Download Genome Organization

Genome Organization
and Evolution
• DNA is associated with architectural proteins
and packaged into chromosomes.
• But, genetic information has to be accessible
for processes such as replication and
transcription.
• Genomes are mosaic and reflect a complex
evolutionary history.
Genome organization varies in
different organisms
The domains of life
• Scientists first divided life into prokaryotes
and eukaryotes.
• Comparison of 16S rRNA sequences and
ribosome structure revealed the archaea.
• Three major groups of living things:
eukaryotes, bacteria, archaea
Two models for the divisions of life
• Three domain tree: bacteria, eukaryotes,
archaea
• Eocyte tree: bacteria and archaea
Eukaryotes are a type of archaea derived from
ancestral cells called eocytes.
Viruses with DNA genomes
• Not considered organisms because they
are not made of cells.
• But, viruses have a genome and they
evolve.
Two classes of genomes
• Small genomes of viruses, archaea,
bacteria (<10 Mb), and many unicellular
eukaryotes (<20 Mb)
– Protein-coding and RNA-coding sequences
occupy most of the nucleotide sequences.
• Large genomes of multicellular and some
unicellular eukaryotes (>100 Mb)
– The majority of the nucleotide sequence is
non-coding.
Packaging of the eukaryotic
genome
The problem:
• How to fit 2 meters of DNA into a <10
µm space.
The solution:
• Double-stranded linear DNA molecules
are packed into chromatin.
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
Diversity in the number of chromosomes
that make up eukaryotic genomes
•
•
•
•
•
Butterflies: >200 chromosomes
Kangaroos: 12
Humans: 46
Adder tongue fern: 1260
Male jack jumper ant: 1
Histones are small, positively
charged proteins
1928: Albrecht Kossel isolated histones, small
basic proteins, from the nuclei of goose
erythrocytes.
1970s: Electron microscopic and biochemical
studies showed that the fundamental packing
unit of chromatin is the nucleosome.
Two types of histones:
• Highly conserved core histones.
• More variable linker histones.
Core histones
• Small, positively-charged, basic proteins.
• Molecular weight 11,000-16,000 daltons.
• Histones H2A, H2B, H3, and H4.
• Rich in arginine and lysine (basic amino acids)
• Bound to DNA in eukaryote chromosomes to
form core octamers.
Linker histones
• Slightly larger, positively-charged, basic proteins.
• Molecular weight >20,000 daltons.
• Histones H1, H5, H1, etc.
• Occur between core octamers.
• Most eukaryotes package their genomes
with histones.
• There are some exceptions:
– Dinoflagellates package their DNA with small
basic non-histone proteins.
– Sperm DNA is compacted with basic proteins
known as protamines.
Eukaryotic chromosomal organization
• Histone proteins
– Abundant
– Histone protein sequence is highly conserved among
eukaryotes—conserved function
– Provide the first level of packaging for the chromosome;
compact the chromosome by a factor of approximately 7
– DNA is wound around histone proteins to produce
nucleosomes; stretch of unwound DNA between each
nucleosome
Chapter 12: Organization
in Chromosomes
20
Eukaryotic chromosomal organization
• Nonhistone proteins
– Other proteins that are associated with the chromosomes
– Many different types in a cell; highly variable in cell types,
organisms, and at different times in the same cell type
– Amount of nonhistone protein varies
– May have role in compaction or be involved in other
functions requiring interaction with the DNA
– Many are acidic and negatively charged; bind to the
histones; binding may be transient
Chapter 12: Organization
in Chromosomes
21
Eukaryotic chromosomal organization
• Histone proteins
– 5 main types
• H1—attached to the nucleosome and involved in
further compaction of the DNA (conversion of 10
nm chromatin to 30 nm chromatin)
• H2A
• H2B
Two copies in each nucleosome
• H3
‘histone octomer’; DNA wraps
• H4
around this structure1.75 times
– This structure produces 10nm chromatin
Chapter 12: Organization
in Chromosomes
22
Fig. 8.17 A possible nucleosome structure
Chapter 12: Organization
in Chromosomes
Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
23
Fig. 8.18 Nucleosomes connected together by linker DNA and H1 histone to
produce the “beads-on-a-string” extended form of chromatin
H1
Histone octomer
Linker DNA
10 nm chromatin is produced in the first level of packaging.
