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Nucleus and
Chromosomal Structure,
(Euchromatin & Heterochromatin)
Karyotype
Prof. A. B. Das
Department of Botany, Utkal University, Vani Vihar,
Bhubaneswar 751004
Nucleus is the most important organelle in cell. In
mammalian cells, excepting RBC, all cells else are the
nucleus contained cells. In prokaryotic cells, there is no
membrane to package the nucleic acid substance, so,
we call this nucleic substance enriched area as
“Nucleoid”.
The major structures of nucleus include: ① nuclear
envelope. ② nucleolus. ③ nuclear matrix. ④ chromatin.
⑤ nuclear lamina.
The major functions of nucleus:
① inheritance: maintain the genetic continuity of
generation by the replication of DNA chromatin and the
proliferation of cell.
② development: regulate the cell differentiation by the
regulation of spatiotemporal sequence of gene
expression.
Structure of nucleus:
(n: nucleolus; N:
euchromatin)
I. Nuclear envelope (Nuclear membrane)
Nuclear envelope is the lipid bilayer that packages the nucleus.
Nuclear envelope separates the DNA from cell plasma and forms a stable
inner environment to:
① protect the DNA from damage,
② separate the replication of DNA from the translation of RNA
spatiotemporally,
③ the chromatin is anchored on to the nuclear envelope, that is beneficial to
be despiraled, replicated, condensed, and distributed into new nuclei
equally,
④ the pores on the envelope are the channels for the substance exchange.
Nuclear envelope is bilayer membrane:
Nuclear envelope is composed of inner nuclear membrane, outer nuclear
membrane, and perinuclear space. There are nuclear pores on the membrane that are
linked with plasma.
Ribosome is attached to the plasma side of outer nuclear membrane, and the
ribosome is linked with ER. The perinuclear space is linked with ER space. The
intermediate filament (10nm) is attached to the outer nuclear membrane, so, the
locations of nucleus and ER are not movable because of the intermediate filament.
The unmovable locations are convenient to the co-function of nucleus and ER.
The nuclear lamina (meshwork filament proteins) attached to the inner side of
the inner nuclear membrane can stabilize nuclear membrane shape.
The photo of nuclear envelope by TEM
Structure of nuclear envelope
The functions of nuclear lamina:
1.Keeps nuclear shape no changed: If you use the high
concentration salt solution, detergent or nuclease to move away
the nuclear substance, the remaining (nuclear lamina) still
presents a nuclear shape. In addition, the nuclear lamina links
nuclear skeleton meshwork and intermediate filament together to
form a continued meshwork for nucleus.
2.Is associated with the assembly of chromatin and
nucleus: The shape of nuclear lamina can be changed during the
cell proliferation phases.
In the G1 phase, nuclear lamina can present the anchoring sites
for heterochromatin on the inner side of inner nuclear membrane.
At the ending of the G1 phase, the nuclear lamina will be
phosphorylated and the nuclear envelope will disappear.
The B type of nuclear lamina will combine to the residual
vesicles of nuclear membrane, and A type of lamina will be
dissolved in plasma.
In the later of M phase, All types of lamina will be
dephosphorylated and assembled again to form nuclear lamina
and mediate the nuclear envelope construction.
Structure of nuclear lamina
The nuclear pores are the channels for the substance transportation:
Nuclear proteins are synthesized in plasma, then will be imported into
nucleus by the pores.
The RNAs and the ribosome subunits synthesized in nucleus will be
exported into plasma by the pores also. In addition, it is indicated by a
injection experiment that small molecules can enter the nucleus by diffusion
from the pores.
Nuclear pores are composed of 50 different nucleoporins at least, and
we call these pore structure as nuclear pore complex (NPC).
Usually, a mammalian nucleus contains 3,000 nuclear pores.
The more activities a cell takes, the more nuclear pores the cell
contains.
For example, a frog ovum can contain 37.7X106 nuclear pores, but a
matured cell contains 150~300 nuclear pores only.
The structures of nuclear pore include
① cytoplasmic ring located on the cell plasma part of the pore complex contains 8
filaments extending into plasma.
② nuclear ring located on the nuclear plasma part of the pore complex extending 8
filaments also.
③ transporter located in center of the pore as a plug particle.
④ Spoke located on the edge of the pore as the spines.
The nuclear pore structures on the cell plasma side after an extraction
The nuclear pore structures on the nuclear plasma side after an extraction
12
A model
structure of
the nuclear
pore
The transportation by nuclear pore is associated with signal transduction:
1982, R. Laskey identified a signal sequence on the C terminal of
nucleoplasmin enriched in nucleus, and the signal can lead protein to enter
nucleus.
This signal sequence was named as nuclear localization signal
(NLS).
The firstly identified NLS is the T antigen of SV40.
This antigen is synthesized in cell plasma, and transported into
nucleus quickly.
Its NLS is pro-pro-lys-lys-lys-Arg-Lys-val.
NLS is composed of 4 – 8 amino acids containing Pro, Lys and Arg.
NLS is not specific to target protein and will not be cleaved by protease.
Karyopherin is a protein family that is associated with the selective
transportation by the pore, and it is a receptor family actually. The imporin
of them imports proteins into nucleus from cell plasma and the exportin of
them exports the proteins on an opposite direction.
Ran is another protein involved in the transportation by the pore
complex. Ran is a G protein that regulates the assembly and disassembly of
the complex of the protein transported and the receptor used. Ran-GTP
concentration is much higher in the nucleus than in cell plasma.
Gold labeled
nucleoplasmin
is passing
through the
nuclear pore
Nuclear plasma protein (nucleoplasmin) is transported by the
following steps:
① The protein combines to the α / β dimer of the receptor (imporin).
② The complex of the protein transported and the receptor used
combines to the filaments located on the NPC cytoplasmic ring.
③ The filaments curve to the nuclear center, the transporter structure
will be changed to form a hydrophilic channel, and the protein passes
through the channel.
④ The complex of the protein transported and the receptor used
combines to Ran-GTP, the complex is disassembled and releases out
the protein transported. ⑤ The imporin β combined with Ran-GTP will
be exported out of the nucleus, the GTP combined with Ran will be
hydrolyzed in cell plasma, and the Ran-GDP will go back to nucleus to
be transformed to Ran-GTP again.
⑥ The imporin α will be transported back to cell plasma with the help
from exportin.
We know a little about how the macromolecules are
transported to cell plasma from nucleus. In most of
cases, the RNA in nucleus is combined with protein
to form an RNP complex, then, transported into cell
plasma. There is nuclear exportation signal (NES)
on the protein of RNP complex that can combine to
the intracellular receptor, exportin, to form the
complex of RNP-exportin-Ran-GTP. In the cell
plasma, this complex will be disassembled and
release out the Ran-GTP, RNA, Ran-GDP, exportin,
and RNP protein.
The nucleoplasmin is transported into nucleus
II. Chromosome
Chromatin was named by W. Flemming in 1879.
Chromosome was named by Waldeyer in 1888.
Chromatin and chromosome are same substance with different shape
presentation in different cell cycle phases.
The chemical components of chromatin:
Chromatin is composed of DNA, histone, nonhistone protein, and
some RNA at ratio about 1:1:(1-1.5):0.05.
