1. Chap. 6 Genes, Genomics, and
Chromosomes (Part B)
Topics
• Genomics: Genome-wide Analysis of Gene Structure and
Expression
• Structural Organization of Eukaryotic Chromosomes
• Morphology and Functional Elements of Eukaryotic Chromosomes
Goals
• Learn about computer-based
methods for analyzing
sequence data.
• Learn how DNA and proteins
are packaged in chromatin.
• Learn the large-scale
structure organization of
chromosomes.
• Learn the functional elements
required for chromosome
replication and segregation. RxFISH-painted human chromosomes.
2. Mining Sequence Data: BLAST Searches
An enormous amount of DNA sequence information is available
from genome sequencing and sequencing of cloned genes. This
data is stored in data banks such as GenBank at the NIH in
Bethesda, MD and the EMBL Sequence Data Base at the
European Molecular Biology Laboratory in Heidelberg, Germany.
Scientists working in the area of bioinformatics use this data to
find genes, analyze their properties, and determine phylogenetic
relationships between organisms and proteins. A common
procedure in which this data is used is the BLAST search (basic
local alignment search tool) which is used to compare protein and
DNA sequences. An example BLAST search alignment is shown
for the human neurofibromatosis 1 (NF1) gene in Fig. 6.25. The
alignment shows NF1 is related to the S. cerevisiae Ira
GTPase-activating protein (GAP) and suggests the disease is
caused by aberrant signal transduction.
Computer programs similar
to BLAST are used to
identify protein sequence
motifs (e.g., zinc fingers)
in unknown proteins. The
identification of structure
regions with known function
sheds light on overall
protein function and helps
guide experimental analysis
of unknown proteins and
genes.
3. BLAST search analysis can identify the members of a protein
family originating from gene duplication and speciation mutations.
As illustrated for the a- and ß-tubulin protein family in Fig.
6.26, an early gene duplication event created the paralogous a-
and ß-tubulin genes. Later speciation mutations lead to evolution
of the orthologous members of the a- and ß-tubulin subfamilies.
Orthologous proteins are most likely to share the same function.
Sequence Comparisons Establish
Evolutionary Relationships Among Proteins
x
4. Genome Size vs Complexity
Genome sequencing has revealed that the morphological complexity
of an organism is not strongly correlated with the size of its
genome (Fig. 6.27). Alternative splicing of RNAs and post-
translational modification of proteins are thought to greatly
increase the complexity of the proteins encoded by the genomes
of higher organisms. In addition, the relative number of cells
formed in a tissue such as the cerebral cortex can be important in
increasing complexity (e.g., mice vs humans). Genes can be
identified within the sequenced genomes of simple organisms such
as yeast and bacteria by searching for open reading frames
(ORFS). ORFs are long stretches of triplet codons lacking stop
codons. Gene annotation (assignment of likely function) is based on
knowledge from biochemical studies and/or alignments with known
sequences. In complex organisms
such as humans whose genes
typically contain introns, more
sophisticated algorithms that ID
intron splice sites and compare
cDNA and other sequence
information to genomic DNA
sequences must be applied to
locate and annotate genes. Using
such methods ~25,000 genes
have been identified in humans.
However, conclusive evidence for
synthesis of protein or RNA
products is lacking for ~10,000
genes.
5. Extended and Condensed Chromatin
Human diploid cells contain about 2 meters of DNA. To fit within
nuclei, DNA must be condensed by ~105-fold. DNA exists in cells
as a nucleoprotein complex known as chromatin. During interphase
when cells are not dividing, chromatin is relatively uncondensed
compared to its state in metaphase chromosomes. When released
from nuclei with low salt buffer, chromatin displays an extended
"beads-on-a-string" morphology, where each bead is a nucleosome
(Fig. 6.28). When released in physiological salt concentrations,
more condensed fibers of 30 nm diameter are observed. In
general, extended chromatin can be transcribed, whereas
condensed forms cannot.
6. Structure of Nucleosomes
Nucleosomes consist of 147 bp of DNA wrapped in almost two turns
around the outside of an octamer of histone proteins (Fig. 6.29).
In most nucleosomes, the octamer has a stoichiometry of
H2A2H2B2H32H42. Histones are the most abundant DNA-binding
proteins in eukaryotic cells. The sequences of the 4 histones that
make up the octamer are highly conserved across all organisms,
indicating their functions were optimized early in evolution. Histones
have a large number of basic amino acids and bind to DNA mostly
by salt-bridge interactions to phosphates in the DNA backbone.
Another histone, H1, binds to the linker DNA between
nucleosomes. Linker DNA is 10-90 bp in length depending upon the
organism.
