Gene expression is controlled after transcription primarily through alternative splicing of the gene after the 5′ cap and 3′ poly-A tail have been added.
The difference between a person's muscle cell and nerve cell is not the DNA contained within each cell. Both cells have the exact same DNA, yet the cells have different shapes and carry out different functions. This is possible because of gene expression—controlling which genes are transcribed and translated in each cell. Transcription is the formation of RNA from the template DNA strand to be used to build proteins. mRNA is an RNA molecule made from a DNA template containing a complementary gene sequence. Translation is the assembly of amino acids into proteins in the ribosomes through the reading of mRNA by tRNA and the ribosome. tRNA is the molecule that carries each amino acid to the mRNA strand during translation. mRNA brings the genetic information from DNA to the ribosome, the organelle which binds both mRNA and tRNA to synthesize proteins. Most RNA molecules are translated into proteins; however, there are instances where some RNA transcripts are created from a DNA template strand and serve a biological role, such as the formation of new RNA molecules.
A common misconception is that one gene always gives rise to one protein and thus one trait. The reality is far more complex. Genes contain both exons—regions that code for proteins—and introns—regions that do not code for proteins. When the initial mRNA message is transcribed, all of the exons and introns are transcribed. Posttranscriptional controls are then applied to make the specific message the cell needs. A posttranscriptional control is a modification to the mRNA applied after transcription.
The first posttranscriptional control applied to all mRNA transcripts is a cap of the 5′ end, where 5 refers to the carbon position in the deoxyribose sugar of DNA. DNA nucleotides include cytosine, thymine, adenine, and guanine. This cap is a nucleotide of DNA called guanosine (G) with a methyl group attached. The cap prevents degradation of the mRNA strand.
The second posttranscriptional control is polyadenylation—which includes the addition of a chain of adenine (A) nucleotides to a specific location in the deoxyribose sugar of the DNA's backbone, called the 3′ end, where 3 refers to the carbon position in the deoxyribose sugar of DNA—of the mRNA transcript. This chain is called a poly-A tail.
Capping and Polyadenylation
Finally, the primary mRNA transcript undergoes RNA splicing. In this process, the introns are excised from the transcript and selected exons are spliced together. Because the gene contains multiple exons, a variety of final mRNAs can be spliced from a single gene.
Many RNAs made in this manner will go on to be translated into proteins. However, not all of them will do so. A noncoding RNA (ncRNA) that serves to regulate gene expression is a functional RNA. Functional RNAs are divided into two types: short ncRNAs and long ncRNAs.
Short ncRNAs typically regulate gene expression by inhibiting transcription or translation. The smallest of these is microRNA (miRNA), a short ncRNA of about 17–25 nucleotides that binds to a specific mRNA and causes degradation or blocks translation of the mRNA. miRNAs are specific to particular mRNA sequences and bind only in certain conditions—for example, to switch off the proteins that form the placenta once the placenta has been fully formed. Within the nucleus, precursor miRNA exists in a double-stranded form. It is exported to the cytoplasm, where it becomes single stranded. miRNA functions by binding to a target sequence that is taken up by a protein complex called the RNA-induced silencing complex (RISC), a complex of proteins that cleaves RNA. If the miRNA has high fidelity with the target (it binds many nucleotides), the double-stranded RNA is rapidly degraded. If it has low fidelity (it binds just a few nucleotides), the double-stranded RNA is slowly degraded.
Similar to miRNA is short interfering RNA (siRNA), double-stranded RNA of about 20–25 nucleotides that protects the cell from infection. These siRNAs target foreign RNA, such as those produced by viruses, and bind to it to form a double-stranded RNA molecule. This is taken up by RISC, similarly to miRNA, which regulates genes to protect the cell from infection. By binding the foreign RNA and transporting it to RISC for cleavage, the siRNA molecule sometimes can prevent a viral infection from occurring. The process of silencing RNA via the binding of complementary RNA is called RNA interference (RNAi).
Long ncRNAs are RNAs of 200 or more nucleotides in length. Some of them are thousands or tens of thousands of nucleotides long. They have different modes of action that are not yet well understood. One mechanism is the formation of heterochromatin, regions of the chromosome that are too tightly packed for transcription to occur. For example, one well-studied long ncRNA may drive X-chromosome inactivation, called Barr body formation, by immediately binding with the DNA from which it is transcribed, preventing further transcription of any gene on the chromosome.