DNA:
DNA is the carrier of genetic information. DNA sequences can be
sorted as 3 types: nonrepeated fraction, moderately repeated
fraction (101-105), and highly repeated fraction (>105). DNA forms:
B-DNA, Z-DNA, and A-DNA.
DNA forms (Red color shows the couple backbones)
Chromosome DNA contains three basic sequences:
① autonomously replicating DNA sequence (ARS). ARS is
the starting site of DNA replication. In yeast genome, there
are 200-400 ARSs included, and most of them contain a AT
enriched 11bp sequence called as ARS consensus
sequence (ACS).
② centromere DNA sequence (CEN) composed of a lot of
repeated sequences.
③ telomere DNA sequence (TEL). TEL is similar in different
bio organisms, and composed of 5 – 10bp repeated
sequences. Human TEL repeated sequence is TTAGGG.
In 1983, A. W. Murray et al constructed yeast artificial
chromosome (YAC) contains ARS, CEN, TEL and exogenous DNA with
the length of 55kb.
YAC is very useful to transgenic technology and construction of cDNA
library because the length of insert to YAC can be much longer than that
to plasmid.
Three basic sequences of chromosome
Histone:
Histone is positively charged and contains arginine and lycine.
Histone is alkaline protein.
Histones can be sorted as two types:
1. Highly conserved core histone including H2A, H2B, H3, and H4.
2. Non conserved linker histone including H1 only.
The core histone is highly conserved, especially the H4 is. For
example, 2 of 102 amino acids of the H4 of cattle and pea are different, but
cattle has been evoluted 300 million years earlier than pea. The reasons for
that may be as the follows:
1. Most of the amino acids of core histone interact with DNA or other
histones, so, any change of them will cause the fatal mutation.
2. In all bio organisms, the DNA phosphodiester skeleton that
interacts with histone is same.
The core histone head part makes DNA winded round the histone
center by the electronic force between arginine residue and
phosphodiester skeleton.
By the described as above, nucleosome can be formed. The tail part of
core histone containing a lot of arginine and lysine residues. The tail part
is the site to be modified after translation.
H1 is easy to be mutated, and it is species specific and tissue
specific.
Nonhistone protein:
Nonhistone protein is the protein that binds to the specific DNA
sequence of chromosome, so, we call it as sequence specific DNA
binding protein.
The features of nonhistone protein are as the follows:
① Nonhistone protein is negatively charged and acidic protein that
contains a large number of aspartic acids and glutamic acids.
② Nonhistone protein can be synthesized during the whole cell cycle,
but histone protein is synthesized during the S phase only.
③ Nonhistone protein can recognize the specific DNA sequence.
The functions of nonhistone are as the follows:
① Help DNA molecules to be pleated and form different structure
domains that are beneficial to DNA replication and gene transcription.
② Help to start DNA replication reaction.
③ Regulate transcription and gene expression.
From DNA to chromosome:
There are 23 pairs of chromosomes in a human
nucleus. If you open and extend the DNA molecule in each
chromosome, it will be 5cm long.
If you link all DNA molecules in a nucleus together, it will be
1.7 – 2.0 m long. But, the diameter of nucleus is shorter
than 10μm.
That is why the genome information is packaged into the
space of a cell nucleus —— thousands of times smaller
than the dot. The primary structure formed by the powerful
compaction is called as nucleosome.
Nucleosome:
If the chromatin is treated by a nonspecific nuclease,
the DNA fragments around 200bp can be obtained in most
of cases.
If you treat the null DNA with that enzyme, you will obtain
the randomly degenerated fragments of DNA.
From DNA to chromosome:
Nucleosome:
Based on this experiment, R. Kornberg figured out the
model of nucleosome.
Nucleosome is a beaded structure composed of core
particles and linker DNA.
We can describe the structure as the follows:
① Each nucleosome includes about 200bp DNA, one
histone core, and an H1.
② The octameric histone core is composed of 8 molecules
from H2A, H2B, H3, and H4 by two molecules from each.
③ DNA molecule winds the core particle with a left hand
helix and 80bp for each circle. 1.75 circles for each
structure.
④ Adjacent core particles are linked by a 60bp linker DNA.
Structures of nucleosome
Chromosome Morphology
• Telomere: chromosome
ends
• Centromere: site of spindle
attachment
– Constriction of the
metaphase chromosome
at the centromere defines
two arms
• Nucleosome: DNA double
helix wrapped around
histone proteins
Chromatin DNA filament:
The DNA is compacted to be shortened by 7
folds and forms the DNA filament in 11nm diameter
when it was transformed to the beaded
nucleosome chain.
Chromatin DNA exists in another style by that
the beaded nucleosome chain is condensed by 6
folds.
Under electron microscope, we can see the
chromatin DNA filament in 30nm diameter that is
formed by the overlapped helix structure of the
beaded nucleosome chain.
The DNA filaments in 30nm and 11nm diameter
(A) Is composed of (B)
For the advanced package of the chromosome, we keep detail unknown
so far. Probably, it is the serial overlapped or pleated like the follows:
From DNA to Chromosome:
DNA 11nm filament (beaded nucleosome chain) 30nm filament
pleat as loop chain bind to the sites on nuclear skeleton where is AT
enriched assembly of chromosome
Assembly of chromosome
Heterochromatin and euchromatin:
In the inter phase (G1 and G2) of cell cycle, the
chromatin in the nucleus can be sorted as heterochromatin
and euchromatin.
Euchromatin is the DNA regions where the
transcription is very active. Euchromatin looks like loose
loop and bright staining under electron microscope.
Euchromatin is easy to be cleaved by nuclease at some
hypersensitive sites.
Heterochromatin is condensed in G phase without any
transcription, so, it was named as inactive chromatin.
Heterochromatin is the genetic lazy regions, and replicated
lately, condensed early, that is called as heteropyknosis.
Heterochromatin
(dark staining)
and euchromatin
(bright staining)
Heterochromatin
Euchromatin
Constitutive
hetero-
chromatin is
hetero-
pyknosed
chromatin in
each type of
cell and
located in
centromere
region.
The Fig shows
you the
Constitutive
hetero-
chromatin
displayed by
fluorescence
hybridization in
situ.
Facultative heterochromatin
is heterochromatin appeared
in some special cell type or
developing stage.
The X chromosome of female
mammalians is the facultative
heterochromatin.
Usually, female mammalian
cell contains double X
chromosomes, and one of
them is heterochromatin
called barr body.
When a human embryo is
developed after 16 days, one
X chromosome will be
transformed as barr body with
dark staining.
So, we can identify the sex of
a human embryo by checking
the barr body of the embryo
cells in the amniotic fluid.
The barr body like a drumstick in a white cell
The structure of chromosome:
In the M phase of cell cycle, chromatin will be transformed as chromosomes
by the powerful condensation.
Chromosomes are stick shape with different length.
The metaphase chromosome is the best stage to observe and number
them because the morphology of chromosome is stable at this time.
The number of chromosome is same in the same type of cells from different
individuals of one species.
The chromosomes of sex cells are haploid, we mark it as n. The
chromosomes of other cells are diploid, we mark it as 2n.
The chromosomes of some cells of some species are polyploid, such as,
4n, 6n, and 8n.
The different cells from same individual can be different chromosome types.
For example, body cells of rat are 2n, but its liver cells can be 4n, 8n, and 16n.