7. Structure of 30-nm Chromatin Fibers
In 30-nm fibers, nucleosomes
bind to one another in a
double helical arrangement
(Fig. 6.30). Histone H1
molecules bind to linker DNA
between nucleosomes and help
stabilize the 30-nm fiber. The
stability of 30-nm fibers is
modulated by post-
translational modification of
the tails of histones in the
octamers (H4 in particular).
8. Histone Tails and Chromatin Condensation
The N- and C-terminal tails of histones project out from the
nucleosome core (Fig. 6.31a). They also contain numerous residues
that can be modified by acetylation, methylation, etc. (Fig.
6.31b). Acetylation of lysine side-chains by histone acetylases
(HATs) neutralizes positive charge and promotes decondensation of
30-nm fibers. Methylation, on the other hand, blocks lysine
acetylation, maintains positive charge, and promotes 30-nm fiber
condensation. Studies have shown that chromatin condensation is
not controlled simply by the net acetylation state of histones.
Rather, the sites where acetylation and other modifications occur
also are important. The combinations of modifications that specify
condensation/decondensation are referred to as the "histone code".
9. Interphase Chromatin
Interphase chromatin exists in two
different condensation states (Fig.
6.33a). Heterochromatin is a
condensed form that has a
condensation state similar to
chromatin found in metaphase
chromosomes. Euchromatin is
considerably less condensed.
Heterochromatin typically is found
at centromere and telomere
regions, which remain relatively
condensed during interphase. The
inactivated copy of the X-
chromosome (Barr body) that
occurs in cells in females also
occurs as heterochromatin. In
contrast, most transcribed genes
are located in regions of
euchromatin. Common modifications
occurring in histone H3 in hetero-
and euchromatin are illustrated in
Fig. 6.33b.
10. Formation of
Heterochromatin
The trimethylation of histone H3 at
lysine 9 (H3K9Me3) plays an
important role in promoting chromatin
condensation to heterochromatin (Fig.
6.34a). Trimethylated sites are
bound by heterochromatin protein 1
(HP1) which self-associates and
oligomerizes resulting in
heterochromatin. Heterochromatin
condensation is thought to spread
laterally between “boundary
elements” that mark the ends of
transcriptionally active euchromatin
(Fig. 6.34b). Recruitment of the
H3K9 histone methyl transferase
(HMT) to HP1 sites promotes
heterochromatin spreading by
catalyzing H3 methylation.
11. Structure of Interphase Chromosomes
FISH analysis performed with fluorescent probes that bind to
sequential sequence sites along DNA supports a looped structure
for interphase chromosomes (Fig. 6.35). Loops range in size
from 1 to 4 million base pairs in mammalian interphase cells.
The bases of the loops are located near the center of the
chromosome at scaffold-associated regions (SARs), and matrix-
attachment regions (MARs). The DNA fibers at the base of the
loops are held together by structural maintenance of
chromosome (SMC) proteins (Fig. 6.36c) and other non-histone
proteins. Transcription units containing expressed genes are
located in uncondensed loop regions, away from the more
condensed center of the chromosome.
12. Interphase Chromosome Territories
In situ hybridization of interphase nuclei with chromosome-
specific fluorescently-labeled probes indicates that
chromosomes reside within restricted regions of the nucleus
rather than appearing throughout the nucleus (Fig. 6.37).
Interestingly, the precise positions of chromosomes are not
reproducible between cells.
13. Structure of Metaphase Chromosomes
In metaphase chromosomes,
the number of loops of
chromatin is increased and the
lengths of the loops are
decreased compared to what
occurs in interphase
chromosomes. In addition,
more folded structures called
chromonema fibers and higher
order structures occur in
prophase and metaphase
chromatids (Fig. 6.38).
14. Microscopic Structure of Metaphase
Chromosomes
Because interphase chromosomes
are not easily visualized by
microscopy techniques, chromosome
morphology has been studied mostly
using metaphase chromosomes.
Metaphase chromosomes are
duplicated structures formed after
DNA replication is complete. They
contain two sister chromatids joined
at a structure called the
centromere (Fig. 6.39). The ends
of chromatids are called telomeres.
Centromeres are required for
chromatid separation late in mitosis.
Telomeres are important in
preventing chromosome shortening
during replication. The number,
sizes, and shapes of metaphase
chromosomes constitute the
karyotype, which is distinctive for
each species.
15. Chromosome Banding Patterns
A number of dyes, such as Giemsa reagent, selectively stain
different regions of chromosomes forming distinctive bands. For
Giemsa reagent, banding is affected by G + C content. Banding
patterns are very important in chromosome ID and in looking for
chromosomal abnormalities and mapping the locations of genes.
