Chapter 3: Genome Organization: From Nucleotides To Chromatin
I. Introduction
A. Introduction: Genomes; Prokaryotic and Eukaryotic
1. The human genome is approximately 3.4 billion bases and
encodes about 19,000 genes
2. If you were to stretch out the 3.4 billion bases, one would find
that the DNA molecule would be about 2m long
a. A human cell nucleus is going to be approximately 10
μm in diameter
b. Represents a packing ratio of 1000 – 10,000 fold
3. Another way of looking at this is if we were to take a string the
length of the Sears Tower, and fit it into a tennis ball, how easy
would it be to do that?
4. Somehow, the cell must have a way to actually package all of
the DNA into the nucleus
5. “The way in which eukaryotic DNA is packaged in the cell
nucleus is one of the wonders of macromolecular structure”
–G. Michael Blackburn, Nucleic Acids in Chemistry and Biology
(1990) p. 65
B. Introduction: Important Definitions
1. Genome: The entire complement of genetic material of the cell
of an organism or virus – will contain all of the genes
2. Genomic DNA: The full complement of DNA found in the
genome of an organism/virus
3. Throughout this chapter, we will study the genome
organization of several different types of organisms or viruses
a. Eukaryotes: Organisms with cells that contain
membrane bound organelles have multiple chromosomes
b. Prokaryotes: Organisms that do not contain membrane
bound organelles have single circular chromosomes
c. DNA Viruses: Viruses whose genome is stored as DNA
d. RNA Viruses: Viruses whose genome is stored as RNA
e. Organelles: Mitochondria and Chloroplasts have
genomes
C. Introduction: Dealing With Genome Size
1. Many organisms have a genome size that is significantly larger
than the space that it needs to fit into
2. Organisms must have ways to organize the genome in such a
way that it fits into the appropriate space
a. The cell for prokaryotes
b. The nucleus for eukaryotes
c. Viral capsid for viruses
3. Organisms have found creative ways to deal with the problem
of fitting a larger genome into a small space
a. Dividing the genome (Chromosomes)
b. Winding the DNA around proteins to form tight
structures known as nucleosomes
II. Eukarytic Genome Structure
A. Eukaryotic Genome Structure: Introduction
1. Along with dividing the genome into linear chromosomes,
eukaryotic cells must pack the linear DNA molecules into
chromatin
a. Chromatin is defined as the genomic DNA and its
associated proteins
b. This allows for sufficient packing of the genomic DNA
into the nucleus
2. To form chromatin, the genomic DNA must be wound around a
specific structure called a nucleosome
a. Genomic DNA is first wound around a histone complex
b. Allows for compaction
3. Genomic DNA is not just wound around one nucleosome, but
many nucleosomes
B. Eukaryotic Genome Structure: Building The Nucleosome Starting
With The Histones
1. In 1928 Albrecht Kossel was the first to isolate histones
a. Isolated from goose erythrocytes
b. Discovered that they were basic (have a positive charge)
2. Two types of histones exist
a. Highly conserved core histones (MW of 11-16 kD)
b. More variable linker histones
3. Core histones, form the core of the nucleosome, and are
present as an octamer
a. Histone H2A
b. Histone H2B
c. Histone H3
d. Histone H4
4. The core histones are rich in lysine and arginine
5. Histone H3 and Histone H4 form a central tetramer
6. Histone H2A and Histone H2B form heterodimers at each end
of the central tetramer
7. Compared to the core histones, the linker histones are larger,
with a molecular weight of greater than 20 kD
8. There are three types of linker histones
a. Histone H1
b. Histone H10
c. Histone H5 (only found in avian erythrocytes)
9. The most commonly used linker histone is Histone H1
10. The linker histone is generally found between core octamers
C. Eukaryotic Genome Structure: Forming the Nucleosome Structure
1. The term nucleosome refers to the core octamer, the linker
histone and about 180 bp of DNA
2. Nucleosomes were first visualized by the labs of Roger
Kornberg and Pierre Chambon by electron microscopy
3. The core nucleosome particle consists of the core histones plus
180 bp of DNA
a. The core histones act as a spool
b. The negatively charged DNA will wind around the
positively charged core histones
c. 146 bp of DNA wind around the core histone complex
4. The 146 bp of DNA wil wrap nearly twice around the positively
charged histones in 1.67 left-handed superhelical turns