The chromosome number of human endometrial cell is variable from 2n =17 - 2n
=103, that is not euploidy.
The chromosome number can be different in different species cells.
For examples, human 2n = 46, chimpanzee 2n = 48, fruit fly 2n = 8,
wheat 2n = 42, rice 2n = 24, onion 2n=16.
The terms used to the structure of chromosome:
1.Chromatid: Metaphase chromosome is composed of two chromatids with a
junction at the centromere site. Each chromatid is formed by the overlapped and
pleated DNA double strands. When the cell is dividing the chromatids can be
separated into two new cells.
2.Chromonema: In the S or G phase cells, each chromonema indicates a
chromatid.
3.Chromomere: Chromomere is the linear beaded particles chain DNA. The
chromomere of heterochromatin is bigger than that of euchromatin.
4.Primary constriction: It is a bright stained hang ditch on the metaphase
chromosome where the centromere is located, so, it can be called as centromere
region. Each chromosome has one localized centromere.
The chromosome from some species has centromere function every
where. We call this chromosome as holocentromere chromosome. For examples,
ascarid (round worm) and other nemas, butterfly.
The chromosomes can be sorted by the location of centromere as
following: ① metacentric chromosome. ② submetacentric chromosome. ③
subtelocentric chromosome. ④ telocentric chromosome.
5.Secondary constriction: Excepting primary constriction, the second ditch is
called as secondary constriction. The location of secondary constriction is
unmovable by that we can identify chromosome.
The terms of chromosome structure
6.Nucleolar organizing regions (NORs): They are the areas where the
genes for ribosome RNA are located. They can synthesize the 28S, 18S, and
5.8S rRNA for ribosome. NORs can exist in secondary constriction.
7.Satellite: It is a ball part located at the terminal of chromosome, and
linked to the main part of chromosome by secondary constriction. The
satellite located at terminal of chromosome is called as terminal satellite, and
located between two secondary constrictions is called as intermediate
satellite.
8.Telomere: It is the specialized part located at the terminal of
chromosome. The function of telomere is maintenance of the stability of
chromosome. Telomere is composed of the highly repeated fractions, and it
is so conserved that it is similar between the totally different life beings. The
component of human telomere is TTAGGG.
Telomere is associated with aging.
After each replication of telomere DNA, the telomere will be shortened by 50
– 100bp.
The replication of telomere is droved by telomerase that has reverse
transcriptase activity.
This enzyme lacks in normal cells, so, telomere will become short with the
cell proliferation. So, cell will be aging during this action.
The nucleolus will be formed in the center of nucleolar organizing regions
The telomeres
displayed using
fluorescence
hybridization in situ.
The sequences of
telomere
The structure of
centromere:
Centromere means the
special region by that the
chromatids of metaphase
chromosome are linked
together.
Kinetochore means the
outer surface structure
located on the primary
constriction that is linked to
spindle fibers.
Centromere contains 3
domains:
kinetochore domain,
central domain,
paring domain.
Three domains of centromere
Kinetochore
domain:
Kinetochore domain
is composed of outer
plate, inner plate,
interzone, and
fibrous corona.
The inner plate
combines to the
heterochromatin of
central domain, outer
plate combines to
filaments of spindle
fibers.
Their motor proteins
located on the
fibrous corona to
supply energy to the
chromosomes
separation.
Central domain: It is located below the centromere and contains the
heterochromatin composed of highly repeated α satellite DNA.
Paring domain: It is located in centromere by that the chromatids of metaphase
chromosome are linked together. There are two types of proteins in this domain:
inner centromere protein (INCENP), and chromatid linking protein (CLIP).
By using anti-centromere antibodies (ACA), INCENP or CENP (centromere protein)
can be identified and sorted as the follows:
Types Functions
CENP-A Specific histone to centromere
CENP-B Binds to satellite DNA in central domain
CENP-C Binds to kinetochore
CENP-D Binds to kinetochore
CENP-E Drive motor protein
CENP-F Binds to kinetochore
INCENP-A Link partner chromatid
INCENP-B Link partner chromatid
Karyotype and bands display:
The bands display technology of chromosome was
developed in 1960s to 1970s, and it brought the
chromosome researches to a new and fast developing
stage. The result data about chromosome bands is the very
useful background research for modern genome research
programs, gene molecular research programs, and genetic
research programs.
Karyotype is the total features of the chromosomes
in M phase. It includes the number, size, and shape of
chromosome. If the paired chromosomes are arranged by
shape and size, a figure will be obtained, and we call it as
karyogram. Karyogram is of characters of species.
Karyotype
• International System for Human
Cytogenetic Nomenclature (ISCN)
– 46, XX – normal female
– 46, XY – normal male
• G-banded chromosomes are identified by
band pattern.
Centromere
Telomere
Metacentric Submetacentric Acrocentric
Telomere
Arm
Long
arm (q)
Short
arm (p)
Chromosome Morphology
p
q
Arm Region Band Subband
2
1
1
2
2
1
1
1
2
3
4
3
2
1
2
1
5
4
3
2
1
1
2
3
1
2
3
1
2, 3
4
1
2
3
17q11.2
Chromosome 17
Defining Chromosomal Location
Chromosome Morphology Changes
During the Cell Division Cycle.
• DNA double helix: 2nm diameter
Interphase (G1, S, G2)
• Chromatin “beads on a string:” 11nm
• Chromatin in nucleosomes: 30nm
Metaphase (Mitosis)
• Extended metaphase chromosomes: 300 nm
• Condensed metaphase chromosomes: 700 nm
Cell Division Cycle
G1 S
G2
Interphase
(11–30 nm fibers)
Metaphase
(300–700 nm fibers)
M
Mitosis:
Prophase
Anaphase
Metaphase
Telophase
Visualizing Metaphase
Chromosomes (Banding)
• Giemsa-, reverse- or centromere-stained
metaphase chromosomes
G-Bands R-Bands C-Bands
Normal Female Karyotype (46, XX)
(G Banding)
Normal Female Karyotype
(High-Resolution G Banding)
Chromosome Number Abnormality
Aneuploidy (48, XXXX)
Chromosome Number Abnormality
Trisomy 21 (47, XX, +21)
Translocation Deletion
Insertion
Inversion Isochromosome
Ring
chromosome
Derivative
chromosome
Chromosome Structure
Abnormalities
Chromosome Structure Abnormality:
Balanced Translocation 45, XY, t(14q21q)
Probe
Interphase or metaphase
cells on slide (in situ)
Microscopic
signal (interphase)
Fluorescent in situ Hybridization
(FISH)
 Hybridization of complementary gene- or
region-specific fluorescent probes to
chromosomes.
Fluorescent in situ Hybridization
(FISH)
• Metaphase FISH
– Chromosome painting
– Spectral karyotyping
• Interphase FISH
Uses of Fluorescent in situ
Hybridization (FISH)
• Identification and characterization of
numerical and structural chromosome
abnormalities.
• Detection of microscopically invisible
deletions.
• Detection of sub-telomeric aberrations.
• Prenatal diagnosis of the common
aneuploidies (interphase FISH).
