Virtually everyone knows that the genes, located in the nuclei of all cells of the body, control heredity from parents to children, but most people do not realize that these same genes also control day-to-day function of all the body’s cells. The genes control cell function by determining which substances are synthesized within the cell—which structures, which enzymes, which chemicals.
Figure 3-1 shows the general schema of genetic control. Each gene, which is a nucleic acid called deoxyribonucleic acid (DNA), automatically controls the formation of another nucleic acid, ribonucleic acid(RNA); this RNA then spreads throughout the cell to control the formation of a specific protein. The entire process, from transcription of the genetic code in the nucleus to translation of the RNA code and formation or proteins in the cell cytoplasm, is often referred to as gene expression.
Figure 3-1 General schema by which the genes control cell function.
Because there are approximately 30,000 different genes in each cell, it is theoretically possible to form a large number of different cellular proteins.
Some of the cellular proteins are structural proteins, which, in association with various lipids and carbohydrates, form the structures of the various intracellular organelles discussed in Chapter 2. However, the majority of the proteins are enzymes that catalyze the different chemical reactions in the cells. For instance, enzymes promote all the oxidative reactions that supply energy to the cell, and they promote synthesis of all the cell chemicals, such as lipids, glycogen, and adenosine triphosphate (ATP).
Genes in the Cell Nucleus
In the cell nucleus, large numbers of genes are attached end on end in extremely long double-stranded helical molecules of DNA having molecular weights measured in the billions. A very short segment of such a molecule is shown in Figure 3-2. This molecule is composed of several simple chemical compounds bound together in a regular pattern, details of which are explained in the next few paragraphs.
Figure 3-2 The helical, double-stranded structure of the gene. The outside strands are composed of phosphoric acid and the sugar deoxyribose. The internal molecules connecting the two strands of the helix are purine and pyrimidine bases; these determine the “code” of the gene.
Basic Building Blocks of DNA
Figure 3-3 shows the basic chemical compounds involved in the formation of DNA. These include (1) phosphoric acid, (2) a sugar called deoxyribose, and (3) four nitrogenous bases (two purines, adenine and guanine, and two pyrimidines, thymine and cytosine). The phosphoric acid and deoxyribose form the two helical strands that are the backbone of the DNA molecule, and the nitrogenous bases lie between the two strands and connect them, as illustrated in Figure 3-6.
Figure 3-3 The basic building blocks of DNA.
Nucleotides
The first stage in the formation of DNA is to combine one molecule of phosphoric acid, one molecule of deoxyribose, and one of the four bases to form an acidic nucleotide. Four separate nucleotides are thus formed, one for each of the four bases: deoxyadenylic, deoxythymidylic, deoxyguanylic, and deoxycytidylic acids. Figure 3-4 shows the chemical structure of deoxyadenylic acid, and Figure 3-5 shows simple symbols for the four nucleotides that form DNA.
Figure 3-4 Deoxyadenylic acid, one of the nucleotides that make up DNA.
Figure 3-5 Symbols for the four nucleotides that combine to form DNA. Each nucleotide contains phosphoric acid (P), deoxyribose (D), and one of the four nucleotide bases: A, adenine; T, thymine; G,guanine; or C, cytosine.
Organization of the Nucleotides to Form Two Strands of DNA Loosely Bound to Each Other
Figure 3-6 shows the manner in which multiple numbers of nucleotides are bound together to form two strands of DNA. The two strands are, in turn, loosely bonded with each other by weak cross-linkages, illustrated in Figure 3-6by the central dashed lines. Note that the backbone of each DNA strand is composed of alternating phosphoric acid and deoxyribose molecules. In turn, purine and pyrimidine bases are attached to the sides of the deoxyribose molecules. Then, by means of loose hydrogen bonds (dashed lines) between the purine and pyrimidine bases, the two respective DNA strands are held together. But note the following:
1. Each purine base adenine of one strand always bonds with a pyrimidine base thymine of the other strand, and
2. Each purine base guanine always bonds with a pyrimidine base cytosine.
Figure 3-6 Arrangement of deoxyribose nucleotides in a double strand of DNA.
Thus, in Figure 3-6, the sequence of complementary pairs of bases is CG, CG, GC, TA, CG, TA, GC, AT, and AT. Because of the looseness of the hydrogen bonds, the two strands can pull apart with ease, and they do so many times during the course of their function in the cell.
To put the DNA of Figure 3-6 into its proper physical perspective, one could merely pick up the two ends and twist them into a helix. Ten pairs of nucleotides are present in each full turn of the helix in the DNA molecule, as shown in Figure 3-2.
Genetic Code
The importance of DNA lies in its ability to control the formation of proteins in the cell. It does this by means of a genetic code. That is, when the two strands of a DNA molecule are split apart, this exposes the purine and pyrimidine bases projecting to the side of each DNA strand, as shown by the top strand in Figure 3-7. It is these projecting bases that form the genetic code.
Figure 3-7 Combination of ribose nucleotides with a strand of DNA to form a molecule of RNA that carries the genetic code from the gene to the cytoplasm. The RNA polymerase enzyme moves along the DNA strand and builds the RNA molecule.
The genetic code consists of successive “triplets” of bases—that is, each three successive bases is a code word. The successive triplets eventually control the sequence of amino acids in a protein molecule that is to be synthesized in the cell. Note in Figure 3-6 that the top strand of DNA, reading from left to right, has the genetic code GGC, AGA, CTT, the triplets being separated from one another by the arrows. As we follow this genetic code through Figures 3-7 and 3-8, we see that these three respective triplets are responsible for successive placement of the three amino acids, proline, serine, and glutamic acid, in a newly formed molecule of protein.
Figure 3-8 Portion of an RNA molecule, showing three RNA “codons”—CCG, UCU, and GAA—that control attachment of the three amino acids, proline, serine, and glutamic acid, respectively, to the growing RNA chain.
The DNA Code in the Cell Nucleus Is Transferred to an RNA Code in the Cell Cytoplasm—The Process of Transcription
Because the DNA is located in the nucleus of the cell, yet most of the functions of the cell are carried out in the cytoplasm, there must be some means for the DNA genes of the nucleus to control the chemical reactions of the cytoplasm. This is achieved through the intermediary of another type of nucleic acid, RNA, the formation of which is controlled by the DNA of the nucleus. Thus, as shown in Figure 3-7, the code is transferred to the RNA; this process is called transcription. The RNA, in turn, diffuses from the nucleus through nuclear pores into the cytoplasmic compartment, where it controls protein synthesis.
Synthesis of RNA
During synthesis of RNA, the two strands of the DNA molecule separate temporarily; one of these strands is used as a template for synthesis of an RNA molecule. The code triplets in the DNA cause formation of complementarycode triplets (called codons) in the RNA; these codons, in turn, will control the sequence of amino acids in a protein to be synthesized in the cell cytoplasm.
