THE EUKARYOTIC

CHROMOSOME
Chapter’s Content:
• Chromosomal DNA and Proteins
• Chromosome Structure and Compaction
• Chromosomal Packaging and Gene Expression
• Replication of Eukaryotic Chromosomes
• Chromosome Segregation
• Artificial Chromosomes
Chromosomal
DNA and Proteins
Each chromosome
within a cell nucleus
contains one long linear
molecule of double-
stranded DNA
Chromatin
• is the generic term for complexes of DNA
and protein found in a cell’s nucleus.
Histone Protein
• Highly basic proteins abundant in lysine
and arginine residues
• Its strong positive charge enables it to
bind to and neutralize the negatively
charged DNA
• Classified into five molecules:
• H1, H2A, H2B, H3, and H4
Nonhistone Proteins
• They play a crucial role in the
organization and compaction of
chromosomes into higher-order structures
• Nonhistone chromosomal proteins are
classified into several groups based on
their functions, including structural,
regulatory, and motor protein
Example of Nonhistone Proteins

• Some nonhistone
proteins play a purely
structural role, helping to
package DNA into more
complex structures.
Sample are the proteins
that form the structural
backbone, or scaffold of
the chromosome
©Don Fawcett/J.R. Paulson, U.K. Laemmli/ Science Source
Chromosome
Structure and Compaction
 The Nucleosome
• The fundamental unit of
chromosome
compaction
• It is a section of DNA
that is wrapped around a
core of proteins called
histones
• A nucleosome contains
roughly 160 bp of DNA
wrapped around a core
composed of eight
histones.
• An additional 40 or so
base pairs form linker
DNA, which connects
one nucleosome with the
next.
Histone H1 lies
outside the core,
associating with
DNA entering
and leaving the
nucleosome
• DNA does not coil smoothly around the histone core.
• The DNA bends sharply at some positions and barely at all at
others. Because the sharp bending required may occur only with
some DNA sequences and not others, base sequence helps dictate
preferred nucleosome positions along the chromosome.
• Duplication of Basic Nucleosomal
Structure occurs in conjunction with
DNA Replication
• Synthesis of the four basic histone
proteins increases during S phase of the
cell cycle
• Histone chaperone proteins mediate the
assembly of nucleosomes.
• The spacing and structure of nucleosomes correlate with genetic
function.
• The spacing of nucleosomes along the chromosome matters because
DNA in the regions between nucleosomes is more readily available
than the DNA within nucleosomes for interactions with the proteins
that initiate expression, replication, and further compaction
The Process of Looping
Higher-Order Packaging Condenses
Chromosomes Further
•Biochemists recreated chromosome
assembly in a lab using Xenopus egg
extracts.
•The process involved four essential
proteins: histones, histone chaperones,
condensins, and topoisomerase II.
•The assembled chromatids closely
resembled metaphase chromosomes.
•The key steps in mitotic chromosome
condensation involve the assembly of
nucleosomes using histones and histone
chaperones.
•Chromatin loops were extruded with the
help of condensins in cooperation with
topoisomerase II.
The structures underlying
these additional levels of
chromosome compaction are
at present unknown:
Possibilities:
• within the loops,
nucleosomes interact with
each other to form some
kind of superhelix
• condensin rings might
interact with each other in
the scaffold to bring loops
closer together.
 Giemsa Staining
Reveals Reproducible Chromosome Banding Patterns
G-banding
is a technique used in
cytogenetics to produce a visible
karyotype by staining condensed
chromosomes, allowing each
chromosome to be identified by its
characteristic banding pattern and
distinguishing chromosomal
abnormalities or rearrangements.
•The reproducibility of
chromosomal patterns enables
geneticists to locate genes on
chromosomes by describing their
positions in relation to bands on the
p (short) or q (long) arm.
•Chromosome arms are subdivided
into regions, with each region
having consecutively numbered
dark and light bands.
•Idiograms illustrate these banding
patterns
Fluorescence In Situ Hybridization
Fluorescence In Situ Hybridization
• Provides a convenient bridge between
the low resolution of a karyotype and
the ultra-high resolution of a complete
genomic sequence. I
• It is a molecular cytogenetic technique
that uses fluorescent probes to detect
and locate specific DNA sequences on
chromosome.
Chromosomal Packaging and
Gene Expression
 Transcription Requires Changes in
Chromatin Structure and Nucleosome
Position
• In eukaryotes, a key observation is that less frequently
transcribed DNA segments are more compacted.
• Gene expression primarily occurs during interphase when
chromosomes are decondensed, while minimal transcription
occurs on highly compacted metaphase chromosomes.
• Even during the relatively de-compacted interphase, further
unwinding is necessary to expose the DNA within
nucleosomes for transcription.
• Gene promoters remain concealed from RNA polymerase and
transcription factors when the promoter DNA is wrapped
around the histone core of a nucleosome.
Most Genes in Heterochromatin Regions
are Silenced
 Human Chromosome in metaphase that was stained
using a special technique
. ©Doug Chapman, University of Washington Medical Center Cytogenetics Laboratory
CONSTITUTIVE HETEROCHROMATIN