Chapter 12: Organization
in Chromosomes
Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
24
Nucleosomes are the fundamental
packing unit of chromatin
Beads-on-a-string: the 10 nm fiber
• Visualized by electron microscopy as 10-11 nm
fiber after low salt extraction.
• Beads represent DNA wrapped around the
histone core octamer.
• String represents the DNA double helix.
Nucleosomes
• Repeating structural element in eukaryotic
chromosomes.
• Core octamer of histones plus one molecule of
the linker histone.
• 180 bp DNA wound around.
Core histone octamer
• Dimer of histones H2A and H2B at each end.
• Tetramer of histones H3 and H4 in the center.
• 146 bp of negatively charged DNA wraps nearly
twice around the positively charged histones.
Carboxyl (C) terminal end
• Extended histone-fold domain
• Histone-histone interactions
• Histone-DNA interactions
Amino (N) terminal charged “tails”
• Lysine-rich
• Sites of many post-translational modifcations
Higher order structure:
the 30 nm fiber
• Visualized by electron microscopy in
higher salt.
• Two models:
1. Classic solenoid model
2. Currently favored zig-zag ribbon model
Further packaging of DNA involves
loop domains
• Further compaction of the 30 nm fiber into loops
that contain 50-100 kb of DNA.
• Insight into loop structure comes from studies of
lampbrush chromosomes in amphibian oocytes.
• In interphase of the cell cycle, the packing ratio
is 1000-fold.
Fig. 8.20b Packaging of nucleosomes into the 30-nm chromatin fiber
Chapter 12: Organization
in Chromosomes
Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
32
Eukaryotic chromosomal organization
• Compaction continues by forming looped domains
from the 30 nm chromatin, which seems to compact
the DNA to 300 nm chromatin
• Human chromosomes contain about 2000 looped
domains
• 30 nm chromatin is looped and attached to a
nonhistone protein scaffolding
• DNA in looped domains are attached to the nuclear
matrix via DNA sequences called MARs (matrix
attachment regions)
Chapter 12: Organization
in Chromosomes
34
Fig. 8.21 Model for the organization of 30-nm chromatin fiber into looped
domains that are anchored to a nonhistone protein chromosome scaffold
Chapter 12: Organization
in Chromosomes
35
Fully condensed chromatin:
metaphase chromosomes
• Condensation requires ATP-hydrolyzing
enzymes and the condensin complex.
• Packing ratio of 10,000-fold.
• Each chromosome is composed of one linear,
double-stranded molecule of DNA.
Fig. 8.22 The many different orders of chromatin packing that give rise to the
highly condensed metaphase chromosome
Chapter 12: Organization
in Chromosomes
37
The centromere provides the site of
attachment for segregation
during cell division
• A fully condensed metaphase chromosome
consists of two sister chromatids connected at
the centromere.
• From the centromere, the kinetochore captures
spindle microtubules, which ensure that sister
chromatids segregate correctly to daughter cells.
During mitosis, chromosomes:
•
•
•
•
•
Condense
Congregate at the metaphase plate
Orient
Attach to microtubules
Are pulled apart
Centromere DNA typically is:
• Localized to a specific region of the
chromosomes.
• Consists of many repeated DNA
sequences spanning 0.1-4 Mb.
• Centromere DNA has little or no sequence
conservation.
• Centromere location is specified by the
formation of a specialized chromatin
structure.
• The histone variant CenH3 triggers a
complex network of interactions, leading to
the fully assembled kinetochore.
Each chromosome must contain:
• A centromere
• One or more origins of replication
• A telomere at each end
Chromosome classification
• Metacentric: centromere in the middle
• Acrocentric: centromere toward one end
• Telocentric: centromere at the end
Autosomes and sex chromosomes
• Chromosomes are classified as sex
chromosomes or autosomes.