Basic Building Blocks of RNA
The basic building blocks of RNA are almost the same as those of DNA, except for two differences. First, the sugar deoxyribose is not used in the formation of RNA. In its place is another sugar of slightly different composition, ribose, containing an extra hydroxyl ion appended to the ribose ring structure. Second, thymine is replaced by another pyrimidine, uracil.
Formation of RNA Nucleotides
The basic building blocks of RNA form RNA nucleotides, exactly as previously described for DNA synthesis. Here again, four separate nucleotides are used in the formation of RNA. These nucleotides contain the bases adenine, guanine, cytosine, and uracil. Note that these are the same bases as in DNA, except that uracil in RNA replaces thymine in DNA.
“Activation” of the RNA Nucleotides
The next step in the synthesis of RNA is “activation” of the RNA nucleotides by an enzyme, RNA polymerase. This occurs by adding to each nucleotide two extra phosphate radicals to form triphosphates (shown in Figure 3-7 by the two RNA nucleotides to the far right during RNA chain formation). These last two phosphates are combined with the nucleotide by high-energy phosphate bonds derived from ATP in the cell.
The result of this activation process is that large quantities of ATP energy are made available to each of the nucleotides, and this energy is used to promote the chemical reactions that add each new RNA nucleotide at the end of the developing RNA chain.
Assembly of the RNA Chain from Activated Nucleotides Using the DNA Strand as a Template—The Process of “Transcription”
Assembly of the RNA molecule is accomplished in the manner shown in Figure 3-7 under the influence of an enzyme, RNA polymerase. This is a large protein enzyme that has many functional properties necessary for formation of the RNA molecule. They are as follows:
1. In the DNA strand immediately ahead of the initial gene is a sequence of nucleotides called the promoter. The RNA polymerase has an appropriate complementary structure that recognizes this promoter and becomes attached to it. This is the essential step for initiating formation of the RNA molecule.
2. After the RNA polymerase attaches to the promoter, the polymerase causes unwinding of about two turns of the DNA helix and separation of the unwound portions of the two strands.
3. Then the polymerase moves along the DNA strand, temporarily unwinding and separating the two DNA strands at each stage of its movement. As it moves along, it adds at each stage a new activated RNA nucleotide to the end of the newly forming RNA chain by the following steps:
a. First, it causes a hydrogen bond to form between the end base of the DNA strand and the base of an RNA nucleotide in the nucleoplasm.
b. Then, one at a time, the RNA polymerase breaks two of the three phosphate radicals away from each of these RNA nucleotides, liberating large amounts of energy from the broken high-energy phosphate bonds; this energy is used to cause covalent linkage of the remaining phosphate on the nucleotide with the ribose on the end of the growing RNA chain.
c. When the RNA polymerase reaches the end of the DNA gene, it encounters a new sequence of DNA nucleotides called the chain-terminating sequence; this causes the polymerase and the newly formed RNA chain to break away from the DNA strand. Then the polymerase can be used again and again to form still more new RNA chains.
d. As the new RNA strand is formed, its weak hydrogen bonds with the DNA template break away, because the DNA has a high affinity for rebonding with its own complementary DNA strand. Thus, the RNA chain is forced away from the DNA and is released into the nucleoplasm.
Thus, the code that is present in the DNA strand is eventually transmitted in complementary form to the RNA chain. The ribose nucleotide bases always combine with the deoxyribose bases in the following combinations:
|
DNA Base |
RNA Base |
|
|
guanine |
……………… |
cytosine |
|
cytosine |
……………… |
guanine |
|
adenine |
……………… |
uracil |
|
thymine |
……………… |
adenine |
Four Different Types of RNA
Each type of RNA plays an independent and entirely different role in protein formation:
1. Messenger RNA (mRNA), which carries the genetic code to the cytoplasm for controlling the type of protein formed.
2. Transfer RNA (tRNA), which transports activated amino acids to the ribosomes to be used in assembling the protein molecule.
3. Ribosomal RNA, which, along with about 75 different proteins, forms ribosomes, the physical and chemical structures on which protein molecules are actually assembled.
4. MicroRNA (miRNA), which are single-stranded RNA molecules of 21 to 23 nucleotides that can regulate gene transcription and translation.
Messenger RNA—The Codons
mRNA molecules are long, single RNA strands that are suspended in the cytoplasm. These molecules are composed of several hundred to several thousand RNA nucleotides in unpaired strands, and they contain codons that are exactly complementary to the code triplets of the DNA genes. Figure 3-8 shows a small segment of a molecule of messenger RNA. Its codons are CCG, UCU, and GAA. These are the codons for the amino acids proline, serine, and glutamic acid. The transcription of these codons from the DNA molecule to the RNA molecule is shown in Figure 3-7.
RNA Codons for the Different Amino Acids
Table 3-1 gives the RNA codons for the 22 common amino acids found in protein molecules. Note that most of the amino acids are represented by more than one codon; also, one codon represents the signal “start manufacturing the protein molecule,” and three codons represent “stop manufacturing the protein molecule.” In Table 3-1, these two types of codons are designated CI for “chain-initiating” and CT for “chain-terminating.”
Table 3-1 RNA Codons for Amino Acids and for Start and Stop
Transfer RNA—The Anticodons
Another type of RNA that plays an essential role in protein synthesis is called tRNA because it transfers amino acid molecules to protein molecules as the protein is being synthesized. Each type of tRNA combines specifically with 1 of the 20 amino acids that are to be incorporated into proteins. The tRNA then acts as a carrier to transport its specific type of amino acid to the ribosomes, where protein molecules are forming. In the ribosomes, each specific type of transfer RNA recognizes a particular codon on the mRNA (described later) and thereby delivers the appropriate amino acid to the appropriate place in the chain of the newly forming protein molecule.
Transfer RNA, which contains only about 80 nucleotides, is a relatively small molecule in comparison with mRNA. It is a folded chain of nucleotides with a cloverleaf appearance similar to that shown in Figure 3-9. At one end of the molecule is always an adenylic acid; it is to this that the transported amino acid attaches at a hydroxyl group of the ribose in the adenylic acid.
Figure 3-9 A messenger RNA strand is moving through two ribosomes. As each “codon” passes through, an amino acid is added to the growing protein chain, which is shown in the right-hand ribosome. The transfer RNA molecule transports each specific amino acid to the newly forming protein.
