Eukaryotic Genomes: Organization, Regulation, and Evolution
I. Chromatin structure is based on successive levels of DNA packing.
A. Eukaryotic DNA is precisely combined with large amounts of protein.
B. Eukaryotic chromosomes contain an enormous amount of DNA relative to th8ir
condensed length. Each human chromosome averages about 1.5 × 10 nucleotide
pairs. If extended, each DNA molecule would be about 4 cm long, thousands of
times longer than the cell diameter.
C. The chromosomes fit into the nucleus through an elaborate, multilevel system of
D. Histone proteins are responsible for the first level of DNA packaging.
1. The mass of histone in chromatin is approximately equal to the mass of
2. Their positively charged amino acids bind tightly to negatively charged
3. The five types of histones are very similar from one eukaryote to another,
and similar proteins are found in prokaryotes.
4. The conservation of histone genes during evolution reflects their pivotal
role in organizing DNA within cells.
5. Unfolded chromatin has the appearance of beads on a string.
a. In this configuration, a chromatin fiber is 10 nm in diameter (the
b. Each bead of chromatin is a nucleosome, the basic unit of DNA
c. The ―string‖ between the beads is called linker DNA.
6. A nucleosome consists of DNA wound around a protein core composed of
two molecules each of four types of histone: H2A, H2B, H3, and H4.
a. A molecule of a fifth histone, H1, attaches to the DNA near the
7. The beaded string seems to remain essentially intact throughout the cell
8. Histones leave the DNA only transiently during DNA replication and they
stay with the DNA during transcription.
a. By changing shape and position, nucleosomes allow RNA-
synthesizing polymerases to move along the DNA.
E. The next level of packing is due to the interactions between the histone tails of one
nucleosome and the linker DNA and nucleosomes to either side.
1. With the aid of histone H1, these interactions cause the 10-nm to coil to
form the 30-nm chromatin fiber.
2. This fiber forms looped domains attached to a scaffold of nonhistone
proteins to make up a 300-nm fiber.
3. In a mitotic chromosome, the looped domains coil and fold to produce the
characteristic metaphase chromosome. 4. An interphase chromosome lacks an obvious scaffold, but its looped
domains seem to be attached to the nuclear lamina on the inside of the
nuclear envelope, and perhaps also to fibers of the nuclear matrix.
5. The chromatin of each chromosome occupies a specific restricted area
within the interphase nucleus.
6. Interphase chromosomes have highly condensed
areas, heterochromatin, and less compacted areas, euchromatin.
a. Heterochromatin DNA is largely inaccessible to transcription
enzymes presumably because they cannot reach the DNA .
b. Looser packing of euchromatin makes its DNA accessible to
enzymes and available for transcription.
II. In addition to its role in packing DNA inside the nucleus, chromatin organization
regulates gene expression.
A. Histone acetylation (addition of an acetyl group —COCH ) and d3acetylation
appear to play a direct role in the regulation of gene transcription.
1. Acetylated histones grip DNA less tightly, providing easier access for
transcription proteins in this region.
2. Some of the enzymes responsible for acetylation or deacetylation are
associated with or are components of transcription factors that bind to
3. Thus histone acetylation enzymes may promote the initiation of
transcription not only by modifying chromatin structure, but also by
binding to and recruiting components of the transcription machinery.
B. DNA methylation is the attachment by specific enzymes of methyl groups (—
CH )3to DNA bases after DNA synthesis.
1. Inactive DNA is generally highly methylated compared to DNA that is
2. DNA methylation proteins recruit histone deacetylation enzymes,
providing a mechanism by which DNA methylation and histone
deacetylation cooperate to repress transcription.
3. Once methylated, genes usually stay that way through successive cell
4. Methylation enzymes recognize sites on one strand that are already
methylated and correctly methylate the daughter strand after each round of
5. This methylation patterns accounts for genomic imprinting in which
methylation turns off either the maternal or paternal alleles of certain
genes at the start of development.
a. The chromatin modifications just discussed do not alter DNA
sequence, and yet they may be passed along to future generations
b. Inheritance of traits by mechanisms not directly involving the
nucleotide sequence is called epigenetic inheritance.
III. Transcription initiation is controlled by proteins that interact with DNA and with each
other. A. Chromatin-modifying enzymes provide initial control of gene expression by
making a region of DNA either more available or less available for transcription.
B. A cluster of proteins called a transcription initiation complex assembles on the
promoter sequence at the ―upstream‖ end of the gene.
C. One component, RNA polymerase II, transcribes the gene, synthesizing a primary
RNA transcript or pre-mRNA.
D. Multiple control elements are associated with most eukaryotic genes.
1. Control elements are noncoding DNA segments that regulate transcription
by binding certain proteins.
2. These control elements and the proteins they bind are critical to the precise
regulation of gene expression in different cell types.
E. To initiate transcription, eukaryotic RNA polymerase requires the assistance of
proteins called transcription factors.
1. Only a few general transcription factors independently bind a DNA
sequence such as the TATA box within the promoter.
2. Others in the initiation complex are involved in protein-protein
interactions, binding each other and RNA polymerase II.
3. The interaction of general transcription factors and RNA polymerase II
with a promoter usually leads to only a low rate of initiation and
production of few RNA transcripts.
4. In eukaryotes, high levels of transcription of particular genes depend on
the interaction of control elements with specific transcription factors.
