where is the energy going to come from?
These are only some core questions. One can dig deeper if they wish. However, these are already good enough for us to get a good feel for this process. Notice, too, that many of these questions are remarkably similar to those we inferred might be necessary to understand DNA replication.
The building blocks of transcription
The building blocks of RNA
Recall from our discussion on the structure of nucleotides that the building blocks of RNA are very similar to those in DNA. In RNA, the building blocks comprise nucleotide triphosphates that
Figure 1. The basic chemical components of nucleotides.
Proteins responsible for creating an RNA copy of a specific piece of DNA (transcription) must first be able to recognize the beginning of the element to
Figure 2. (a) A general diagram of a gene. The gene includes the promoter sequence, an untranslated region (UTR), and the coding sequence. (
Bacterial vs. eukaryotic promoters
In bacterial cells, the -10 consensus sequence, called the -10 region, is AT rich, often TATAAT. The -35 sequence, TTGACA,
Eukaryotic promoters are much larger and more complex than prokaryotic promoters, but both have an AT-rich region—in eukaryotes, it
Instead of a single bacterial polymerase, the genomes of most eukaryotes encode three different RNA polymerases, each made up of ten protein subunits or more. Each eukaryotic polymerase also requires a distinct set of proteins known as transcription factors to recruit it to a promoter. In addition, an army of other transcription factors, proteins known as enhancers, and silencers help to regulate the synthesis of RNA from each promoter. Enhancers and silencers affect the efficiency of transcription but are
The initiation of transcription begins with the binding of RNA polymerase to the promoter. Transcription requires the DNA double helix
Transcription always proceeds from the template strand, one of the two strands of the double-stranded DNA. The RNA product is complementary to the template strand and is almost identical to the
Figure 4. During elongation, RNA polymerase tracks along the DNA template, synthesizing
Bacterial vs. eukaryotic elongation
In bacteria, elongation begins with the release of the
In eukaryotes, following the formation of the preinitiation complex, the polymerase
Possible NB Discussion Point
Compare and contrast the energy story for DNA replication initiation + elongation to the energy story for transcription initiation + elongation.
Once a gene
The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA polymerase II in eukaryotes takes place
Termination of transcription in the archaea is far less studied than in the other two domains of life and
In bacteria and archaea
In bacteria and archaea, transcription occurs in the
In eukaryotes, the process of transcription
5' G-cap and 3' poly-A tail
Possible NB Discussion Point
Transcriptomics is a branch of “-omics” that involves studying an organism or population’s transcriptome or, the complete set of all RNA molecules. What kind of information can you obtain from studying the transcriptome(s)? Can you think of any cool scientific questions that a transcriptomic analysis might help resolve? What are some constraints to transcriptomic approaches one might keep in mind when conducting analyses?
Splicing occurs on most eukaryotic