Because the function of tRNA is to cause attachment of a specific amino acid to a forming protein chain, it is essential that each type of tRNA also have specificity for a particular codon in the mRNA. The specific code in the tRNA that allows it to recognize a specific codon is again a triplet of nucleotide bases and is called an anticodon. This is located approximately in the middle of the tRNA molecule (at the bottom of the cloverleaf configuration shown in Figure 3-9). During formation of the protein molecule, the anticodon bases combine loosely by hydrogen bonding with the codon bases of the mRNA. In this way, the respective amino acids are lined up one after another along the mRNA chain, thus establishing the appropriate sequence of amino acids in the newly forming protein molecule.
Ribosomal RNA
The third type of RNA in the cell is ribosomal RNA; it constitutes about 60 percent of the ribosome. The remainder of the ribosome is protein, containing about 75 types of proteins that are both structural proteins and enzymes needed in the manufacture of protein molecules.
The ribosome is the physical structure in the cytoplasm on which protein molecules are actually synthesized. However, it always functions in association with the other two types of RNA as well: tRNAtransports amino acids to the ribosome for incorporation into the developing protein molecule, whereas mRNA provides the information necessary for sequencing the amino acids in proper order for each specific type of protein to be manufactured.
Thus, the ribosome acts as a manufacturing plant in which the protein molecules are formed.
Formation of Ribosomes in the Nucleolus
The DNA genes for formation of ribosomal RNA are located in five pairs of chromosomes in the nucleus, and each of these chromosomes contains many duplicates of these particular genes because of the large amounts of ribosomal RNA required for cellular function.
As the ribosomal RNA forms, it collects in the nucleolus, a specialized structure lying adjacent to the chromosomes. When large amounts of ribosomal RNA are being synthesized, as occurs in cells that manufacture large amounts of protein, the nucleolus is a large structure, whereas in cells that synthesize little protein, the nucleolus may not even be seen. Ribosomal RNA is specially processed in the nucleolus, where it binds with “ribosomal proteins” to form granular condensation products that are primordial subunits of ribosomes. These subunits are then released from the nucleolus and transported through the large pores of the nuclear envelope to almost all parts of the cytoplasm. After the subunits enter the cytoplasm, they are assembled to form mature, functional ribosomes. Therefore, proteins are formed in the cytoplasm of the cell, but not in the cell nucleus, because the nucleus does not contain mature ribosomes.
MicroRNA
A fourth type of RNA in the cell is miRNA. These are short (21 to 23 nucleotides) single-stranded RNA fragments that regulate gene expression (Figure 3-10). The miRNAs are encoded from the transcribed DNA of genes, but they are not translated into proteins and are therefore often called noncoding RNA. The miRNAs are processed by the cell into molecules that are complementary to mRNA and act to decrease gene expression. Generation of miRNAs involves special processing of longer primary precursor RNAs called pri-miRNAs, which are the primary transcripts of the gene. The pri-miRNAs are then processed in the cell nucleus by the microprocessor complex to pre-miRNAs, which are 70 nucleotide stem-loop structures. These pre-miRNAs are then further processed in the cytoplasm by a specific dicer enzyme that helps assemble an RNA-induced silencing complex (RISC) and generates miRNAs.
Figure 3-10 Regulation of gene expression by microRNA (miRNA). Primary miRNA (pri-miRNA), the primary transcripts of a gene processed in the cell nucleus by the microprocessor complex to pre-miRNAs. These pre-miRNAs are then further processed in the cytoplasm by dicer, an enzyme that helps assemble an RNA-induced silencing complex (RISC) and generates miRNAs. The miRNAs regulate gene expression by binding to the complementary region of the RNA and repressing translation or promoting degradation of the mRNA before it can be translated by the ribosome.
The miRNAs regulate gene expression by binding to the complementary region of the RNA and promoting repression of translation or degradation of the mRNA before it can be translated by the ribosome. miRNAs are believed to play an important role in the normal regulation of cell function, and alterations in miRNA function have been associated with diseases such as cancer and heart disease.
Another type of microRNA is small interfering RNA (siRNA), also called silencing RNA or short interfering RNA. The siRNAs are short, double-stranded RNA molecules, 20 to 25 nucleotides in length, that interfere with the expression of specific genes. siRNAs generally refer to synthetic miRNAs and can be administered to silence expression of specific genes. They are designed to avoid the nuclear processing by the microprocessor complex, and after the siRNA enters the cytoplasm it activates the RISC silencing complex, blocking the translation of mRNA. Because siRNAs can be tailored for any specific sequence in the gene, they can be used to block translation of any mRNA and therefore expression by any gene for which the nucleotide sequence is known. Some researchers have proposed that siRNAs may become useful therapeutic tools to silence genes that contribute to the pathophysiology of diseases.
Formation of Proteins on the Ribosomes—The Process of “Translation”
When a molecule of messenger RNA comes in contact with a ribosome, it travels through the ribosome, beginning at a predetermined end of the RNA molecule specified by an appropriate sequence of RNA bases called the “chain-initiating” codon. Then, as shown in Figure 3-9, while the messenger RNA travels through the ribosome, a protein molecule is formed—a process called translation. Thus, the ribosome reads the codons of the messenger RNA in much the same way that a tape is “read” as it passes through the playback head of a tape recorder. Then, when a “stop” (or “chain-terminating”) codon slips past the ribosome, the end of a protein molecule is signaled and the protein molecule is freed into the cytoplasm.
Polyribosomes
A single messenger RNA molecule can form protein molecules in several ribosomes at the same time because the initial end of the RNA strand can pass to a successive ribosome as it leaves the first, as shown at the bottom left in Figure 3-9 and in Figure 3-11. The protein molecules are in different stages of development in each ribosome. As a result, clusters of ribosomes frequently occur, 3 to 10 ribosomes being attached to a single messenger RNA at the same time. These clusters are called polyribosomes.
Figure 3-11 Physical structure of the ribosomes, as well as their functional relation to messenger RNA, transfer RNA, and the endoplasmic reticulum during the formation of protein molecules.
(Courtesy Dr. Don W. Fawcett, Montana.)
It is especially important to note that a messenger RNA can cause the formation of a protein molecule in any ribosome; that is, there is no specificity of ribosomes for given types of protein. The ribosome is simply the physical manufacturing plant in which the chemical reactions take place.
Many Ribosomes Attach to the Endoplasmic Reticulum
In Chapter 2, it was noted that many ribosomes become attached to the endoplasmic reticulum. This occurs because the initial ends of many forming protein molecules have amino acid sequences that immediately attach to specific receptor sites on the endoplasmic reticulum; this causes these molecules to penetrate the reticulum wall and enter the endoplasmic reticulum matrix. This gives a granular appearance to those portions of the reticulum where proteins are being formed and entering the matrix of the reticulum.