• The number, size, and shape of the
chromosomes make a species-specific set
or karyotype.
Examples of diversity in sex chromosome
systems
•
•
•
•
Humans: XX (female) and XY (male)
Birds: ZW (female) and ZZ (male)
Insects: XX (female), and X (male)
Duck-billed platypus: XXXXX,XXXXX
(female) and XXXXX, YYYYY (male)
Organization and expression of the
genetic material
Heterochromatin: chromatin that is
condensed suppresses transcription
Euchromatin: chromatin that is more open
and allows for gene activation
• Euchromatin is uncoiled and active,
whereas heterochromatin remains
condensed and is inactive.
G-banding is due to differential staining
along the length of each chromosome.
Figure 12.12
Eukaryotic gene expression is regulated at
three levels
• DNA sequence: DNA-binding proteins associate
with regulatory elements in the DNA.
• Chromatin structure: changes in the way the
DNA is wrapped around the histones.
• Nuclear architecture: positioning of
chromosomes in “territories” in the nucleus.
• Early insights into how chromatin structure
changes during transcription have come
from studies of polytene chromosomes.
• Chromosome puffs represent sites of high
transcriptional activity.
5.4 The majority of the
eukaryotic genome is noncoding
C-value paradox
• The observation that the amount of DNA in
the haploid genome is not related to an
organism’s evolutionary complexity.
– e.g. wheat has 16,000 Mb of DNA, while
humans only have 3,200 Mb.
• Most genomic DNA consists of various
classes of repetitive DNA sequences.
Organization of the human genome
• Less than 40% of the human genome is
comprised of genes and gene-related
sequences.
• Intergenic DNA consists of unique or low
copy number sequences and moderately
to highly repetitive sequences.
Repetitive DNA sequences are divided
into two major classes
• Interspersed elements
• Tandem repetitive elements
Interspersed elements are primarily
transposable elements
Genome-wide repeats that are primarily
degenerate copies of transposable
elements
• Short interspersed nuclear elements (SINEs)
• Long interspersed nuclear elements (LINEs)
Tandem repetitive sequences are
arranged in arrays with variable
numbers of repeats
Three subdivisions based on length
• Satellite DNA
• Minisatellites
• Short tandem repeats (STRs)
Satellite DNA
• Very highly repetitive DNA with repeat
lengths of one to several thousand base
pairs.
• Buoyant density during density gradient
centrifugation differs from that of the bulk
of the DNA.
Figure 12.14
5.5 Lateral gene transfer in the
eukaryotic genome
• Lateral or horizontal transfer is the transfer of
DNA between two different species, especially
distantly related species.
• Important mechanism for bacterial evolution; in
particular, through movement of transposable
elements.
• Evidence is accumulating for the importance of
lateral transfer in fungi, animal, and plant
evolution.
Organelle genomes reflect an
endosymbiont origin
• Both mitochondria and chloroplasts contain their
own genetic information.
• Endosymbiont hypothesis: both organelles are
derived from primitive, free-living, bacterial-like
organisms.
• Inherited independently of the nuclear genome.
• Uniparental mode of inheritance: organelles are
only contributed from the maternal gamete.
Chloroplast DNA (cpDNA)
• Circular (?) or linear (?) double-stranded DNA
molecule.
• 120-160 kb
• Multiple copies (20-40) per organelle.
• Different buoyant density and base composition
compared with nuclear DNA.
Mitochondrial DNA (mtDNA)
• Typically a circular, double-stranded DNA
molecule.
• Linear in yeast and some other fungi.
• In animals, typically 16-18 kb.
• In plants, 100 kb to 2.5 Mb.
• Multiple copies (several to 30) per organelle.
Mitochondrial DNA and disease
• Defects in mtDNA can lead to
degenerative disorders, e.g.
Leber’s hereditary optic neuropathy (LHON)
Kearns-Sayre syndrome
• Heteroplasmy leads to differences in the
severity and the kind of symptoms.