FISH Probes
• Chromosome-specific centromere probes (CEP)
– Hybridize to centromere region
– Detect aneuploidy in interphase and metaphase
• Chromosome painting probes (WCP)
– Hybridize to whole chromosomes or regions
– Characterize chromosomal structural changes in metaphase
cells
• Unique DNA sequence probes (LSI)
– Hybridize to unique DNA sequences
– Detect gene rearrangements, deletions, and amplifications
Telomere
(TTAGGG)n
100–200 kb 3–20 kb
Unique sequences Telomere associated repeats
Probe binding site
FISH Probes
• Telomere-specific probes (TEL)
– Hybridize to subtelomeric regions
– Detect subtelomeric deletions and rearrangements
Normal diploid signal
Trisomy or insertion
Monosomy or deletion
Cell
nucleus
Genetic Abnormalities by
Interphase FISH LSI Probe
• Greater or less than two signals per
nucleus is considered abnormal.
Structural Abnormality by Interphase
FISH LSI Probe (Fusion Probe)
Structural Abnormality by Interphase
FISH LSI Probe (Break Apart Probe)
Translocation by Metaphase FISH
WCP Probe (Whole-Chromosome Painting)
Karyogram of Platypleura kaempferi
The chromosome banding technology is
very important to genetics research, species
classification, and others. This technology
includes the cell and chromosome treatments by
physical and chemical methods, chromosome
staining and bands display.
Bands display technologies can be sorted as
two types:
1. The bands distribute on entire chromosome,
such as G, Q, and R banding technologies.
2. The bands distribute in localized region of
chromosome, such as C, Cd, T, and N banding
technologies.
Human G Karyotype. G bands display the regions where AT is enriched
Human Q Karyotype. Q bands display same thing of G bands
Human C Karyotype. C bands display the centromere heterochromatin
Special chromosomes:
Polytene chromosome:
It was identified in some insect saliva cells in 1881.
Polytene chromosome: ① 1,000 – 2,000 folds huger than
others. It is the reason that chromosomes are replicated
without separation. ② Polytene. Each polytene
chromosome is composed by 500 – 4,000 helix opened
chromosomes. ③ Cell junction and homologous
chromosomes combination. ④ Striation. ⑤ In some life
stage of insects, some bands of polytene chromosome
become loosed and form puff and Balbiani ring. Puff can be
labeled by H3-TdR, that means puff is the region where the
gene transcription is very active.
The chromosomes from saliva cells
Lamp-brush chromosome:
Lamp-brush chromosome was identified in fishes firstly. There are lateral loops
on the chromosome like lamp brush. It is composed of two homologous
chromosomes. Lateral loops are the region with RNA active transcription.
B chromosome:
In 1928, Randolph, a scientist, call normal chromosomes as A chromosomes, and
call abnormal chromosomes existed in many animals and plants as B chromosome.
III. Nucleolus
Nucleolus may be visible in G phase nucleus. They are spherical and 1 – 2 for
each cell usually. The number and size of nucleolus are depended on the cell type
and function. The more proteins synthesis and the faster proliferation the cell
takes, the more and bigger nucleoli the cell has. Nucleolus disappears before the
cell division, and appears in the end of division. The major functions of nucleolus
are rRNA transcription and ribosome assembly.
Structure of nucleolus:
No any membrane packages nucleolus area. There are three special areas
can be identified under electron microscope: ① fibrillar centers (FC) that are
surrounded by dense fibers, and low electric density. FC contains RNA
polymerase and rDNA that is naked molecule. ② dense fibrillar component (DFC)
that is a loop or half loop to surround FC. Transcription is carried out in the border
region of FC and DFC. ③ granular component (GC) composed of 15-20nm
particles that are the RNPs in different manufactured steps. RNP means the RNA
combined with protein.
Nucleolus chromatins can be sorted as two types: heterochromatin and
euchromatin. The nucleolus heterochromatin is always located around the
nucleolus, so we call them as nucleolus peripheral chromatin. The nucleolus
euchromatin is located in nucleolus, and nucleolus organizing region in that the
rDNA is located.
Structure of nucleolus
IV. Ribosome
Ribosome is the manufacturing shop to synthesize proteins. There are about
20,000 ribosomes in an actively growing bacterium. Ribosome proteins are 10% of
total proteins of cell, and its RNA is 80% of cell total RNA.
Structure of ribosome:
The ratios of protein and RNA to ribosome components are 40% and 60%.
The ribosome subunits are composed of the combination of the protein and RNA.
The catalytic activities needed by the translation are presented by ribosome
protein, rRNA and other helper factors.
The ribosomes can be sorted as two types. 70S ribosome exists in bacteria,
mitochondrion, and chloroplast. 80S ribosome exists in the plasma of eukaryotic
cells.
Ribosome is composed of a large subunit and a small subunit. The both
subunits will be combined together when the ribosome synthesizes protein with
mRNA as template. After the translation, the ribosome will be separated as two
parts again. When a protein is translated on an mRNA, many ribosomes can bind
to the mRNA to synthesize the protein. We call these ribosomes for one protein
synthesis as polyribosome. The longer mRNA is used, the more ribosomes are
combined. The polyribosome enhances the efficiency of protein synthesis.
Prokaryotic 5S rRNA and eukaryotic 5.8S rRNA are very conserved for their
structures, so, they can be used to research the bio-evolution.
Assembly of ribosome:
The DNA fragment encoding rRNA is called as
rRNA gene. There are about 200 copies of this
gene in a human cell. rDNA contains no histone
core, so, it is a naked DNA.
To transcript rRNA, the RNA polymerase
moves ahead along the DNA molecule. The
synthesized rRNA molecules extend out their
molecules from the complex of polymerase and
DNA, and form a featherlike structure under
microscope.
rRNA transcription
The filaments are the
new synthesized 45S
rRNA that combines to
protein to form RNP
complex. The
methylated 45S rRNA
can be cleaved as the
two parts by RNase:
18S rRNA and 32S
rRNA,the latter is
cleaved as 28S rRNA
and 5.8S rRNA. The
synthesized 5S rRNA
will be transported into
nucleolus to join the
assembly of the large
subunits of ribosome.
There is a 60bp non-transcription DNA
fragment between adjacent rRNA genes
Assembly of ribosome
Model of a
ribosome
mRNA
Synthesized protein
V. Nuclear matrix
Nuclear matrix is called as nucleoskeleton that is a meshwork in
eukaryotic cells, that is what I told you before. Because nuclear matrix is
associated with DNA replication, RNA transcription and modification,
chromosome assembly, and virus replication, nuclear matrix is now paid
more attentions to.
Components of nuclear matrix:
① Non-histone filaments at ratio of 96%. The nucleoskeleton
contains three scaffold proteins: SC Ⅰ, SCⅡ, and SC Ⅲ.
② A little RNA and DNA: The RNA is important to maintain the
skeleton structure. The DNA is called as matrix /scaffold associated
region (MAR or SAR) where the AT is enriched to form the
heterochromatin binding sites.
③ A little phospholipids (1.6%) and sugars (0.9%).
Nuclear skeleton – nuclear lamina – inter filaments – pore complex
is a meshwork system with very good stability.
The function of nuclear skeleton:
1. Present the scaffolds for DNA replication. DNA can be
anchored on to the scaffold with a replication loop. The
enzymes needed by DNA replication are located on the
skeleton, such as DNA polymerase α, DNA primerase,
DNA topoisomerase II.
2. Is the place where gene can be transcripted and
modified. There are RNA polymerase binding sites on the
skeleton. New synthesized RNA is combined to the
skeleton for further modification.