Figure 3-11 shows the functional relation of messenger RNA to the ribosomes and the manner in which the ribosomes attach to the membrane of the endoplasmic reticulum. Note the process of translation occurring in several ribosomes at the same time in response to the same strand of messenger RNA. Note also the newly forming polypeptide (protein) chains passing through the endoplasmic reticulum membrane into the endoplasmic matrix.
Yet it should be noted that except in glandular cells in which large amounts of protein-containing secretory vesicles are formed, most proteins synthesized by the ribosomes are released directly into the cytosol instead of into the endoplasmic reticulum. These proteins are enzymes and internal structural proteins of the cell.
Chemical Steps in Protein Synthesis
Some of the chemical events that occur in synthesis of a protein molecule are shown in Figure 3-12. This figure shows representative reactions for three separate amino acids, AA1, AA2, and AA20. The stages of the reactions are the following: (1) Each amino acid is activated by a chemical process in which ATP combines with the amino acid to form an adenosine monophosphate complex with the amino acid,giving up two high-energy phosphate bonds in the process. (2) The activated amino acid, having an excess of energy, then combines with its specific transfer RNA to form an amino acid–tRNA complex and, at the same time, releases the adenosine monophosphate. (3) The transfer RNA carrying the amino acid complex then comes in contact with the messenger RNA molecule in the ribosome, where the anticodon of the transfer RNA attaches temporarily to its specific codon of the messenger RNA, thus lining up the amino acid in appropriate sequence to form a protein molecule. Then, under the influence of the enzyme peptidyl transferase (one of the proteins in the ribosome), peptide bonds are formed between the successive amino acids, thus adding progressively to the protein chain. These chemical events require energy from two additional high-energy phosphate bonds, making a total of four high-energy bonds used for each amino acid added to the protein chain. Thus, the synthesis of proteins is one of the most energy-consuming processes of the cell.
Figure 3-12 Chemical events in the formation of a protein molecule.
Peptide Linkage
The successive amino acids in the protein chain combine with one another according to the typical reaction:
In this chemical reaction, a hydroxyl radical (OH−) is removed from the COOH portion of the first amino acid and a hydrogen (H+) of the NH2 portion of the other amino acid is removed. These combine to form water, and the two reactive sites left on the two successive amino acids bond with each other, resulting in a single molecule. This process is called peptide linkage. As each additional amino acid is added, an additional peptide linkage is formed.
Synthesis of Other Substances in the Cell
Many thousand protein enzymes formed in the manner just described control essentially all the other chemical reactions that take place in cells. These enzymes promote synthesis of lipids, glycogen, purines, pyrimidines, and hundreds of other substances. We discuss many of these synthetic processes in relation to carbohydrate, lipid, and protein metabolism in Chapters 67 through 69. It is by means of all these substances that the many functions of the cells are performed.
Control of Gene Function and Biochemical Activity in Cells
From our discussion thus far, it is clear that the genes control both the physical and chemical functions of the cells. However, the degree of activation of respective genes must be controlled as well; otherwise, some parts of the cell might overgrow or some chemical reactions might overact until they kill the cell. Each cell has powerful internal feedback control mechanisms that keep the various functional operations of the cell in step with one another. For each gene (approximately 30,000 genes in all), there is at least one such feedback mechanism.
There are basically two methods by which the biochemical activities in the cell are controlled: (1) genetic regulation, in which the degree of activation of the genes and the formation of gene products are themselves controlled and (2) enzyme regulation, in which the activity levels of already formed enzymes in the cell are controlled.
Genetic Regulation
Genetic regulation, or regulation of gene expression, covers the entire process from transcription of the genetic code in the nucleus to the formation or proteins in the cytoplasm. Regulation of gene expression provides all living organisms the ability to respond to changes in their environment. In animals that have many different types of cells, tissues, and organs, differential regulation of gene expression also permits the many different cell types in the body to each perform their specialized functions. Although a cardiac myocyte contains the same genetic code as a renal tubular epithelia cell, many genes are expressed in cardiac cells that are not expressed in renal tubular cells. The ultimate measure of gene “expression” is whether (and how much) of the gene products (proteins) are produced because proteins carry out cell functions specified by the genes. Regulation of gene expression can occur at any point in the pathways of transcription, RNA processing, and translation.
The Promoter Controls Gene Expression
Synthesis of cellular proteins is a complex process that starts with the transcription of DNA into RNA. The transcription of DNA is controlled by regulatory elements found in the promoter of a gene (Figure 3-13). In eukaryotes, which includes all mammals, the basal promoter consists of a sequence of seven bases (TATAAAA) called the TATA box, the binding site for the TATA-binding protein (TBP) and several other important transcription factors that are collectively referred to as the transcription factor IID complex. In addition to the transcription factor IID complex, this region is where transcription factor IIB binds to both the DNA and RNA polymerase 2 to facilitate transcription of the DNA into RNA. This basal promoter is found in all protein-coding genes and the polymerase must bind with this basal promoter before it can begin traveling along the DNA strand to synthesize RNA. The upstream promoteris located farther upstream from the transcription start site and contains several binding sites for positive or negative transcription factors that can effect transcription through interactions with proteins bound to the basal promoter. The structure and transcription factor binding sites in the upstream promoter vary from gene to gene to give rise to the different expression patterns of genes in different tissues.
Figure 3-13 Gene transcriptional in eukaryotic cells. A complex arrangement of multiple clustered enhancer modules interspersed with insulator elements, which can be located either upstream or downstream of a basal promoter containing TATA box (TATA), proximal promoter elements (response elements, RE), and Initiator sequences (INR).
Transcription of genes in eukaryotes is also influenced by enhancers, which are regions of DNA that can bind transcription factors. Enhancers can be located a great distance from the gene they act on or even on a different chromosome. They can also be located either upstream or downstream of the gene that they regulate. Although enhancers may be located a great distance away from their target gene, they may be relatively close when DNA is coiled in the nucleus. It is estimated that there are 110,000 gene enhancer sequences in the human genome.
In the organization of the chromosome, it is important to separate active genes that are being transcribed from genes that are repressed. This can be challenging because multiple genes may be located close together on the chromosome. This is achieved by chromosomal insulators. These insulators are gene sequences that provide a barrier so that a specific gene is isolated against transcriptional influences from surrounding genes. Insulators can vary greatly in their DNA sequence and the proteins that bind to them. One way an insulator activity can be modulated is by DNA methylation. This is the case for the mammalian insulin-like growth factor 2 (IGF-2) gene. The mother’s allele has an insulator between the enhancer and promoter of the gene that allows for the binding of a transcriptional repressor. However, the paternal DNA sequence is methylated such that the transcriptional repressor cannot bind to the insulator and the IGF-2 gene is expressed from the paternal copy of the gene.