• Chromosomal
regions that remain
condensed in
heterochromatin at
most times in all
cells
 EUROCHROMATIN HETEROCHROMATIN
• contains most of the sites of • transcriptionally inactive for
transcription and thus the most part;
almost all of the genes.
• Located in the Regions of Constitutive
Heterochromatins are:
– DNA consist of long repetitive sequences
– Transposable Elements
 Heterochromatin Can Spread Along
the Chromosome and Silence Nearby
Eurochromatic Genes
Such rearrangement produces POSITION
EFFECT VARIEGATION (PEV)
Heterochromatin can spread over more than 1000 kb of
previously euchromatic chromatin
Heterochromatin can spread over more than 1000 kb of
previously euchromatic chromatin
 BOUNDARY BETWEEN
HETEROCHROMATIN and
EUROCHROMATIN

Barrier Elements
Heterochromatin and Eurochromatin:
Different Histone
Modifications
The N-terminal regions of
the four core histones form
tails that extend outward
from the nucleosome
• Enzymes can add or
remove several diff.
kinds of chemical
groups
HISTONE TAILS
can influence the
packing of
nucleosomes, and the
modified tails can also
serve as platforms to
which chromatin
modifier proteins can
bind
 Examples of Histone Tail Modifications:
Enzymes Involve Effect

Acetylation Histone “opens” chromatin

acetyltransferases by preventing the
(HATs), close packing of
nucleosomes.
Deacetylation Histone deacetylases closed chromatin
(HDACs) and repressed
transcription
Examples of Histone Tail Modifications:
Enzymes Involve

Methylation Histone methyltransferases

(HMTs)

Demethylation Histone demethylases

• One of the genes whose loss-of-function mutant alleles act as PEV
suppressors in Drosophila codes for an HMT enzyme adds methyl
groups to a specific lysine (K9) in histone H3.
• This specific methylation marks the chromatin for assembly into
heterochromatin by providing binding sites for heterochromatin-
specific proteins
In Drosophila, a suppressor gene related to Position Effect
Variegation (PEV) encodes HP1, a crucial protein involved
in heterochromatin formation. HP1 specifically binds to
histone H3 tails with methylated K9. This interaction
facilitates chromatin compaction into heterochromatin
through two mechanisms.
 Heterochromatin Formation Inactivates an
X-Chromosome In Cells of Female Mammals
Replication of Eukaryotic
Chromosomes
Chromosomal DNA Replication
Begins at Specific Origin
• Eukaryotic chromosomes use multiple origins of replication
that can function simultaneously.
• Most Mammalian Cells carry about 10,000 origins
positioned in the chromosomes.
• Eukaryotic chromosomes use multiple origins of replication
that can function simultaneously.
• Most Mammalian Cells carry about 10,000 origins
positioned in the chromosomes.
New Nucleosomes during
DNA Replication
• The replication fork disassembles nucleosomes in the parental chromosome.
• New nucleosomes start assembling immediately after the replication fork passes.
First, a tetramer containing two molecules each of histones H3 and H4
associates with DNA to form a half nucleosome, followed by two dimers each
containing one molecule of H2A and one of H2B.
• The new nucleosomes can contain various random combinations of H3/H4
tetramers and H2A/H2B dimers that were either newly synthesized or that
existed previously in parental nucleosomes
Telomeres
 TELOMERES
- Composed of special
DNA sequences
associated with specific
proteins, these caps
contain no genes but are
crucial in preserving the
structural integrity of each
chromosome
 Telomeres
and The Replication Of Chromosome Ends

