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Biology for AP® Courses

16.5 Eukaryotic Post-transcriptional Gene Regulation

Biology for AP® Courses16.5 Eukaryotic Post-transcriptional Gene Regulation

Learning Objectives

In this section, you will explore the following question:

  • How is gene expression controlled through post-transcriptional modifications of RNA molecules?

Connection for AP® Courses

Post-transcriptional regulation can occur at any stage after transcription. One important post-transcriptional mechanism is RNA splicing. After RNA is transcribed, it is often modified to create a mature RNA that is ready to be translated. As we studied in previous chapters, processing messenger RNA involves the removal of introns that do not code for protein. Spliceosomes remove the introns and ligate the exons together, often in different sequences than their original order on the newly transcribed (immature) messenger RNA. A GTP cap is added to the 5’-end and a poly-A tail is added to the 3’-end. This mature messenger RNA then leaves the nucleus and enters the cytoplasm. Once in the cytoplasm, the length of time the messenger RNA resides there before being degraded—a characteristic lifespan or “shelf-life” of the molecule called RNA stability—can be altered to control the amount of protein that is synthesized. RNA stability is controlled by several factors, including microRNAs (miRNA or RNAi, RNA interference); miRNAs always decrease stability and promote decay of messenger RNA.

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP® Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP® Biology course, an inquiry-based laboratory experience, instructional activities, and AP® exam questions. A learning objective merges required content with one or more of the seven science practices.

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes.
Enduring Understanding 3.A Heritable information provides for continuity of life.
Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information.
Science Practice 6.5 The student can evaluate alternative scientific explanations.
Learning Objective 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, RNA are the primary source of heritable information.
Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information.
Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models.
Learning Objective 3.6 The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression.

Teacher Support

Introduce mRNA modifications using videos such as this one about 5'caps and 3'poly-A tails.

Students may not realize that splicing occurs with variation, not all introns are excised in exactly the same way all of the time. Differential splicing produces different protein products. This one introduces RNA splicing.

RNA is transcribed, but must be processed into a mature form before translation can begin. This processing after an RNA molecule has been transcribed, but before it is translated into a protein, is called post-transcriptional modification. As with the epigenetic and transcriptional stages of processing, this post-transcriptional step can also be regulated to control gene expression in the cell. If the RNA is not processed, shuttled, or translated, then no protein will be synthesized.

RNA Splicing, the First Stage of Post-transcriptional Control

In eukaryotic cells, the RNA transcript often contains regions, called introns, that are removed prior to translation. The regions of RNA that code for protein are called exons (Figure 16.11). After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by splicing.

A pre-mRNA has four exons separated by three introns. The pre-mRNA can be alternatively spliced to create two different proteins, each with three exons. One protein contains exons one, two, and three. The other protein contains exons one, three and four.
Figure 16.11 Pre-mRNA can be alternatively spliced to create different proteins.

Evolution Connection

Alternative RNA Splicing

In the 1970s, genes were first observed that exhibited alternative RNA splicing. Alternative RNA splicing is a mechanism that allows different protein products to be produced from one gene when different combinations of introns, and sometimes exons, are removed from the transcript (Figure 16.12). This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation, with the frequency of different splicing alternatives controlled by the cell as a way to control the production of different protein products in different cells or at different stages of development. Alternative splicing is now understood to be a common mechanism of gene regulation in eukaryotes; according to one estimate, 70 percent of genes in humans are expressed as multiple proteins through alternative splicing.

Diagram shows five methods of alternative splicing of pre-mRNA. When exon skipping occurs, an exon is spliced out in one mature mRNA product and retained in another. When mutually exclusive exons are present in the pre-mRNA, only one is retained in the mature mRNA. When an alternative 5’ donor site is present, the location of the 5’ splice site is variable. When an alternative 3’ acceptor site is present, the location of the 3’ splice site is variable. Intron retention results in an intron being retained in one mature mRNA and spliced out in another.
Figure 16.12 There are five basic modes of alternative splicing.
Does alternative gene splicing increase or decrease the flexibility of gene expression? Explain your answer.
  1. Flexibility increases because mRNA can be altered after transcription is completed.
  2. Flexibility increases because genes can be divided and recombined into new genes.
  3. Flexibility decreases because the mRNA molecule becomes smaller.
  4. Flexibility decreases because DNA is degraded during alternative splicing.