Other Mechanisms for Control of Transcription by the Promoter
Variations in the basic mechanism for control of the promoter have been discovered with rapidity in the past 2 decades. Without giving details, let us list some of them:
1. A promoter is frequently controlled by transcription factors located elsewhere in the genome. That is, the regulatory gene causes the formation of a regulatory protein that in turn acts either as an activator or a repressor of transcription.
2. Occasionally, many different promoters are controlled at the same time by the same regulatory protein. In some instances, the same regulatory protein functions as an activator for one promoter and as a repressor for another promoter.
3. Some proteins are controlled not at the starting point of transcription on the DNA strand but farther along the strand. Sometimes the control is not even at the DNA strand itself but during the processing of the RNA molecules in the nucleus before they are released into the cytoplasm; rarely, control might occur at the level of protein formation in the cytoplasm during RNA translation by the ribosomes.
4. In nucleated cells, the nuclear DNA is packaged in specific structural units, the chromosomes. Within each chromosome, the DNA is wound around small proteins called histones, which in turn are held tightly together in a compacted state by still other proteins. As long as the DNA is in this compacted state, it cannot function to form RNA. However, multiple control mechanisms are beginning to be discovered that can cause selected areas of chromosomes to become decompacted one part at a time so that partial RNA transcription can occur. Even then, specific transcriptor factors control the actual rate of transcription by the promoter in the chromosome. Thus, still higher orders of control are used for establishing proper cell function. In addition, signals from outside the cell, such as some of the body’s hormones, can activate specific chromosomal areas and specific transcription factors, thus controlling the chemical machinery for function of the cell.
Because there are more than 30,000 different genes in each human cell, the large number of ways in which genetic activity can be controlled is not surprising. The gene control systems are especially important for controlling intracellular concentrations of amino acids, amino acid derivatives, and intermediate substrates and products of carbohydrate, lipid, and protein metabolism.
Control of Intracellular Function by Enzyme Regulation
In addition to control of cell function by genetic regulation, some cell activities are controlled by intracellular inhibitors or activators that act directly on specific intracellular enzymes. Thus, enzyme regulation represents a second category of mechanisms by which cellular biochemical functions can be controlled.
Enzyme Inhibition
Some chemical substances formed in the cell have direct feedback effects in inhibiting the specific enzyme systems that synthesize them. Almost always the synthesized product acts on the first enzyme in a sequence, rather than on the subsequent enzymes, usually binding directly with the enzyme and causing an allosteric conformational change that inactivates it. One can readily recognize the importance of inactivating the first enzyme: this prevents buildup of intermediary products that are not used.
Enzyme inhibition is another example of negative feedback control; it is responsible for controlling intracellular concentrations of multiple amino acids, purines, pyrimidines, vitamins, and other substances.
Enzyme Activation
Enzymes that are normally inactive often can be activated when needed. An example of this occurs when most of the ATP has been depleted in a cell. In this case, a considerable amount of cyclic adenosine monophosphate (cAMP) begins to be formed as a breakdown product of the ATP; the presence of this cAMP, in turn, immediately activates the glycogen-splitting enzyme phosphorylase, liberating glucose molecules that are rapidly metabolized and their energy used for replenishment of the ATP stores. Thus, cAMP acts as an enzyme activator for the enzyme phosphorylase and thereby helps control intracellular ATP concentration.
Another interesting instance of both enzyme inhibition and enzyme activation occurs in the formation of the purines and pyrimidines. These substances are needed by the cell in approximately equal quantities for formation of DNA and RNA. When purines are formed, they inhibit the enzymes that are required for formation of additional purines. However, they activate the enzymes for formation of pyrimidines. Conversely, the pyrimidines inhibit their own enzymes but activate the purine enzymes. In this way, there is continual cross-feed between the synthesizing systems for these two substances, resulting in almost exactly equal amounts of the two substances in the cells at all times.
Summary
In summary, there are two principal methods by which cells control proper proportions and proper quantities of different cellular constituents: (1) the mechanism of genetic regulation and (2) the mechanism of enzyme regulation. The genes can be either activated or inhibited, and likewise, the enzyme systems can be either activated or inhibited. These regulatory mechanisms most often function as feedback control systems that continually monitor the cell’s biochemical composition and make corrections as needed. But on occasion, substances from without the cell (especially some of the hormones discussed throughout this text) also control the intracellular biochemical reactions by activating or inhibiting one or more of the intracellular control systems.
The DNA-Genetic System Also Controls Cell Reproduction
Cell reproduction is another example of the ubiquitous role that the DNA-genetic system plays in all life processes. The genes and their regulatory mechanisms determine the growth characteristics of the cells and also when or whether these cells will divide to form new cells. In this way, the all-important genetic system controls each stage in the development of the human being, from the single-cell fertilized ovum to the whole functioning body. Thus, if there is any central theme to life, it is the DNA-genetic system.
Life Cycle of the Cell
The life cycle of a cell is the period from cell reproduction to the next cell reproduction. When mammalian cells are not inhibited and are reproducing as rapidly as they can, this life cycle may be as little as 10 to 30 hours. It is terminated by a series of distinct physical events called mitosis that cause division of the cell into two new daughter cells. The events of mitosis are shown in Figure 3-14 and are described later. The actual stage of mitosis, however, lasts for only about 30 minutes, so more than 95 percent of the life cycle of even rapidly reproducing cells is represented by the interval between mitosis, called interphase.
Figure 3-14 Stages of cell reproduction. A, B, and C, Prophase. D, Prometaphase. E, Metaphase. F, Anaphase. G and H, Telophase.
(From Margaret C. Gladbach, Estate of Mary E. and Dan Todd, Kansas.)
Except in special conditions of rapid cellular reproduction, inhibitory factors almost always slow or stop the uninhibited life cycle of the cell. Therefore, different cells of the body actually have life cycle periods that vary from as little as 10 hours for highly stimulated bone marrow cells to an entire lifetime of the human body for most nerve cells.
Cell Reproduction Begins with Replication of DNA
As is true of almost all other important events in the cell, reproduction begins in the nucleus itself. The first step is replication (duplication) of all DNA in the chromosomes. Only after this has occurred can mitosis take place.
The DNA begins to be duplicated some 5 to 10 hours before mitosis, and this is completed in 4 to 8 hours. The net result is two exact replicas of all DNA. These replicas become the DNA in the two new daughter cells that will be formed at mitosis. After replication of the DNA, there is another period of 1 to 2 hours before mitosis begins abruptly. Even during this period, preliminary changes that will lead to the mitotic process are beginning to take place.
Chemical and Physical Events of DNA Replication
DNA is replicated in much the same way that RNA is transcribed in response to DNA, except for a few important differences:
1. Both strands of the DNA in each chromosome are replicated, not simply one of them.
2. Both entire strands of the DNA helix are replicated from end to end, rather than small portions of them, as occurs in the transcription of RNA.