Homoplasmy
• All of the mtDNA within cells of an individual are
identical.
Heteroplasmy
• Mutation occurring in one copy of mtDNA can
result in both mutant and normal mtDNA within
the same cell.
• An individual may have some tissues enriched
for normal mtDNA and others enriched for
mutant mtDNA.
Intercompartmental DNA
transfer
• A special form of lateral gene transfer.
• Associated with the gradual loss of an
endosymbiont’s independence on the path
to becoming an organelle.
Known types of interorganelle
transfer:
•
•
•
•
•
Mitochondrion to nucleus
Chloroplast to nucleus
Chloroplast to mitochondrion
Nucleus to mitochondrion
Mitochondrion to chloroplast
• Eukaryotic genomes are mosaic―the product of
a complicated evolutionary history.
• Most human genes were transferred from an
endosymbiont:
– Genes of archael origin are involved in
information processing.
– Genes of bacterial origin are associated with
metabolism and cell structure.
– The proteins that make the nuclear envelope
are encoded by genes of both archael and
bacterial origin.
5.6 Prokaryotic and viral
genome organization
Bacterial genome organization
• A single, covalently closed circular DNA
molecule.
• Condensation involving histone-like
proteins into a structure called a
nucleoid.
• Further condensation into supercoiled
domains.
Histone-like or nucleoid-associated proteins
• HU (heat-unstable protein)
• IHF (integration host factor)
• HNS (heat-stable nucleoid structuring)
• SMC (structural maintenance of chromosomes)
• Lateral gene transfer provides a source of
genetic material for bacteria.
• This allows for their rapid response to
changing environments.
– e.g. In Japan, a human gut bacterium has
acquired a gene from a marine bacterium that
encodes an enzyme involved in digesting the
seaweed used to wrap sushi.
Plasmid DNA
• Small, double-stranded circular or linear DNA
molecules.
• Carried by bacteria, some fungi, and some
higher plants.
• Extrachromosomal, independent, and selfreplicating.
Plasmids from bacteria
• Small, covalently closed circular DNA molecules.
• Carriers of resistance to antibiotics.
• Vehicles for genetic engineering.
Archael genome organization
• One double-stranded circular DNA molecule (0.5
to 5.5 Mb)
• Some archaea have two distinct histones, each
with a single histone fold domain.
• 60 bp of DNA wraps around a histone tetramer.
• Some archaea use non-histone packaging
proteins.
• The evolutionary origins of histones can
be traced back to the archael histones.
• A “doublet histone” in some archaea may
represent an intermediate in the transition
from archael to eukaryotic histones.
Viral genome organization
Bacteriophages and mammalian DNA
viruses
• Double-stranded linear, single-stranded circular,
and double-stranded circular genomes.
• Model systems for molecular biology.
• Provide a cloned set of genes on a single DNA
molecule.
Prokaryotic viruses (phages)
Bacteriophage (bacterial viruses)
• Genome typically consists of a single DNA
molecule, largely devoid of associated proteins.
• Commonly used bacteriophages in molecular
biology:
Bacteriophage  (double-stranded linear genome)
M13 (single-stranded circular genome)
• Many recent advances in the study of
bacteriophages and viruses of archaea.
• Metagenomics: the sequencing of
genomes of entire populations within the
“virosphere.”
• Isolation of many new virus-host systems
of major environmental importance.
• Many phage genes have no known
functions or homologs: “ORFans.”
• But, viruses and cellular organisms also
share a common gene pool by lateral gene
transfer.
Mammalian DNA viruses
• Infect mammalian cells and make use of the
host machinery for their replication.
• Genomes come in a diversity of forms:
Human papilloma virus (circular, double-stranded)
Simian virus 40 (circular, double-stranded)
Adenovirus (linear, double-stranded)
• Little is known about how many
mammalian DNA viruses package their
genome into the viral capsid.
• Some encode their own basic proteins.
• Simian virus 40 (SV40) uses host cell
histones (H2A, H2B, H3, and H4).