3. Is associated with the assembly of chromosome. The
nuclear skeleton may be same thing to chromosome
skeleton. 30nm chromatin fibers are combined to nuclear
skeleton to form loops that will be packaged further in M
phase to be assembled as chromosome.
Chromatin bound on nuclear skeleton or chromosome skeleton
Summary
• Mutations are heritable changes in DNA.
• Mutations include changes in chromosome number,
structure, and gene mutations.
• Chromosomes are analyzed by Giemsa staining and
karyotyping.
• Karyotyping detects changes in chromosome number
and large structural changes.
• Structural changes include translocation, duplication,
and deletion of chromosomal regions.
• More subtle chromosomal changes can be detected by
metaphase or interphase FISH.
Thank You!!!

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Chromosome & nuclear structure.pdf

  • 1. Nucleus and Chromosomal Structure, (Euchromatin & Heterochromatin) Karyotype Prof. A. B. Das Department of Botany, Utkal University, Vani Vihar, Bhubaneswar 751004
  • 2. Nucleus is the most important organelle in cell. In mammalian cells, excepting RBC, all cells else are the nucleus contained cells. In prokaryotic cells, there is no membrane to package the nucleic acid substance, so, we call this nucleic substance enriched area as “Nucleoid”. The major structures of nucleus include: ① nuclear envelope. ② nucleolus. ③ nuclear matrix. ④ chromatin. ⑤ nuclear lamina. The major functions of nucleus: ① inheritance: maintain the genetic continuity of generation by the replication of DNA chromatin and the proliferation of cell. ② development: regulate the cell differentiation by the regulation of spatiotemporal sequence of gene expression.
  • 3. Structure of nucleus: (n: nucleolus; N: euchromatin)
  • 4. I. Nuclear envelope (Nuclear membrane) Nuclear envelope is the lipid bilayer that packages the nucleus. Nuclear envelope separates the DNA from cell plasma and forms a stable inner environment to: ① protect the DNA from damage, ② separate the replication of DNA from the translation of RNA spatiotemporally, ③ the chromatin is anchored on to the nuclear envelope, that is beneficial to be despiraled, replicated, condensed, and distributed into new nuclei equally, ④ the pores on the envelope are the channels for the substance exchange. Nuclear envelope is bilayer membrane: Nuclear envelope is composed of inner nuclear membrane, outer nuclear membrane, and perinuclear space. There are nuclear pores on the membrane that are linked with plasma. Ribosome is attached to the plasma side of outer nuclear membrane, and the ribosome is linked with ER. The perinuclear space is linked with ER space. The intermediate filament (10nm) is attached to the outer nuclear membrane, so, the locations of nucleus and ER are not movable because of the intermediate filament. The unmovable locations are convenient to the co-function of nucleus and ER. The nuclear lamina (meshwork filament proteins) attached to the inner side of the inner nuclear membrane can stabilize nuclear membrane shape.
  • 5. The photo of nuclear envelope by TEM
  • 7. The functions of nuclear lamina: 1.Keeps nuclear shape no changed: If you use the high concentration salt solution, detergent or nuclease to move away the nuclear substance, the remaining (nuclear lamina) still presents a nuclear shape. In addition, the nuclear lamina links nuclear skeleton meshwork and intermediate filament together to form a continued meshwork for nucleus. 2.Is associated with the assembly of chromatin and nucleus: The shape of nuclear lamina can be changed during the cell proliferation phases. In the G1 phase, nuclear lamina can present the anchoring sites for heterochromatin on the inner side of inner nuclear membrane. At the ending of the G1 phase, the nuclear lamina will be phosphorylated and the nuclear envelope will disappear. The B type of nuclear lamina will combine to the residual vesicles of nuclear membrane, and A type of lamina will be dissolved in plasma. In the later of M phase, All types of lamina will be dephosphorylated and assembled again to form nuclear lamina and mediate the nuclear envelope construction.
  • 9. The nuclear pores are the channels for the substance transportation: Nuclear proteins are synthesized in plasma, then will be imported into nucleus by the pores. The RNAs and the ribosome subunits synthesized in nucleus will be exported into plasma by the pores also. In addition, it is indicated by a injection experiment that small molecules can enter the nucleus by diffusion from the pores. Nuclear pores are composed of 50 different nucleoporins at least, and we call these pore structure as nuclear pore complex (NPC). Usually, a mammalian nucleus contains 3,000 nuclear pores. The more activities a cell takes, the more nuclear pores the cell contains. For example, a frog ovum can contain 37.7X106 nuclear pores, but a matured cell contains 150~300 nuclear pores only. The structures of nuclear pore include ① cytoplasmic ring located on the cell plasma part of the pore complex contains 8 filaments extending into plasma. ② nuclear ring located on the nuclear plasma part of the pore complex extending 8 filaments also. ③ transporter located in center of the pore as a plug particle. ④ Spoke located on the edge of the pore as the spines.
  • 10. The nuclear pore structures on the cell plasma side after an extraction
  • 11. The nuclear pore structures on the nuclear plasma side after an extraction
  • 13. The transportation by nuclear pore is associated with signal transduction: 1982, R. Laskey identified a signal sequence on the C terminal of nucleoplasmin enriched in nucleus, and the signal can lead protein to enter nucleus. This signal sequence was named as nuclear localization signal (NLS). The firstly identified NLS is the T antigen of SV40. This antigen is synthesized in cell plasma, and transported into nucleus quickly. Its NLS is pro-pro-lys-lys-lys-Arg-Lys-val. NLS is composed of 4 – 8 amino acids containing Pro, Lys and Arg. NLS is not specific to target protein and will not be cleaved by protease. Karyopherin is a protein family that is associated with the selective transportation by the pore, and it is a receptor family actually. The imporin of them imports proteins into nucleus from cell plasma and the exportin of them exports the proteins on an opposite direction. Ran is another protein involved in the transportation by the pore complex. Ran is a G protein that regulates the assembly and disassembly of the complex of the protein transported and the receptor used. Ran-GTP concentration is much higher in the nucleus than in cell plasma.
  • 15. Nuclear plasma protein (nucleoplasmin) is transported by the following steps: ① The protein combines to the α / β dimer of the receptor (imporin). ② The complex of the protein transported and the receptor used combines to the filaments located on the NPC cytoplasmic ring. ③ The filaments curve to the nuclear center, the transporter structure will be changed to form a hydrophilic channel, and the protein passes through the channel. ④ The complex of the protein transported and the receptor used combines to Ran-GTP, the complex is disassembled and releases out the protein transported. ⑤ The imporin β combined with Ran-GTP will be exported out of the nucleus, the GTP combined with Ran will be hydrolyzed in cell plasma, and the Ran-GDP will go back to nucleus to be transformed to Ran-GTP again. ⑥ The imporin α will be transported back to cell plasma with the help from exportin.
  • 16. We know a little about how the macromolecules are transported to cell plasma from nucleus. In most of cases, the RNA in nucleus is combined with protein to form an RNP complex, then, transported into cell plasma. There is nuclear exportation signal (NES) on the protein of RNP complex that can combine to the intracellular receptor, exportin, to form the complex of RNP-exportin-Ran-GTP. In the cell plasma, this complex will be disassembled and release out the Ran-GTP, RNA, Ran-GDP, exportin, and RNP protein.