5. The double helix is curved around the nucleosome core and is
stretched on average about 1-2 bp, which results in a difference
of 10.17 bp per helical turn, as compared to 10.5 bp/helical turn
for naked DNA
6. The interactions holding the DNA to the nucleosomes are
electrostatic, as the histones can be removed by washing with
solutions with high salt concentration
D. Eukaryotic Genome Structure: Determining That 180 bp of DNA is
Wound Around a Single Nucleosome
1. In order to figure out the amount of DNA wound around a
nucleosome, the enzyme Micrococcal nuclease was used
a. Micrococcal nuclease will digest free double stranded
DNA
b. Micrococcal nuclease will not digest double stranded
DNA associated with proteins
2. To perform the experiment, chromatin was first subjected to
treatment with a low concentration of micrococcal nuclease
3. Once treatment was finished, protein components were
removed, leaving only the DNA that was associated with the
nucleosomes
4. The DNA was then run on an agarose gel
5. On the agarose gel, they saw DNA bands at mutliples of 180 bp
E. Eukaryotic Genome Structure: The Beads-on-a-String Theory of
Genome Structure
1. In 1975, Chambon’s lab published electron micrographs of the
eukaryotic genome revealed the existence of uniformly sized
particles with a repeating pattern
2. The genome looked like “Beads-on-a-string”
3. The Beads-on-a-string appearance can be visualized by
electron microscopy after low salt extraction of the genomic DNA
a. The beads represent DNA wrapped around the histone
core octamer
b. The string represents the free DNA helix between
nucleosomes
c. Note: these methods of extraction are non-physiological
and therefore, it is unknown whether this conformation
exists in vivo
F. Eukaryotic Genome Structure: The 30 nm Fiber
1. Chromatin in situ show nucleosomal arrays forming a compact
fiber of approximately 30 nm in diamter
a. Observed by electron microscopy
b. Difficult to maintain the 30 nm structure upon
purification and so the structure remains poorly
understood
2. Two possible models have been proposed for the structure of
the 30 nm fiber-based on high salt extractions
a. Selenoid model
b. Zig-Zag model
3. The selenoid model involves six consectutive nucleosomes
arranged in a turn of a helix
a. Once thought to be the physiologically relevant model
b. Doesn’t form at physiological salt concentrations (150
nM)-probably not relevant in situ
4. The zig-zag ribbon structure twists and supercoils, and
through X-ray crystallography has been seen in transcriptionally
active cells
G. Eukaryotic Genome Structure: Loop Domains
1. The 30 nm fiber is compacted further to form more elaborate
structure, which allow for better packing
2. Compaction allows for formation of loop domains containing
50-100 kb of DNA (0.25μm)
3. The loops are created by attaching DNA to the proteins
associated with the underlying nuclear scaffold
4. In the interphase cell, the packing ratio is about 1000-fold
H. Eukaryotic Genome Structure: Metaphase Chromosomes
1. The eukaryotic genome structures we have talked about
pertain to interphase cells where the chromosomes are generally
decondensed
2. As the cell enters mitosis the chromosomes begin to condense
a. Condensation begins in prophase
b. The chromosomes become fully condensed in
metaphase
3. In condensing the genomic DNA, the cell is going to have to
incorporate even greater chromatin structure
5. Condensation requires of chromatin to achieve the metaphase
chromosome structure requires several ATP-hydrolyzing
enzymes and the condensin complex
6. Condensin is a large protein complex
a. Composed of five subunits
b. One of the most abundant structural components of the
condensed metaphase chromosomes
7. Supplemental figure: Eukaryotic Genome Structure: Metaphase
Chromosomes
III. Other Genome Structures
A. Other Genome Structures: Prokaryotic Genome Structure
1. Bacteria do not have a nucleus, however they must compact
their single chromosome that is 1000 times the length of the cell
2. The single bacterial chromosome is circular
a. No free 5’ and 3’ ends
b. About 4700 kb in size
3. Bacterial chromosomal DNA is organized into a condensed
ovoid structure called a nucleoid
4. Several proteins are responsible for compacting the DNA into
the nucleoid, which are “histone-like”
a. HU protein (Stands for Heat Unstable)
b. IHF protein (Stands for Integration host factor)
c. HNS protein (Heat stable nucleoid structuring)
d. SMC (Structural maintenance of chromosomes)
