In the appropriate cell type and at the correct developmental stage, ribonucleic acid (RNA) polymerase transcribes an RNA copy of a gene, the primary transcript. However, the primary transcript may contain many more nucleotides than are needed to create the intended protein. In addition, the primary transcript is vulnerable to breakdown by RNA-degrading enzymes.
Before the primary transcript can be used to guide protein synthesis, it must be processed into a mature transcript, called messenger RNA (mRNA). This is especially true in eukaryotic cells . Processing events include protection of both ends of the transcript and removal of intervening nonprotein-coding regions.
β-thalassemia, a hemoglobin disease, can be caused by an intron mutation that prevents recognition of a splice site.
On an RNA molecule, the end formed earliest is known as the 5′ (5-prime) end, whereas the trailing end is the 3′ end. The ends of the primary transcript are particularly susceptible to a class of degradative enzymes called exonucleases. During processing, the 5′ end of the primary transcript is protected against the effects of these enzymes by the addition of a CAP. The CAP uses an unusual linkage between nucleotides. Exonucleases do not recognize this unusual structure and therefore cannot remove the CAP. Since exonucleases work only from an end, if the CAP nucleotide cannot be removed, the entire 5′ end of the mRNA is protected. The 5′ CAP also aids in transport out of the nucleus and helps bind the mRNA to the ribosome .
To protect the 3′ end against degradative exonucleases, a poly-A tail is added by poly-A polymerase. Poly-A is a chain of adenine nucleotides, one hundred to two hundred units long. The poly-A tail has typical bonds that are susceptible to degradation by exonucleases, but it does not have any protein coding function so it does not particularly matter if some of the A residues are degraded. It actually takes quite some time for the poly-A tail to be completely lost, and during this time the protein coding portion of the mRNA remains intact. Without the poly-A tail, however, the exonucleases would rapidly degrade into the protein coding portion of the mRNA. An exception to the poly-A strategy is seen in the mRNA for histones, proteins that wrap deoxyribonucleic acid (DNA) into chromosomes. Instead of poly-A, histone mRNA uses a much smaller structure that is regulated by factors present during DNA synthesis.
The most striking event in RNA processing occurs because the protein coding region in eukaryotic genes is not continuous. A typical eukaryotic gene is composed of a number of protein coding regions, called exons, that are separated by noncoding regions called introns. In fact, the number of nucleotides in the introns can be much larger than the number of nucleotides in the combined exons. The DNA gene contains the code for both the exons and the introns, as does the primary RNA transcript, but the noncoding intron sequences must be removed to form the mRNA before protein synthesis.
The process by which introns are removed and exons are joined to one another is called RNA splicing, and it is catalyzed by complexes of proteins and RNA called SNuRPs (small nuclear ribonucleoprotein particles). These complexes locate special RNA sequences that flank the exon/intron junctions, bind to them, and catalyze the splicing reactions. Some primary transcripts can be spliced in a few different ways. Such "alternate splicing" yields a range of related proteins.
After addition of the CAP to the 5′ end, the poly-A tail to the 3′ end, and splicing of the introns, the processing is complete and the mRNA is transported through nuclear pores to the cytoplasm of the eukaryotic cell where translation (protein synthesis) will occur.
James E. Blankenship
Alberts, Bruce, et al. Molecular Biology of the Cell, 4th ed. New York: Garland Publishing, 2000.
Stryer, Lubert. Biochemistry, 4th ed. New York: W. H. Freeman and Company, 1995.
RNA serves a multitude of functions within cells. These functions are primarily involved in converting the genetic information contained in a cell's DNA into the proteins that determine the cell's structure and function. All RNAs are originally transcribed from DNA by RNA polymerases, which are specialized enzyme complexes, but most RNAs must be further modified or processed before they can carry out their roles. Thus, RNA processing refers to any modification made to RNA between its transcription and its final function in the cell. These processing steps include the removal of extra sections of RNA, specific modifications of RNA bases, and modifications of the ends of the RNA.
Types of RNA
There are different types of RNA, each of which plays a specific role, including specifying the amino acid sequence of proteins (performed by messenger RNAs, or mRNAs), organizing and catalyzing the synthesis of proteins (ribosomal RNAs or rRNAs), translating codons in the mRNA into amino acids (transfer RNAs or tRNAs) and directing many of the RNA processing steps (performed by small RNAs in the nucleus, called snRNAs and snoRNAs).
All of these types of RNAs begin as primary transcripts copied from DNA by one of the RNA polymerases. One of the features that separates eukaryotes and prokaryotes is that eukaryotes isolate their DNA inside a nucleus while protein synthesis takes place in the cytoplasm. This separates the processes of transcription and translation in space and time. Prokaryotes, which lack a nucleus, can translate an mRNA as soon as it is transcribed by RNA polymerase. As a consequence, there is very little processing of prokaryotic mRNAs. By contrast, in eukaryotic cells many processing steps occur between mRNA transcription and translation. Unlike the case of mRNAs, both eukaryotes and prokaryotes process their rRNAs and tRNAs in broadly similar ways.