The most detailed staining is achieved via multicolor FISH
chromosome painting. In this technique, staining is performed
using a mixture of DNA probes coupled to several fluorescent
dyes (See Slide 1). In Fig. 6.40 below, FISH staining patterns
have been converted to false-color images to visualize
chromosomes. Standard terminology is used for naming band and
gene locations in chromosomes. The short arm is designated "p",
and the long arm "q". Arms are further divided into major
sections and subsections that are numbered consecutively out
from the centromere.
16. Detection of Translocations
The analysis of chromosome banding patterns is used to detect
anomalies such as truncations and translocations associated with
certain genetic disorders and cancers. In chronic myelogenous
leukemia, leukemic cells contain a shortened chromosome 22 and
a longer chromosome 9 resulting from a translocation event in the
q arms of these two chromosomes (Fig. 6.41). The shortened
chromosome is distinctive and is referred to as the "Philadelphia
chromosome". Multicolor FISH staining (right) is useful in
identification of such chromosomes in a chromosome spread.
17. Evolution of Human Chromosomes
Through the determination of
locations of common chromosomal
segments in modern primate
chromosomes, investigators have
calculated the most likely
karyotype of the common
ancestor of all primates (Fig.
6.42c). In addition, they have
proposed a model for how the
human karyotype evolved from
that ancestor. Major events in
the evolution of the human
karyotype include 1) formation of
chromosome 2 by fusion of
ancestral chromosomes 9 and 11,
2) formation of chromosomes 14
and 15 by breakage of ancestral
chromosome 5, and 3) formation
of chromosomes 12 and 22 by
translocations between ancestral
chromosomes 14 and 21. In other
cases (e.g., chromosome 1), no
significant rearrangements have
occurred over time.
18. ID of Functional Chromosomal Elements (I)
Studies with yeast have demonstrated that all chromosomes must
contain 3 functional elements to replicate and segregate correctly:
1) replication origins, 2) a centromere, and 3) telomeres. Yeast
replication origins were identified in plasmid cloning studies. Only
yeast plasmids containing a copy of a sequence referred to as the
autonomously replicating sequence (ARS) could be transfected into
yeast cells (Fig. 6.44a). The haploid S. cerevisiae genome contains
many ARSs distributed among its 16 chromosomes.
19. ID of Functional Chromosomal Elements (II)
While only ARSs are needed for plasmid replication, an additional
sequence identified by cloning procedures was found to be required
for efficient segregation of plasmids to yeast daughter cells (Fig.
6.44b). This DNA proved to contain chromosomal centromere
sequences (CEN sequences). Yeast CEN sequences are relatively
simple (Fig. 6.45, not covered). In humans, they consist of 2-4 x
106 bp of simple sequence DNA composed of a 171 bp repeat unit.
The human centromere sequence is bound by specialized nucleosomes
containing a centromere-specific histone H3 variant (CENP-A). A
large complex of non-histone proteins (the kinetochore) binds to
centromeres and attaches them to microtubules of the mitotic
spindle apparatus.
20. ID of Functional Chromosomal Elements (III)
Yeast transfection studies also showed that linearized plasmids
containing ARS and CEN sequences could be maintained in cells
only if telomere (TEL) sequences were attached at their ends
(Fig. 6.44c). The function of TEL sequences in replication of
chromosome ends is illustrated in the next two slides.
21. Function of Telomeres
A special mechanism is needed to
complete the replication of DNA
in DNA strands that have their
3’ ends located at the ends of
chromosomes. DNA polymerases
cannot complete synthesis of this
region of DNA, and without
synthesis, chromosomes become
shortened with each round of
replication (Fig. 6.46).
Shortening results in the loss of
binding sites for proteins that
protect the ends of linear
chromosomes from attack by
exonucleases. As illustrations of
the importance of telomere
replication, knockout mice lacking
the enzyme that synthesizes DNA
at telomeres, telomerase, cannot
produce viable offspring after six
generations. In addition,
telomerase often is switched on
in cancer cells.
22. Mechanism of Action of Telomerase
Telomere sequences typically consist of
tandemly repeating sequence units with
a high G content in the strand that has
its 3' end at the end of the
chromosome. In humans and other
vertebrates, the repeating sequence is
TTAGGG. This sequence unit repeats
over a few thousand base pairs in
humans. The mechanism of replication of
this DNA is illustrated in Fig. 6.47 for
a protozoan species. Replication is
carried out by the enzyme known as
telomerase. Telomerase is a reverse
transcriptase that carries its own
internal RNA template which binds to
the ssDNA at the chromosome 3’ end
and allows this strand to be elongated.
Ultimately, DNA Pol a/primase can
synthesize a primer on this strand,
which is elongated by DNA Pol . Some
organisms rely on a different mechanism
for replication of telomeric DNA. For
example, flies lack telomerase and
maintain telomere length by regulated
insertion of non-LTR retrotransposons
into telomere DNA.