5. Each of the proteins above are considered non-essential (i.e.
the bacteria can survive and reproduce without them)
6. Further condensation packs the bacterial genome into
supercoiled domains of 20-100kb domains
B. Other Genome Structures: Prokaryotic Plasmids
1. Plasmids are small, double-stranded, circular molecules of
DNA
a. Found mainly in plasmids
b. Specific plasmids that can be found in yeast
c. Generally are about 2 kb-100kb in size
d. Are a few plasmids that are linear
2. Plasmids are extra-chromosomal, meaning they are
completely separate from the host cell’s chromosome
a. Plasmids are independent
b. Plasmids are self-replicating
3. During mitosis, at least one copy of a plasmid is passed onto
each new daughter cell
4. For the bacteria, plasmids are important in that they can carry
genes for resistance to antibiotics
5. For the purpose of the laboratory, they can be used as vecors
for recombinant DNA technology (i.e. molecular cloning of genes)
C. Other Genome Structures: Organelle Genomes
1. Mitochondria (found in all eukaryotes) and chloroplants
(mainly found in plants) have their own circular genomes
a. Usually, but not always circular
b. Circular genomes are very similar to bacterial
chromosomes
2. The fact that organelle genomes look like prokaryotic genomes
led to the development of the “endosymbiont hypothesis”
3. The “endosymbiont hypothesis” states that both mitochondria
and chloroplasts are derived from primitive, free-living
organisms that were much like bacteria
4. Organelle genomes are inherited independently of the nuclear
genome
a. Exhibit a uniparental mechanism of inheritance
b. Organelles are maternally inherited
D. Other Genome Structures: Chloroplast DNA (cpDNA)
1. The main function of the chloroplast is to perform
photosynthesis
2. The cpDNA has evolved to encode enzymes involved in
photosynthesis
3. The cpDNA is most commonly depicted as a double-stranded
circular molecule
a. Size ranges from about 120-160 kb (depending on the
organism)
b. Usually 20-40 copies per organelle
4. Further research into the structure of the cpDNA suggests that
most cpDNA is actually linear, and that only a small amount is
actually circular
5. Compared to the nuclear genoe, the cpDNA is free of the
common proteins (histones) associated with the eukaryotic DNA
a. Has a different buoyant density
b. Has a different base composition
E. Other Genome Structures: Mitochondrial DNA (mtDNA)
1. The main function of the mitochondrion is to carry out cellular
metabolism
2. The mitochondrial genome will encode essential enzymes
involved in ATP production
3. mtDNA is generally found a circular, double-stranded molecule
that is free of histones
a. In some eukaryotes the mtDNA can be linear
b. Yeast and other fungi
4. mtDNA differs in size between organisms
a. Animals: 16-18 kb
b. Plants: 100 kb – 2.5 Mb
5. Many copies of mtDNA can be found per mitochondrion, with
as many as 30 copies in the mitochondrian of Euglena
F. Other Genome Structures: Mitochondrial DNA (mtDNA) and Disease
1. Mutations in the mtDNA can result in significant, inheritable
genetic disease affecting 1 in 8500
2. One example of a mitochondrial disease is Leber’s Hereditary
Optic Neuropathy (LHON)
a. Rapid onset of blindness
b. Blindness occurs in young adults due to optic nerve
atrophy
c. Strong sex bias: ~50% of male carriers have vision loss,
whereas only 10% of females do
3. LHON is due to a substitution 1178A>G in the gene encoding
the ND4 subunit of complex I of the electron transport chain
4. LHON is largely homoplasmic – all of the mtDNA molecules in
the afflicted individual will have this mutation
G. Other Genome Structures: Mammalian DNA Viruses
1. Mammalian DNA viruses infect mammalian cells
2. In order to replicate themselves, the use the host machinery to
carry out their replication
a. Replicating the genome
b. Creation of the viral capsid
3. When it comes to genomes of DNA viruses, there is a large
diversity of forms
a. HPV, which is a causitive agent of cervical cancers has a
double-stranded circular genome
b. Simian virus 40 (SV40) from rhesus monkey has a
circular, double-stranded genome
c. Adenoviruses, which can cause respiratory, or gastrointestinal symptoms have a double- stranded, linear
genome
4. Little is known about how DNA viruses package their genome
into new viral capsids after replications
a. Some viruses use their own proteins for packaging
b. Others will use host proteins
c. Papovaviruses will use the core histones for genome
packaging
H. Other Genome Structures: RNA-Based Genomes
1. RNA can serve as the genome for a variety of different
infectious agents and pathogens
a. RNA viruses
b. Retroviruses
c. Viroids
d. Other subviral pathogens
2. RNA based genomes have rates of mutation that are 1000-fold
higher than DNA based genomes
a. Due to the fact that RNA polymerases lack exonuclease
proofreeading activity
b. Assumption that higher rates of mutation are
advantageous and allow for better evasion of the host
immune system (not supported experimentally)
3. Mutation rate may be explained as a trade-off between
replication rate and replication fidelity - Proofreading would
increase fidelity, but would slow the rate of replication
4. Table 3.3: Other Genome Structures: RNA-Based Genomes
J. Other Genome Structures: Eukaryotic RNA Viruses
1. Eukaryotic RNA viruses can infect a wide variety of organisms
a. Animals
b. Plants
c. Others
2. Some viral RNA genomes are single-stranded, others are
double stranded
3. Typically eukaryotic RNA viruses do not replicate their
genome by using a DNA intermediate
4. There are three main categories of eukaryotic RNA viruses
a. Plus-strand viruses: make protein directly using their
genomic RNA
b. Minus-strand viruses: Must make complementary plusstrand before using it to produce protein (most wide
spread)
c. Double-stranded RNA viruses: generally uncommon, and
contain two complementary strands of RNA
K. Other Genome Structures: Retroviruses
1. Retroviruses are also called RNA tumor viruses
2. Retroviruses have a single-stranded RNA genome, which in
order to replicate must go through a DNA intermediate through
reverse transcription
3. Upon infection, the retroviral RNA genome (single-stranded) is
reverse transcribed into a double- stranded DNA copy
a. Double stranded DNA copy is inserted into the host
genome
b. Retrovirus DNA remains permanently inserted into the
host’s genome
4. Retroviruses include many different well-known animal
pathogens, including HIV