Link to Learning

Visualize how mRNA splicing happens by watching the process in action in this video.

Refer to [link]
Several human diseases are caused by an error in mRNA splicing. Explain why this occurs.
  1. Once an mRNA is spliced, the original mRNA cannot be created again.
  2. Spliced RNA cannot produce proper proteins.
  3. Splicing does not occur at all.
  4. Splicing occurs in the wrong location on mRNA.

Science Practice Connection for AP® Courses

Think About It

What is an evolutionary advantage of alternative gene splicing of introns during post-transcriptional modification of mRNA?

Teacher Support

The question is an application of Learning Objective 3.1 and Science Practice 6.5 and Learning Objective 3.6 and Science Practice 6.4 because students are asked to explain how alternative spicing, i.e., the rearranging on introns following transcription, affects the product(s) produced and why this splicing provides evolutionary advantage(s).


Alternative splicing has many advantages including higher efficiency, because one DNA sequence (one gene) can code for a number of different proteins. It also allows for evolutionary flexibility: different protein isoforms with different functions can be formed through alternative splicing.

Control of RNA Stability

Before the mRNA leaves the nucleus, it is given two protective "caps" that prevent the end of the strand from degrading during its journey. The 5' cap, which is placed on the 5' end of the mRNA, is usually composed of a methylated guanosine triphosphate molecule (GTP). The poly-A tail, which is attached to the 3' end, is usually composed of a series of adenine nucleotides. Once the RNA is transported to the cytoplasm, the length of time that the RNA resides there can be controlled. Each RNA molecule has a defined lifespan and decays at a specific rate. This rate of decay can influence how much protein is in the cell. If the decay rate is increased, the RNA will not exist in the cytoplasm as long, shortening the time for translation to occur. Conversely, if the rate of decay is decreased, the RNA molecule will reside in the cytoplasm longer and more protein can be translated. This rate of decay is referred to as the RNA stability. If the RNA is stable, it will be detected for longer periods of time in the cytoplasm.

Binding of proteins to the RNA can influence its stability. Proteins, called RNA-binding proteins, or RBPs, can bind to the regions of the RNA just upstream or downstream of the protein-coding region. These regions in the RNA that are not translated into protein are called the untranslated regions, or UTRs. They are not introns (those have been removed in the nucleus). Rather, these are regions that regulate mRNA localization, stability, and protein translation. The region just before the protein-coding region is called the 5' UTR, whereas the region after the coding region is called the 3' UTR (Figure 16.13). The binding of RBPs to these regions can increase or decrease the stability of an RNA molecule, depending on the specific RBP that binds.

In the mature RNA molecule, exons are spliced together between the 5' and 3' untranslated regions. A 5' cap is attached to the 5' untranslated region, and a poly-A tail is attached to the 3' untranslated region. RNA-binding proteins associate with the 5' and 3' untranslated regions.
Figure 16.13 The protein-coding region of mRNA is flanked by 5' and 3' untranslated regions (UTRs). The presence of RNA-binding proteins at the 5' or 3' UTR influences the stability of the RNA molecule.

RNA Stability and microRNAs

In addition to RBPs that bind to and control (increase or decrease) RNA stability, other elements called microRNAs can bind to the RNA molecule. These microRNAs, or miRNAs, are short RNA molecules that are only 21–24 nucleotides in length. The miRNAs are made in the nucleus as longer pre-miRNAs. These pre-miRNAs are chopped into mature miRNAs by a protein called dicer. Like transcription factors and RBPs, mature miRNAs recognize a specific sequence and bind to the RNA; however, miRNAs also associate with a ribonucleoprotein complex called the RNA-induced silencing complex (RISC). RISC binds along with the miRNA to degrade the target mRNA. Together, miRNAs and the RISC complex rapidly destroy the RNA molecule.

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