  • 17. The nucleoplasmin is transported into nucleus
  • 18. II. Chromosome Chromatin was named by W. Flemming in 1879. Chromosome was named by Waldeyer in 1888. Chromatin and chromosome are same substance with different shape presentation in different cell cycle phases. The chemical components of chromatin: Chromatin is composed of DNA, histone, nonhistone protein, and some RNA at ratio about 1:1:(1-1.5):0.05. DNA: DNA is the carrier of genetic information. DNA sequences can be sorted as 3 types: nonrepeated fraction, moderately repeated fraction (101-105), and highly repeated fraction (>105). DNA forms: B-DNA, Z-DNA, and A-DNA.
  • 19. DNA forms (Red color shows the couple backbones)
  • 20. Chromosome DNA contains three basic sequences: ① autonomously replicating DNA sequence (ARS). ARS is the starting site of DNA replication. In yeast genome, there are 200-400 ARSs included, and most of them contain a AT enriched 11bp sequence called as ARS consensus sequence (ACS). ② centromere DNA sequence (CEN) composed of a lot of repeated sequences. ③ telomere DNA sequence (TEL). TEL is similar in different bio organisms, and composed of 5 – 10bp repeated sequences. Human TEL repeated sequence is TTAGGG. In 1983, A. W. Murray et al constructed yeast artificial chromosome (YAC) contains ARS, CEN, TEL and exogenous DNA with the length of 55kb. YAC is very useful to transgenic technology and construction of cDNA library because the length of insert to YAC can be much longer than that to plasmid.
  • 21. Three basic sequences of chromosome
  • 22. Histone: Histone is positively charged and contains arginine and lycine. Histone is alkaline protein. Histones can be sorted as two types: 1. Highly conserved core histone including H2A, H2B, H3, and H4. 2. Non conserved linker histone including H1 only. The core histone is highly conserved, especially the H4 is. For example, 2 of 102 amino acids of the H4 of cattle and pea are different, but cattle has been evoluted 300 million years earlier than pea. The reasons for that may be as the follows: 1. Most of the amino acids of core histone interact with DNA or other histones, so, any change of them will cause the fatal mutation. 2. In all bio organisms, the DNA phosphodiester skeleton that interacts with histone is same. The core histone head part makes DNA winded round the histone center by the electronic force between arginine residue and phosphodiester skeleton. By the described as above, nucleosome can be formed. The tail part of core histone containing a lot of arginine and lysine residues. The tail part is the site to be modified after translation. H1 is easy to be mutated, and it is species specific and tissue specific.
  • 23. Nonhistone protein: Nonhistone protein is the protein that binds to the specific DNA sequence of chromosome, so, we call it as sequence specific DNA binding protein. The features of nonhistone protein are as the follows: ① Nonhistone protein is negatively charged and acidic protein that contains a large number of aspartic acids and glutamic acids. ② Nonhistone protein can be synthesized during the whole cell cycle, but histone protein is synthesized during the S phase only. ③ Nonhistone protein can recognize the specific DNA sequence. The functions of nonhistone are as the follows: ① Help DNA molecules to be pleated and form different structure domains that are beneficial to DNA replication and gene transcription. ② Help to start DNA replication reaction. ③ Regulate transcription and gene expression.
  • 24. From DNA to chromosome: There are 23 pairs of chromosomes in a human nucleus. If you open and extend the DNA molecule in each chromosome, it will be 5cm long. If you link all DNA molecules in a nucleus together, it will be 1.7 – 2.0 m long. But, the diameter of nucleus is shorter than 10μm. That is why the genome information is packaged into the space of a cell nucleus —— thousands of times smaller than the dot. The primary structure formed by the powerful compaction is called as nucleosome. Nucleosome: If the chromatin is treated by a nonspecific nuclease, the DNA fragments around 200bp can be obtained in most of cases. If you treat the null DNA with that enzyme, you will obtain the randomly degenerated fragments of DNA.
  • 25. From DNA to chromosome: Nucleosome: Based on this experiment, R. Kornberg figured out the model of nucleosome. Nucleosome is a beaded structure composed of core particles and linker DNA. We can describe the structure as the follows: ① Each nucleosome includes about 200bp DNA, one histone core, and an H1. ② The octameric histone core is composed of 8 molecules from H2A, H2B, H3, and H4 by two molecules from each. ③ DNA molecule winds the core particle with a left hand helix and 80bp for each circle. 1.75 circles for each structure. ④ Adjacent core particles are linked by a 60bp linker DNA.
  • 27. Chromosome Morphology • Telomere: chromosome ends • Centromere: site of spindle attachment – Constriction of the metaphase chromosome at the centromere defines two arms • Nucleosome: DNA double helix wrapped around histone proteins
  • 28. Chromatin DNA filament: The DNA is compacted to be shortened by 7 folds and forms the DNA filament in 11nm diameter when it was transformed to the beaded nucleosome chain. Chromatin DNA exists in another style by that the beaded nucleosome chain is condensed by 6 folds. Under electron microscope, we can see the chromatin DNA filament in 30nm diameter that is formed by the overlapped helix structure of the beaded nucleosome chain.
  • 29. The DNA filaments in 30nm and 11nm diameter (A) Is composed of (B)
  • 30. For the advanced package of the chromosome, we keep detail unknown so far. Probably, it is the serial overlapped or pleated like the follows: From DNA to Chromosome: DNA 11nm filament (beaded nucleosome chain) 30nm filament pleat as loop chain bind to the sites on nuclear skeleton where is AT enriched assembly of chromosome
  • 32. Heterochromatin and euchromatin: In the inter phase (G1 and G2) of cell cycle, the chromatin in the nucleus can be sorted as heterochromatin and euchromatin. Euchromatin is the DNA regions where the transcription is very active. Euchromatin looks like loose loop and bright staining under electron microscope. Euchromatin is easy to be cleaved by nuclease at some hypersensitive sites. Heterochromatin is condensed in G phase without any transcription, so, it was named as inactive chromatin. Heterochromatin is the genetic lazy regions, and replicated lately, condensed early, that is called as heteropyknosis.
  • 33. Heterochromatin (dark staining) and euchromatin (bright staining) Heterochromatin Euchromatin
  • 34. Constitutive hetero- chromatin is hetero- pyknosed chromatin in each type of cell and located in centromere region. The Fig shows you the Constitutive hetero- chromatin displayed by fluorescence hybridization in situ.
  • 35. Facultative heterochromatin is heterochromatin appeared in some special cell type or developing stage. The X chromosome of female mammalians is the facultative heterochromatin. Usually, female mammalian cell contains double X chromosomes, and one of them is heterochromatin called barr body. When a human embryo is developed after 16 days, one X chromosome will be transformed as barr body with dark staining. So, we can identify the sex of a human embryo by checking the barr body of the embryo cells in the amniotic fluid. The barr body like a drumstick in a white cell
  • 36. The structure of chromosome: In the M phase of cell cycle, chromatin will be transformed as chromosomes by the powerful condensation. Chromosomes are stick shape with different length. The metaphase chromosome is the best stage to observe and number them because the morphology of chromosome is stable at this time. The number of chromosome is same in the same type of cells from different individuals of one species. The chromosomes of sex cells are haploid, we mark it as n. The chromosomes of other cells are diploid, we mark it as 2n. The chromosomes of some cells of some species are polyploid, such as, 4n, 6n, and 8n. The different cells from same individual can be different chromosome types. For example, body cells of rat are 2n, but its liver cells can be 4n, 8n, and 16n. The chromosome number of human endometrial cell is variable from 2n =17 - 2n =103, that is not euploidy. The chromosome number can be different in different species cells. For examples, human 2n = 46, chimpanzee 2n = 48, fruit fly 2n = 8, wheat 2n = 42, rice 2n = 24, onion 2n=16.