3. The principal enzymes for replicating DNA are a complex of multiple enzymes called DNA polymerase, which is comparable to RNA polymerase. It attaches to and moves along the DNA template strand while another enzyme, DNA ligase, causes bonding of successive DNA nucleotides to one another, using high-energy phosphate bonds to energize these attachments.
4. Formation of each new DNA strand occurs simultaneously in hundreds of segments along each of the two strands of the helix until the entire strand is replicated. Then the ends of the subunits are joined together by the DNA ligase enzyme.
5. Each newly formed strand of DNA remains attached by loose hydrogen bonding to the original DNA strand that was used as its template. Therefore, two DNA helixes are coiled together.
6. Because the DNA helixes in each chromosome are approximately 6 centimeters in length and have millions of helix turns, it would be impossible for the two newly formed DNA helixes to uncoil from each other were it not for some special mechanism. This is achieved by enzymes that periodically cut each helix along its entire length, rotate each segment enough to cause separation, and then resplice the helix. Thus, the two new helixes become uncoiled.
DNA Repair, DNA “Proofreading,” and “Mutation.”
During the hour or so between DNA replication and the beginning of mitosis, there is a period of active repair and “proofreading” of the DNA strands. That is, wherever inappropriate DNA nucleotides have been matched up with the nucleotides of the original template strand, special enzymes cut out the defective areas and replace these with appropriate complementary nucleotides. This is achieved by the same DNA polymerases and DNA ligases that are used in replication. This repair process is referred to as DNA proofreading.
Because of repair and proofreading, the transcription process rarely makes a mistake. But when a mistake is made, this is called a mutation. The mutation causes formation of some abnormal protein in the cell rather than a needed protein, often leading to abnormal cellular function and sometimes even cell death. Yet given that there are 30,000 or more genes in the human genome and that the period from one human generation to another is about 30 years, one would expect as many as 10 or many more mutations in the passage of the genome from parent to child. As a further protection, however, each human genome is represented by two separate sets of chromosomes with almost identical genes. Therefore, one functional gene of each pair is almost always available to the child despite mutations.
Chromosomes and Their Replication
The DNA helixes of the nucleus are packaged in chromosomes. The human cell contains 46 chromosomes arranged in 23 pairs. Most of the genes in the two chromosomes of each pair are identical or almost identical to each other, so it is usually stated that the different genes also exist in pairs, although occasionally this is not the case.
In addition to DNA in the chromosome, there is a large amount of protein in the chromosome, composed mainly of many small molecules of electropositively charged histones. The histones are organized into vast numbers of small, bobbin-like cores. Small segments of each DNA helix are coiled sequentially around one core after another.
The histone cores play an important role in the regulation of DNA activity because as long as the DNA is packaged tightly, it cannot function as a template for either the formation of RNA or the replication of new DNA. Further, some of the regulatory proteins have been shown to decondense the histone packaging of the DNA and to allow small segments at a time to form RNA.
Several nonhistone proteins are also major components of chromosomes, functioning both as chromosomal structural proteins and, in connection with the genetic regulatory machinery, as activators, inhibitors, and enzymes.
Replication of the chromosomes in their entirety occurs during the next few minutes after replication of the DNA helixes has been completed; the new DNA helixes collect new protein molecules as needed. The two newly formed chromosomes remain attached to each other (until time for mitosis) at a point called the centromere located near their center. These duplicated but still attached chromosomes are called chromatids.
Cell Mitosis
The actual process by which the cell splits into two new cells is called mitosis. Once each chromosome has been replicated to form the two chromatids, in many cells, mitosis follows automatically within 1 or 2 hours.
Mitotic Apparatus: Function of the Centrioles
One of the first events of mitosis takes place in the cytoplasm, occurring during the latter part of interphase in or around the small structures called centrioles. As shown in Figure 3-14, two pairs of centrioles lie close to each other near one pole of the nucleus. These centrioles, like the DNA and chromosomes, are also replicated during interphase, usually shortly before replication of the DNA. Each centriole is a small cylindrical body about 0.4 micrometer long and about 0.15 micrometer in diameter, consisting mainly of nine parallel tubular structures arranged in the form of a cylinder. The two centrioles of each pair lie at right angles to each other. Each pair of centrioles, along with attached pericentriolar material, is called a centrosome.
Shortly before mitosis is to take place, the two pairs of centrioles begin to move apart from each other. This is caused by polymerization of protein microtubules growing between the respective centriole pairs and actually pushing them apart. At the same time, other microtubules grow radially away from each of the centriole pairs, forming a spiny star, called the aster, in each end of the cell. Some of the spines of the aster penetrate the nuclear membrane and help separate the two sets of chromatids during mitosis. The complex of microtubules extending between the two new centriole pairs is called the spindle, and the entire set of microtubules plus the two pairs of centrioles is called the mitotic apparatus.
Prophase
The first stage of mitosis, called prophase, is shown in Figure 3-14A, B, and C. While the spindle is forming, the chromosomes of the nucleus (which in interphase consist of loosely coiled strands) become condensed into well-defined chromosomes.
Prometaphase
During this stage (see Figure 3-14D), the growing microtubular spines of the aster fragment the nuclear envelope. At the same time, multiple microtubules from the aster attach to the chromatids at the centromeres, where the paired chromatids are still bound to each other; the tubules then pull one chromatid of each pair toward one cellular pole and its partner toward the opposite pole.
Metaphase
During metaphase (see Figure 3-14E), the two asters of the mitotic apparatus are pushed farther apart. This is believed to occur because the microtubular spines from the two asters, where they interdigitate with each other to form the mitotic spindle, actually push each other away. There is reason to believe that minute contractile protein molecules called “molecular motors,” perhaps composed of the muscle protein actin, extend between the respective spines and, using a stepping action as in muscle, actively slide the spines in a reverse direction along each other. Simultaneously, the chromatids are pulled tightly by their attached microtubules to the very center of the cell, lining up to form the equatorial plate of the mitotic spindle.
Anaphase
During this phase (see Figure 3-14F), the two chromatids of each chromosome are pulled apart at the centromere. All 46 pairs of chromatids are separated, forming two separate sets of 46 daughter chromosomes. One of these sets is pulled toward one mitotic aster and the other toward the other aster as the two respective poles of the dividing cell are pushed still farther apart.
Telophase
In telophase (see Figure 3-14G and H), the two sets of daughter chromosomes are pushed completely apart. Then the mitotic apparatus dissolutes, and a new nuclear membrane develops around each set of chromosomes. This membrane is formed from portions of the endoplasmic reticulum that are already present in the cytoplasm. Shortly thereafter, the cell pinches in two, midway between the two nuclei. This is caused by formation of a contractile ring of microfilaments composed of actin and probably myosin (the two contractile proteins of muscle) at the juncture of the newly developing cells that pinches them off from each other.
