Genome Organization and Expression in Eukaryotes

In eukaryotes, gene expression must be controlled to allow cell differentiation and development. Genes are continually turned on and off in response to the internal and external environments. Human cells express between 3-5% of their genes at any given time. In most cases it is the transcription of DNA that is controlled.

1.         Genome Organization

            a.         Eukaryotic genomes are associated with proteins in very specific ways. Normally, the chromatin appears as a diffuse mass. During cell division, however, it condenses to form short, thick, discrete chromosomes.

            b.         DNA packing

                        i.         Nucleosomes (Fig. 18.1 a) - proteins called histones act as spools around which DNA is wound. The amount of histone protein is about the same as the amount of DNA. They contain many positively charged amino acids and so bind to the negatively charged DNA. A nucleosome is a stretch of DNA wound around 4 histone proteins.

                        ii.        30 nm chromatin fibres (Fig. 18.1 b) - groups of 6 nucleosomes wind tightly together to form a cylinder.

                        iii.       Looped domains (Fig. 18.1 c) - long loops of 30 nm fibre form loops which are attached to a nonhistone protein scaffold.

                        iv.       Mitotic chromatin - during mitosis, the looped domains also fold and coil to produce tightly coiled masses of DNA.

                        v.         During interphase, the chromatin is much less tightly coiled but is still associated with a protein scaffold on the inside of the nuclear lamina and each chromosome occupies a specific area within the nucleus.

                        vi.       Even during interphase, some DNA exists in a tightly packed form called heterochromatin. It is known that the DNA of heterochromatin is not transcribed so this likely serves as a way of controlling gene expression. The Barr body is an example of DNA that exists as heterochromatin.

            c.         Noncoding sequences.

                        i.         Repetitive sequences

                                    (1)       Between 10-25% of eukaryotic DNA is made of short sequences (5 - 10 nucleotides) that are repeated thousands or millions of times. Most is located at the tips and centromeres of chromosomes.

                                    (2)       During DNA replication, primers must be placed in front of the section to be replicated. Because DNA polymerase cannot begin de novo, replace of the whole primer at the ends of chromosomes, called telomeres, is impossible. Hence, chromosomes get shorter with each division. Cells prevent this by using an enzyme called telomerase to place repetitive sequences at the ends of chromosomes.

                                    (3)       A decrease in the length of telomeres has been linked to cell aging and death.

                        ii.        Multigene families

                                    (1)       Some genes are present in more than one copy and others are closely related in sequence. These are called multigene families and each family likely evolved from a single ancestral gene. An example is the group of genes that code for rRNA. These are present in groups of hundreds or thousands which enables the cell to make millions of ribosomes very quickly.

                                    (2)       Some copies in a gene family have sequences similar to other members but lack promoters or other elements required for transcription. These are called pseudogenes.

                        iii.       Remember that introns also qualify as noncoding DNA.

2.         Genome expression

            a.         Transcriptional control

                        i.         The binding of transcription factors influences the transcription of a gene

                        ii.        Other proteins bind to sequences called enhancers, located up to thousands of bases upstream of the promoter. The DNA between the enhancer and the promoter loops out so that the two are brought close together, enhancing transcription (Fig. 18.6).

            b.         Posttranscriptional control

                        i.         RNA processing - the addition of the 5' cap and the poly-A tail are further ways in which gene expression can be controlled although little is known about how it might work.

            c.         Translational control

                        i.         Because translation involves several different proteins, it offers several opportunities to control gene expression.

                        ii.        Proteins can bind to the 5'end of mRNA molecules and block translation. This way, a cell can manufacture large quantities of mRNA before they are needed but block their translation. Then, when some trigger occurs, they can experience an explosive burst of protein synthesis.

                        iii.       After translation, many polypeptides are modified to become active. This represents the last opportunity for control.

            d.         Hormones

                        i.         Steroid hormones are soluble in lipids and so can cross the plasma and nuclear membranes. In the nucleus, the hormone binds with a protein and the complex then binds to an enhancer site in DNA, increasing transcription.

                        ii.        Protein hormones are unable to cross membrane so cannot enter the cell or the nucleus. Instead, they initiate a signal transduction pathway that leads to the activation of transcription factors which, in turn, increase the transcription of specific genes.

            e.         DNA methylation - the addition of methyl groups (-CH₃) to bases of DNA can inactivate a stretch of DNA.

3.         Cancer

            a.         Cancer is characterized by cells that have escaped normal control on growth and division. If the genes that regulate cell growth and division become changed by mutation, physical damage, radiation, or viruses, they can cease to function correctly.

            b.         Proto-oncogenes are genes that normally code for proteins that regulate cell growth and division. When these genes escape normal control, they are called oncogenes, and can trigger abnormal cell growth - cancer.

            c.         Tumor-suppressor genes - are genes which tend to inhibit cell growth. Any change that decreases the activity of these genes can also result in cancer.

            d.         Usually, more than one change must occur for cells to become fully cancerous. This explains why risk factors tend to add up and why the incidence of cancer increases with age.