  • 37. The terms used to the structure of chromosome: 1.Chromatid: Metaphase chromosome is composed of two chromatids with a junction at the centromere site. Each chromatid is formed by the overlapped and pleated DNA double strands. When the cell is dividing the chromatids can be separated into two new cells. 2.Chromonema: In the S or G phase cells, each chromonema indicates a chromatid. 3.Chromomere: Chromomere is the linear beaded particles chain DNA. The chromomere of heterochromatin is bigger than that of euchromatin. 4.Primary constriction: It is a bright stained hang ditch on the metaphase chromosome where the centromere is located, so, it can be called as centromere region. Each chromosome has one localized centromere. The chromosome from some species has centromere function every where. We call this chromosome as holocentromere chromosome. For examples, ascarid (round worm) and other nemas, butterfly. The chromosomes can be sorted by the location of centromere as following: ① metacentric chromosome. ② submetacentric chromosome. ③ subtelocentric chromosome. ④ telocentric chromosome. 5.Secondary constriction: Excepting primary constriction, the second ditch is called as secondary constriction. The location of secondary constriction is unmovable by that we can identify chromosome.
  • 38. The terms of chromosome structure
  • 39. 6.Nucleolar organizing regions (NORs): They are the areas where the genes for ribosome RNA are located. They can synthesize the 28S, 18S, and 5.8S rRNA for ribosome. NORs can exist in secondary constriction. 7.Satellite: It is a ball part located at the terminal of chromosome, and linked to the main part of chromosome by secondary constriction. The satellite located at terminal of chromosome is called as terminal satellite, and located between two secondary constrictions is called as intermediate satellite. 8.Telomere: It is the specialized part located at the terminal of chromosome. The function of telomere is maintenance of the stability of chromosome. Telomere is composed of the highly repeated fractions, and it is so conserved that it is similar between the totally different life beings. The component of human telomere is TTAGGG. Telomere is associated with aging. After each replication of telomere DNA, the telomere will be shortened by 50 – 100bp. The replication of telomere is droved by telomerase that has reverse transcriptase activity. This enzyme lacks in normal cells, so, telomere will become short with the cell proliferation. So, cell will be aging during this action.
  • 40. The nucleolus will be formed in the center of nucleolar organizing regions
  • 41. The telomeres displayed using fluorescence hybridization in situ. The sequences of telomere
  • 42. The structure of centromere: Centromere means the special region by that the chromatids of metaphase chromosome are linked together. Kinetochore means the outer surface structure located on the primary constriction that is linked to spindle fibers. Centromere contains 3 domains: kinetochore domain, central domain, paring domain. Three domains of centromere
  • 43. Kinetochore domain: Kinetochore domain is composed of outer plate, inner plate, interzone, and fibrous corona. The inner plate combines to the heterochromatin of central domain, outer plate combines to filaments of spindle fibers. Their motor proteins located on the fibrous corona to supply energy to the chromosomes separation.
  • 44. Central domain: It is located below the centromere and contains the heterochromatin composed of highly repeated α satellite DNA. Paring domain: It is located in centromere by that the chromatids of metaphase chromosome are linked together. There are two types of proteins in this domain: inner centromere protein (INCENP), and chromatid linking protein (CLIP). By using anti-centromere antibodies (ACA), INCENP or CENP (centromere protein) can be identified and sorted as the follows: Types Functions CENP-A Specific histone to centromere CENP-B Binds to satellite DNA in central domain CENP-C Binds to kinetochore CENP-D Binds to kinetochore CENP-E Drive motor protein CENP-F Binds to kinetochore INCENP-A Link partner chromatid INCENP-B Link partner chromatid
  • 45. Karyotype and bands display: The bands display technology of chromosome was developed in 1960s to 1970s, and it brought the chromosome researches to a new and fast developing stage. The result data about chromosome bands is the very useful background research for modern genome research programs, gene molecular research programs, and genetic research programs. Karyotype is the total features of the chromosomes in M phase. It includes the number, size, and shape of chromosome. If the paired chromosomes are arranged by shape and size, a figure will be obtained, and we call it as karyogram. Karyogram is of characters of species.
  • 46. Karyotype • International System for Human Cytogenetic Nomenclature (ISCN) – 46, XX – normal female – 46, XY – normal male • G-banded chromosomes are identified by band pattern.
  • 48. p q Arm Region Band Subband 2 1 1 2 2 1 1 1 2 3 4 3 2 1 2 1 5 4 3 2 1 1 2 3 1 2 3 1 2, 3 4 1 2 3 17q11.2 Chromosome 17 Defining Chromosomal Location
  • 49. Chromosome Morphology Changes During the Cell Division Cycle. • DNA double helix: 2nm diameter Interphase (G1, S, G2) • Chromatin “beads on a string:” 11nm • Chromatin in nucleosomes: 30nm Metaphase (Mitosis) • Extended metaphase chromosomes: 300 nm • Condensed metaphase chromosomes: 700 nm
  • 50. Cell Division Cycle G1 S G2 Interphase (11–30 nm fibers) Metaphase (300–700 nm fibers) M Mitosis: Prophase Anaphase Metaphase Telophase
  • 51. Visualizing Metaphase Chromosomes (Banding) • Giemsa-, reverse- or centromere-stained metaphase chromosomes G-Bands R-Bands C-Bands
  • 52. Normal Female Karyotype (46, XX) (G Banding)
  • 57. Chromosome Structure Abnormality: Balanced Translocation 45, XY, t(14q21q)
  • 58. Probe Interphase or metaphase cells on slide (in situ) Microscopic signal (interphase) Fluorescent in situ Hybridization (FISH)  Hybridization of complementary gene- or region-specific fluorescent probes to chromosomes.
  • 59. Fluorescent in situ Hybridization (FISH) • Metaphase FISH – Chromosome painting – Spectral karyotyping • Interphase FISH
  • 60. Uses of Fluorescent in situ Hybridization (FISH) • Identification and characterization of numerical and structural chromosome abnormalities. • Detection of microscopically invisible deletions. • Detection of sub-telomeric aberrations. • Prenatal diagnosis of the common aneuploidies (interphase FISH).
  • 61. FISH Probes • Chromosome-specific centromere probes (CEP) – Hybridize to centromere region – Detect aneuploidy in interphase and metaphase • Chromosome painting probes (WCP) – Hybridize to whole chromosomes or regions – Characterize chromosomal structural changes in metaphase cells • Unique DNA sequence probes (LSI) – Hybridize to unique DNA sequences – Detect gene rearrangements, deletions, and amplifications
  • 62. Telomere (TTAGGG)n 100–200 kb 3–20 kb Unique sequences Telomere associated repeats Probe binding site FISH Probes • Telomere-specific probes (TEL) – Hybridize to subtelomeric regions – Detect subtelomeric deletions and rearrangements
  • 63. Normal diploid signal Trisomy or insertion Monosomy or deletion Cell nucleus Genetic Abnormalities by Interphase FISH LSI Probe • Greater or less than two signals per nucleus is considered abnormal.