Control of Cell Growth and Cell Reproduction
We know that certain cells grow and reproduce all the time, such as the blood-forming cells of the bone marrow, the germinal layers of the skin, and the epithelium of the gut. Many other cells, however, such as smooth muscle cells, may not reproduce for many years. A few cells, such as the neurons and most striated muscle cells, do not reproduce during the entire life of a person, except during the original period of fetal life.
In certain tissues, an insufficiency of some types of cells causes these to grow and reproduce rapidly until appropriate numbers of them are again available. For instance, in some young animals, seven eighths of the liver can be removed surgically, and the cells of the remaining one eighth will grow and divide until the liver mass returns to almost normal. The same occurs for many glandular cells and most cells of the bone marrow, subcutaneous tissue, intestinal epithelium, and almost any other tissue except highly differentiated cells such as nerve and muscle cells.
We know little about the mechanisms that maintain proper numbers of the different types of cells in the body. However, experiments have shown at least three ways in which growth can be controlled. First, growth often is controlled by growth factors that come from other parts of the body. Some of these circulate in the blood, but others originate in adjacent tissues. For instance, the epithelial cells of some glands, such as the pancreas, fail to grow without a growth factor from the sublying connective tissue of the gland. Second, most normal cells stop growing when they have run out of space for growth. This occurs when cells are grown in tissue culture; the cells grow until they contact a solid object, and then growth stops. Third, cells grown in tissue culture often stop growing when minute amounts of their own secretions are allowed to collect in the culture medium. This, too, could provide a means for negative feedback control of growth.
Regulation of Cell Size
Cell size is determined almost entirely by the amount of functioning DNA in the nucleus. If replication of the DNA does not occur, the cell grows to a certain size and thereafter remains at that size. Conversely, it is possible, by use of the chemical colchicine, to prevent formation of the mitotic spindle and therefore to prevent mitosis, even though replication of the DNA continues. In this event, the nucleus contains far greater quantities of DNA than it normally does, and the cell grows proportionately larger. It is assumed that this results simply from increased production of RNA and cell proteins, which in turn cause the cell to grow larger.
Cell Differentiation
A special characteristic of cell growth and cell division is cell differentiation, which refers to changes in physical and functional properties of cells as they proliferate in the embryo to form the different bodily structures and organs. The description of an especially interesting experiment that helps explain these processes follows.
When the nucleus from an intestinal mucosal cell of a frog is surgically implanted into a frog ovum from which the original ovum nucleus was removed, the result is often the formation of a normal frog. This demonstrates that even the intestinal mucosal cell, which is a well-differentiated cell, carries all the necessary genetic information for development of all structures required in the frog’s body.
Therefore, it has become clear that differentiation results not from loss of genes but from selective repression of different gene promoters. In fact, electron micrographs suggest that some segments of DNA helixes wound around histone cores become so condensed that they no longer uncoil to form RNA molecules. One explanation for this is as follows: It has been supposed that the cellular genome begins at a certain stage of cell differentiation to produce a regulatory protein that forever after represses a select group of genes. Therefore, the repressed genes never function again. Regardless of the mechanism, mature human cells produce a maximum of about 8000 to 10,000 proteins rather than the potential 30,000 or more if all genes were active.
Embryological experiments show that certain cells in an embryo control differentiation of adjacent cells. For instance, the primordial chorda-mesoderm is called the primary organizer of the embryo because it forms a focus around which the rest of the embryo develops. It differentiates into a mesodermal axis that contains segmentally arranged somites and, as a result of inductions in the surrounding tissues, causes formation of essentially all the organs of the body.
Another instance of induction occurs when the developing eye vesicles come in contact with the ectoderm of the head and cause the ectoderm to thicken into a lens plate that folds inward to form the lens of the eye. Therefore, a large share of the embryo develops as a result of such inductions, one part of the body affecting another part, and this part affecting still other parts.
Thus, although our understanding of cell differentiation is still hazy, we know many control mechanisms by which differentiation could occur.
Apoptosis—Programmed Cell Death
The 100 trillion cells of the body are members of a highly organized community in which the total number of cells is regulated not only by controlling the rate of cell division but also by controlling the rate of cell death. When cells are no longer needed or become a threat to the organism, they undergo a suicidal programmed cell death, or apoptosis. This process involves a specific proteolytic cascade that causes the cell to shrink and condense, to disassemble its cytoskeleton, and to alter its cell surface so that a neighboring phagocytic cell, such as a macrophage, can attach to the cell membrane and digest the cell.
In contrast to programmed death, cells that die as a result of an acute injury usually swell and burst due to loss of cell membrane integrity, a process called cell necrosis. Necrotic cells may spill their contents, causing inflammation and injury to neighboring cells. Apoptosis, however, is an orderly cell death that results in disassembly and phagocytosis of the cell before any leakage of its contents occurs, and neighboring cells usually remain healthy.
Apoptosis is initiated by activation of a family of proteases called caspases. These are enzymes that are synthesized and stored in the cell as inactive procaspases. The mechanisms of activation of caspases are complex, but once activated, the enzymes cleave and activate other procaspases, triggering a cascade that rapidly breaks down proteins within the cell. The cell thus dismantles itself, and its remains are rapidly digested by neighboring phagocytic cells.
A tremendous amount of apoptosis occurs in tissues that are being remodeled during development. Even in adult humans, billions of cells die each hour in tissues such as the intestine and bone marrow and are replaced by new cells. Programmed cell death, however, is normally balanced with the formation of new cells in healthy adults. Otherwise, the body’s tissues would shrink or grow excessively. Recent studies suggest that abnormalities of apoptosis may play a key role in neurodegenerative diseases such as Alzheimer’s disease, as well as in cancer and autoimmune disorders. Some drugs that have been used successfully for chemotherapy appear to induce apoptosis in cancer cells.
Cancer
Cancer is caused in all or almost all instances by mutation or by some other abnormal activation of cellular genes that control cell growth and cell mitosis. The abnormal genes are called oncogenes. As many as 100 different oncogenes have been discovered.
Also present in all cells are antioncogenes, which suppress the activation of specific oncogenes. Therefore, loss or inactivation of antioncogenes can allow activation of oncogenes that lead to cancer.
Only a minute fraction of the cells that mutate in the body ever lead to cancer. There are several reasons for this. First, most mutated cells have less survival capability than normal cells and simply die. Second, only a few of the mutated cells that do survive become cancerous, because even most mutated cells still have normal feedback controls that prevent excessive growth.