DNA polymerase, a key

component of the
replication machinery,
functions only in the 5′-
to-3′ direction: It can
add nucleotides only to
the 3′ end of an existing
chain.
As a result, the chromosomes in successive generations of
cells would become shorter and shorter, losing crucial
genes as their DNA diminished.
Telomeres and an enzyme
called telomerase provide a
countermeasure to this
limitation of DNA
polymerase. Telomeres
consist of particular
repetitive DNA sequences
that do not encode proteins.
Human telomeres are
composed of the base
sequence 5′ TTAGGG 3′
(read on one strand)
repeated 250 to 1500 times.
 Telomeres Activity and Cell Proliferation

Two Kinds of Somatic Cells in the Human Bodies that can create Telomerase

that allow tissue renewal, such as the continual

• STEM CELLS
production of blood cells.

somatic cells gone awry that can divide

• TUMOR CELLS
indefinitely, becoming seemingly immortal
 Telomeres and Chromosome Integrity

Chromosomes that are broken and

detached from their telomeres
pose many dangers for cells:
• One problem is that cells
contain nuclease enzymes that
can degrade DNA progressively
inward from the broken ends.
• A second problem results from
the enzyme systems responsible
for non-homologous end-
joining (NHEJ)
The SHELTERIN complex protects telomeres.
The proteins of the shelterin complex bind to telomeres,
folding the DNA ends (gray) so they can neither be
attacked by nucleases nor subjected to nonhomologous
end-joining.
Chromosome Segregation
•Chromatids of replicated
chromosomes must separate
during mitosis or meiosis II to
ensure each daughter cell
receives one chromatid from
each chromosome.
•In meiosis I, homologous
chromosomes must pair and
segregate, with each daughter
cell receiving one chromosome
from each homologous pair
Centromeres play a crucial role in ensuring
precise distribution during cell division, acting as
segregation centers.
 Special DNA Sequences Allow the Formation of
Centromeres
•Centromeres in higher eukaryotic organisms are large and
complex, consisting of repetitive, noncoding sequences
known as SATELLITE DNAS.
•These complex centromeres are comprised of various types
of satellite DNAs, with each type consisting of short
sequences (5–300 base pairs) repeated in tandem thousands
or millions of times.
•The predominant human centromeric satellite DNA, α-
satellite, is a noncoding sequence of 171 base pairs. It forms
large arrays in tandem repeats, extending over a megabase of
DNA in the centromeric region of each chromosome.
Kinetochores Govern Attachment of Chromosomes
to the Spindle
•Kinetochores at the
centromeres are sites
where spindle fibers
attach to the
chromosomes. A cell
cycle checkpoint
ensures that chromatids
do not separate until all
kinetochores are
connected properly to
the spindle.
 Cohesin Complexes Hold
Sister Chromatids Together
•A highly conserved,
multisubunit protein complex
called cohesin acts as the glue
that holds sister chromatids
together during mitosis and
meiosis until segregation
takes place.
•Cohesin encircles the two
double helixes of the sister
chromatids to keep them
together.
Artificial Chromosome
•In the 1980s, molecular geneticists created the first artificial
eukaryotic chromosome called a YEAST ARTIFICIAL
CHROMOSOME (YAC).
•YACs were constructed by combining in a single DNA
molecule the yeast (Saccharomyces cerevisiae) versions of
the three key chromosomal elements: centromeres,
telomeres, and origins of replication.
 Yeast Artificial Chromosomes (YACs)
Help Characterize DNA Elements Required for
Chromosome Replication and Transmission

• YACs has produced many insights into chromosome function.

• The YAC construction process was allowed geneticists to isolate and
analyze the chromosomal regions corresponding to ARSs and
centromeres:
• Plasmids containing only origins of replication but no
centromere or telomere replicate but do not segregate properly.
• Plasmids with origins of replication and a centromere but no
telomeres replicate and segregate fairly well if they are circular;
if they are linear, they degrade and eventually become lost from
the cell.
Yeast Can Survive with a Single Giant Chromosome

Scientists have generated a strain of yeast that has only one giant 11.8 Mb fused
chromosome that is eight times larger than the longest normal yeast chromosome.
 SYNTHETIC CHROMOSOME
• All the DNA in a synthetic chromosome is
entirely human-made in DNA synthesizer
machines; in contrast, a YAC is constructed by
piecing together DNA elements that were
originally in yeast chromosomes.
• The asynthetic chromosome would include
(before any subsequent manipulation) all
genes present on the corresponding yeast
chromosome.
 SYNTHETIC CHROMOSOME
• A yeast synthetic chromosome
lacking most intergenic sequences
functions normally. Such
synthetic chromosomes may help
define a minimal yeast genome.