5. Some control elements, named proximal control elements, are located
close to the promoter.
6. Distant control elements, enhancers, may be thousands of nucleotides
away from the promoter or even downstream of the gene or within an
a. A given gene may have multiple enhancers, each active at a
different time or in a different cell type or location in the organism.
b. An activator is a protein that binds to an enhancer to stimulate
transcription of a gene.
7. Protein-mediated bending of DNA brings bound activators in contact with
a group of mediator proteins that interact with proteins at the promoter.
This helps assemble and position the initiation complex on the promoter.
8. Eukaryotic genes also have repressor proteins to inhibit expression of a
a. Eukaryotic repressors can cause inhibition of gene expression by
blocking the binding of activators to their control elements or to
components of the transcription machinery or by turning off
transcription even in the presence of activators.
9. Some activators and repressors act indirectly to influence chromatin
a. Some activators recruit proteins that acetylate histones near the
promoters of specific genes, promoting transcription. b. Some repressors recruit proteins that deacetylate histones, reducing
transcription or silencing the gene.
c. Recruitment of chromatin-modifying proteins seems to be the most
common mechanism of repression in eukaryotes.
10. For many genes, the particular combination of control elements associated
with the gene may be more important than the presence of a single unique
control element in regulating transcription of the gene. Even with only a
dozen control element sequences, a large number of combinations are
a. A particular combination of control elements will be able to
activate transcription only when the appropriate activator proteins
are present, such as at a precise time during development or in a
particular cell type.
b. The use of different combinations of control elements allows fine
regulation of transcription with a small set of control elements.
11. Remember that in prokaryotes, coordinately controlled genes are often
clustered into an operon with a single promoter and other control elements
upstream. The genes of the operon are transcribed into a single mRNA and
12. In contrast, very few eukaryotic genes are organized this way. Some
coexpressed genes are clustered near each other on the same chromosome.
a. Each eukaryotic gene in these clusters has its own promoter and is
b. The coordinate regulation of clustered genes in eukaryotic cells is
thought to involve changes in the chromatin structure that makes
the entire group of genes either available or unavailable for
c. More commonly, genes coding for the enzymes of a metabolic
pathway are scattered over different chromosomes.
d. Coordinate gene expression in eukaryotes depends on the
association of a specific control element or combination of control
elements with every gene of a dispersed group.
e. A common group of transcription factors binds to all the genes in
the group, promoting simultaneous gene transcription.
IV. Post-transcriptional mechanisms play supporting roles in the control of gene expression.
A. By using regulatory mechanisms that operate after transcription, a cell can rapidly
fine-tune gene expression in response to environmental changes without altering
its transcriptional patterns.
B. RNA processing in the nucleus and the export of mRNA to the cytoplasm provide
opportunities for gene regulation that are not available in bacteria.
C. In alternative RNA splicing, different mRNA molecules are produced from the
same primary transcript, depending on which RNA segments are treated as exons
and which as introns.
1. Regulatory proteins specific to a cell type control intron-exon choices by
binding to regulatory sequences within the primary transcript. D. The life span of an mRNA molecule is an important factor in determining the
pattern of protein synthesis.
1. Prokaryotic mRNA molecules may be degraded after only a few minutes.
2. Eukaryotic mRNAs typically last for hours, days, or weeks.
3. A common pathway of mRNA breakdown begins with enzymatic
shortening of the poly-A tail.
a. This triggers the enzymatic removal of the 5’ cap.
b. This is followed by rapid degradation of the mRNA by nucleases.
4. During the past few years, researchers have found small single-stranded
RNA molecules called microRNAs, or miRNAs, that bind to
complementary sequences in mRNA molecules.
a. miRNAs are formed from longer RNA precursors that fold back on
themselves, forming a long hairpin structure stabilized by
b. An enzyme called Dicer cuts the double-stranded RNA into short
c. One of the two strands is degraded. The other miRNA strand
associates with a protein complex and directs the complex to any
mRNA molecules with a complementary sequence.
d. The miRNA-protein complex then degrades the target mRNA or
blocks its translation.
e. The phenomenon of inhibition of gene expression by RNA
molecules is called RNA interference (RNAi).
f. Small interfering RNAs (siRNAs) are similar in size and function
to miRNAs and are generated by similar mechanisms in eukaryotic
g. Cellular RNAi pathways lead to the destruction of RNAs and may
have originated as a natural defense against infection by RNA
E. Translation of specific mRNAs can be blocked by regulatory proteins that bind to
specific sequences or structures within the 5’ leader region of mRNA. This
prevents attachment of ribosomes.
F. mRNAs may be stored in egg cells without poly-A tails of sufficient size to allow
1. At the appropriate time during development, a cytoplasmic enzyme adds
more A residues, allowing translation to begin.
G. Protein factors required to initiate translation in eukaryotes offer targets for
simultaneously controlling translation of all mRNAs in a cell.
1. This allows the cell to shut down translation if environmental conditions
are poor (for example, shortage of a key constituent) or until the
appropriate conditions exist (for example, after fertilization in an egg or
during daylight in plants).
V. Cancer results from genetic changes that affect the cell cycle.
A. Cancer is a disease in which cells escape the control methods that normally
regulate cell growth and division. B. The gene regulation systems that go wrong during cancer are the very same