Types of RNA Processing
There are three main types of RNA processing events: trimming one or both of the ends of the primary transcript to the mature RNA length; removing internal RNA sequences by a process called RNA splicing; and modifying RNA nucleotides either at the ends of an RNA or within the body of the RNA. We will briefly examine each of these and then discuss how they are applied to the various types of cellular RNAs.
Almost all RNAs have extra sequences at one or both ends of the primary transcripts that must be removed. The removal of individual nucleotides from the ends of the RNA strand is carried out by any of several ribonucleases (enzymes that cut RNA), called exoribonucleases. An entire section of RNA sequence can be removed by cleavage in the middle of an RNA strand. The enzymes responsible for the cleavage in this location are called endoribonucleases. Each of these ribonucleases is targeted so that it only cleaves particular RNAs at particular places.
RNA splicing is similar to trimming in that it removes extra RNA sequences, but it is different because the sequence is removed from the middle of an RNA and the two flanking pieces are joined together again (see figure). The part of the RNA that is removed is called an intron, whereas the two pieces that are joined together, or spliced, are called exons. Just as with the cleavage enzymes, the splicing machinery recognizes particular sites within the RNA, in this case the junctions between exons and introns, and cleaves and rejoins the RNA at those positions.
Modification of RNA nucleotides can occur at the ends of an RNA molecule or at internal positions. Modification of the ends can protect the RNA from degradation by exoribonucleases and can also act as a signal to guide the transport of the molecule to a particular subcellular compartment. Some internal modifications, particularly of tRNAs and rRNAs, are necessary for these RNAs to carry out their functions in protein synthesis. Some internal modifications of mRNAs change the sequence of the message and so change the amino acid sequence of the protein coded for by the mRNA. This process is called RNA editing. As with the other types of RNA processing, the enzymes that modify RNAs are directed to specific sites on the RNA.
Processing of Various Classes of RNAs
Ribosomal RNAs are synthesized as long primary transcripts that contain several different rRNAs separated by spacer regions (see figure). The individual rRNAs are cut apart by endoribonucleases that cleave within the spacer regions. Other enzymes then trim the ends to their final length. Ribosomal RNAs are also modified at many specific sites within the RNA. Ribosomal RNA synthesis and processing occurs in a special structure within the nucleus called the nucleolus . The mature rRNAs bind to ribosomal proteins within the nucleolus and the assembled ribosomes are then transported to the cytoplasm to carry out protein synthesis.
Transfer RNAs are transcribed individually from tRNA genes. The primary transcripts are trimmed at both the 5′ and 3′ ("five prime," or "upstream" and "three prime," or "downstream") ends, and several modifications are made to internal bases. Many eukaryotic tRNAs also contain an intron, which must be removed by RNA splicing. The finished tRNAs are then transported from the nucleus to the cytoplasm.
Messenger RNAs are transcribed individually from their genes as very long primary transcripts. This is because most eukaryotic genes are divided into many exons separated by introns. Genes may contain from zero to more than sixty introns, with a typical gene having around ten. Introns are spliced out of primary RNA transcripts by a large structure called the spliceosome . The spliceosome does not move along the RNA but is assembled around each intron where it cuts and joins the RNA to remove the intron and connect the exons. This must be done many times on a typical primary transcript to produce the mature mRNA.
In addition to removal of the introns, the mRNA is modified at the 5′ end by the addition of a special "cap" structure that is later recognized by the translation machinery. The mRNA is also trimmed at the 3′ end and several hundred adenosine nucleotides are added. This modification, which is called either polyadenylation or poly (A) addition, helps stabilize the 3′ end against degradation and is also recognized by the translation machinery. Finally, the processed mature mRNA is transported from the nucleus to the cytoplasm.
Some RNAs, called small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs), are processed in the nucleus and are themselves part of the RNA processing systems in the nucleus. Most snRNAs are involved in mRNA splicing, while most snoRNAs are involved in rRNA cleavage and modification.
RNA Processing and the Human Genome
The fact that most human genes are composed of many exons has some important consequences for the expression of genetic information. First, we now know that many genes are spliced in more than one way, a phenomenon known as alternative splicing. For example, some types of cells might leave out an exon from the final mRNA that is left in by other types of cells, giving it a slightly different function. This means that a single gene can code for more than one protein. Some complicated genes appear to be spliced to give hundreds of alternative forms. Alternative splicing, therefore, can increase the coding capacity of the genome without increasing the number of genes.
A second consequence of the exon/intron gene structure is that many human gene mutations affect the splicing pattern of that gene. For example, a mutation in the sequence at an intron/exon junction that is recognized by the spliceosome can cause the junction to be ignored. This causes splicing to occur to the next exon in line, leaving out the exon next to the mutation. This is called exon skipping and it usually results in an mRNA that codes for a nonfunctional protein. Exon skipping and other errors in splicing are seen in many human genetic diseases.
see also Alternative Splicing; Nucleotide; Nucleus; Ribosome; RNA; RNA Polymerases.
Richard A. Padgett
Lewin, Benjamin. Genes VII. Oxford, U.K.: Oxford University Press, 2000.
Lodish, Harvey, et al. Molecular Cell Biology, 4th ed. New York: W. H. Freeman, 2000.