Third, those cells that are potentially cancerous are often destroyed by the body’s immune system before they grow into a cancer. This occurs in the following way: Most mutated cells form abnormal proteins within their cell bodies because of their altered genes, and these proteins activate the body’s immune system, causing it to form antibodies or sensitized lymphocytes that react against the cancerous cells, destroying them. In support of this is the fact that in people whose immune systems have been suppressed, such as in those taking immunosuppressant drugs after kidney or heart transplantation, the probability of a cancer’s developing is multiplied as much as fivefold.
Fourth, usually several different activated oncogenes are required simultaneously to cause a cancer. For instance, one such gene might promote rapid reproduction of a cell line, but no cancer occurs because there is not a simultaneous mutant gene to form the needed blood vessels.
But what is it that causes the altered genes? Considering that many trillions of new cells are formed each year in humans, a better question might be, why is it that all of us do not develop millions or billions of mutant cancerous cells? The answer is the incredible precision with which DNA chromosomal strands are replicated in each cell before mitosis can take place, and also the proofreading process that cuts and repairs any abnormal DNA strand before the mitotic process is allowed to proceed. Yet despite all these inherited cellular precautions, probably one newly formed cell in every few million still has significant mutant characteristics.
Thus, chance alone is all that is required for mutations to take place, so we can suppose that a large number of cancers are merely the result of an unlucky occurrence.
However, the probability of mutations can be increased manyfold when a person is exposed to certain chemical, physical, or biological factors, including the following:
1. It is well known that ionizing radiation, such as x-rays, gamma rays, and particle radiation from radioactive substances, and even ultraviolet light can predispose individuals to cancer. Ions formed in tissue cells under the influence of such radiation are highly reactive and can rupture DNA strands, thus causing many mutations.
2. Chemical substances of certain types also have a high propensity for causing mutations. It was discovered long ago that various aniline dye derivatives are likely to cause cancer, so workers in chemical plants producing such substances, if unprotected, have a special predisposition to cancer. Chemical substances that can cause mutation are called carcinogens. The carcinogens that currently cause the greatest number of deaths are those in cigarette smoke. They cause about one quarter of all cancer deaths.
3. Physical irritants can also lead to cancer, such as continued abrasion of the linings of the intestinal tract by some types of food. The damage to the tissues leads to rapid mitotic replacement of the cells. The more rapid the mitosis, the greater the chance for mutation.
4. In many families, there is a strong hereditary tendency to cancer. This results from the fact that most cancers require not one mutation but two or more mutations before cancer occurs. In those families that are particularly predisposed to cancer, it is presumed that one or more cancerous genes are already mutated in the inherited genome. Therefore, far fewer additional mutations must take place in such family members before a cancer begins to grow.
5. In laboratory animals, certain types of viruses can cause some kinds of cancer, including leukemia. This usually results in one of two ways. In the case of DNA viruses, the DNA strand of the virus can insert itself directly into one of the chromosomes and thereby cause a mutation that leads to cancer. In the case of RNA viruses, some of these carry with them an enzyme called reverse transcriptase that causes DNA to be transcribed from the RNA. The transcribed DNA then inserts itself into the animal cell genome, leading to cancer.
Invasive Characteristic of the Cancer Cell
The major differences between the cancer cell and the normal cell are the following: (1) The cancer cell does not respect usual cellular growth limits; the reason for this is that these cells presumably do not require all the same growth factors that are necessary to cause growth of normal cells. (2) Cancer cells are often far less adhesive to one another than are normal cells. Therefore, they tend to wander through the tissues, enter the blood stream, and be transported all through the body, where they form nidi for numerous new cancerous growths. (3) Some cancers also produce angiogenic factors that cause many new blood vessels to grow into the cancer, thus supplying the nutrients required for cancer growth.
Why Do Cancer Cells Kill?
The answer to this question is usually simple. Cancer tissue competes with normal tissues for nutrients. Because cancer cells continue to proliferate indefinitely, their number multiplying day by day, cancer cells soon demand essentially all the nutrition available to the body or to an essential part of the body. As a result, normal tissues gradually suffer nutritive death.
Bibliography
Alberts B., Johnson A., Lewis J., et al. Molecular Biology of the Cell, ed 5. New York: Garland Science, 2008.
Aranda A., Pascal A. Nuclear hormone receptors and gene expression. Physiol Rev. 2001;81:1269.
Brodersen P., Voinnet O. Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol. 2009;10:141.
Cairns B.R. The logic of chromatin architecture and remodelling at promoters. Nature. 2009;461:193.
Carthew R.W., Sontheimer E.J. Origins and mechanisms of miRNAs and siRNAs. Cell. 2009;136:642.
Castanotto D., Rossi J.J. The promises and pitfalls of RNA-interference-based therapeutics. Nature. 2009;457:426.
Cedar H., Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet. 2009;10:295.
Croce C.M. Causes and consequences of microRNA dysregulation in cancer. Nat Rev Genet. 2009;10:704.
Frazer K.A., Murray S.S., Schork N.J., et al. Human genetic variation and its contribution to complex traits. Nat Rev Genet. 2009;10:241.
Fuda N.J., Ardehali M.B., Lis J.T. Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature. 2009;461:186.
Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat Struct Mol Biol. 2004;11:394.
Hastings P.J., Lupski J.R., Rosenberg S.M., et al. Mechanisms of change in gene copy number. Nat Rev Genet. 2009;10:551.
Hoeijmakers J.H. DNA damage, aging, and cancer. N Engl J Med. 2009;361:1475.
Hotchkiss R.S., Strasser A., McDunn J.E., et al. Cell death. N Engl J Med. 2009;361:1570.
Jinek M., Doudna J.A. A three-dimensional view of the molecular machinery of RNA interference. Nature. 2009;457:40.
Jockusch B.M., Hüttelmaier S., Illenberger S. From the nucleus toward the cell periphery: a guided tour for mRNAs. News Physiol Sci. 2003;18:7.
Kim V.N., Han J., Siomi M.C. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol. 2009;10:126.
Misteli T., Soutoglou E. The emerging role of nuclear architecture in DNA repair and genome maintenance. Nat Rev Mol Cell Biol. 2009;10:243.
Moazed D. Small RNAs in transcriptional gene silencing and genome defence. Nature. 2009;457:413.
Siller K.H., Doe C.Q. Spindle orientation during asymmetric cell division. Nat Cell Biol. 2009;11:365.
Sims R.J.3rd, Reinberg D. Is there a code embedded in proteins that is based on post-translational modifications? Nat Rev Mol Cell Biol. 2008;9:815.
Stappenbeck T.S., Miyoshi H. The role of stromal stem cells in tissue regeneration and wound repair. Science. 2009;324:1666.
Sutherland H., Bickmore W.A. Transcription factories: gene expression in unions? Nat Rev Genet. 2009;10:457.