  • 64. Structural Abnormality by Interphase FISH LSI Probe (Fusion Probe)
  • 65. Structural Abnormality by Interphase FISH LSI Probe (Break Apart Probe)
  • 66. Translocation by Metaphase FISH WCP Probe (Whole-Chromosome Painting)
  • 68. The chromosome banding technology is very important to genetics research, species classification, and others. This technology includes the cell and chromosome treatments by physical and chemical methods, chromosome staining and bands display. Bands display technologies can be sorted as two types: 1. The bands distribute on entire chromosome, such as G, Q, and R banding technologies. 2. The bands distribute in localized region of chromosome, such as C, Cd, T, and N banding technologies.
  • 69. Human G Karyotype. G bands display the regions where AT is enriched
  • 70. Human Q Karyotype. Q bands display same thing of G bands
  • 71. Human C Karyotype. C bands display the centromere heterochromatin
  • 72. Special chromosomes: Polytene chromosome: It was identified in some insect saliva cells in 1881. Polytene chromosome: ① 1,000 – 2,000 folds huger than others. It is the reason that chromosomes are replicated without separation. ② Polytene. Each polytene chromosome is composed by 500 – 4,000 helix opened chromosomes. ③ Cell junction and homologous chromosomes combination. ④ Striation. ⑤ In some life stage of insects, some bands of polytene chromosome become loosed and form puff and Balbiani ring. Puff can be labeled by H3-TdR, that means puff is the region where the gene transcription is very active.
  • 73. The chromosomes from saliva cells
  • 74. Lamp-brush chromosome: Lamp-brush chromosome was identified in fishes firstly. There are lateral loops on the chromosome like lamp brush. It is composed of two homologous chromosomes. Lateral loops are the region with RNA active transcription. B chromosome: In 1928, Randolph, a scientist, call normal chromosomes as A chromosomes, and call abnormal chromosomes existed in many animals and plants as B chromosome.
  • 75. III. Nucleolus Nucleolus may be visible in G phase nucleus. They are spherical and 1 – 2 for each cell usually. The number and size of nucleolus are depended on the cell type and function. The more proteins synthesis and the faster proliferation the cell takes, the more and bigger nucleoli the cell has. Nucleolus disappears before the cell division, and appears in the end of division. The major functions of nucleolus are rRNA transcription and ribosome assembly. Structure of nucleolus: No any membrane packages nucleolus area. There are three special areas can be identified under electron microscope: ① fibrillar centers (FC) that are surrounded by dense fibers, and low electric density. FC contains RNA polymerase and rDNA that is naked molecule. ② dense fibrillar component (DFC) that is a loop or half loop to surround FC. Transcription is carried out in the border region of FC and DFC. ③ granular component (GC) composed of 15-20nm particles that are the RNPs in different manufactured steps. RNP means the RNA combined with protein. Nucleolus chromatins can be sorted as two types: heterochromatin and euchromatin. The nucleolus heterochromatin is always located around the nucleolus, so we call them as nucleolus peripheral chromatin. The nucleolus euchromatin is located in nucleolus, and nucleolus organizing region in that the rDNA is located.
  • 77. IV. Ribosome Ribosome is the manufacturing shop to synthesize proteins. There are about 20,000 ribosomes in an actively growing bacterium. Ribosome proteins are 10% of total proteins of cell, and its RNA is 80% of cell total RNA. Structure of ribosome: The ratios of protein and RNA to ribosome components are 40% and 60%. The ribosome subunits are composed of the combination of the protein and RNA. The catalytic activities needed by the translation are presented by ribosome protein, rRNA and other helper factors. The ribosomes can be sorted as two types. 70S ribosome exists in bacteria, mitochondrion, and chloroplast. 80S ribosome exists in the plasma of eukaryotic cells. Ribosome is composed of a large subunit and a small subunit. The both subunits will be combined together when the ribosome synthesizes protein with mRNA as template. After the translation, the ribosome will be separated as two parts again. When a protein is translated on an mRNA, many ribosomes can bind to the mRNA to synthesize the protein. We call these ribosomes for one protein synthesis as polyribosome. The longer mRNA is used, the more ribosomes are combined. The polyribosome enhances the efficiency of protein synthesis. Prokaryotic 5S rRNA and eukaryotic 5.8S rRNA are very conserved for their structures, so, they can be used to research the bio-evolution.
  • 78. Assembly of ribosome: The DNA fragment encoding rRNA is called as rRNA gene. There are about 200 copies of this gene in a human cell. rDNA contains no histone core, so, it is a naked DNA. To transcript rRNA, the RNA polymerase moves ahead along the DNA molecule. The synthesized rRNA molecules extend out their molecules from the complex of polymerase and DNA, and form a featherlike structure under microscope.
  • 79. rRNA transcription The filaments are the new synthesized 45S rRNA that combines to protein to form RNP complex. The methylated 45S rRNA can be cleaved as the two parts by RNase: 18S rRNA and 32S rRNA,the latter is cleaved as 28S rRNA and 5.8S rRNA. The synthesized 5S rRNA will be transported into nucleolus to join the assembly of the large subunits of ribosome. There is a 60bp non-transcription DNA fragment between adjacent rRNA genes
  • 82. V. Nuclear matrix Nuclear matrix is called as nucleoskeleton that is a meshwork in eukaryotic cells, that is what I told you before. Because nuclear matrix is associated with DNA replication, RNA transcription and modification, chromosome assembly, and virus replication, nuclear matrix is now paid more attentions to. Components of nuclear matrix: ① Non-histone filaments at ratio of 96%. The nucleoskeleton contains three scaffold proteins: SC Ⅰ, SCⅡ, and SC Ⅲ. ② A little RNA and DNA: The RNA is important to maintain the skeleton structure. The DNA is called as matrix /scaffold associated region (MAR or SAR) where the AT is enriched to form the heterochromatin binding sites. ③ A little phospholipids (1.6%) and sugars (0.9%). Nuclear skeleton – nuclear lamina – inter filaments – pore complex is a meshwork system with very good stability.
  • 83. The function of nuclear skeleton: 1. Present the scaffolds for DNA replication. DNA can be anchored on to the scaffold with a replication loop. The enzymes needed by DNA replication are located on the skeleton, such as DNA polymerase α, DNA primerase, DNA topoisomerase II. 2. Is the place where gene can be transcripted and modified. There are RNA polymerase binding sites on the skeleton. New synthesized RNA is combined to the skeleton for further modification. 3. Is associated with the assembly of chromosome. The nuclear skeleton may be same thing to chromosome skeleton. 30nm chromatin fibers are combined to nuclear skeleton to form loops that will be packaged further in M phase to be assembled as chromosome.
  • 84. Chromatin bound on nuclear skeleton or chromosome skeleton
  • 85. Summary • Mutations are heritable changes in DNA. • Mutations include changes in chromosome number, structure, and gene mutations. • Chromosomes are analyzed by Giemsa staining and karyotyping. • Karyotyping detects changes in chromosome number and large structural changes. • Structural changes include translocation, duplication, and deletion of chromosomal regions. • More subtle chromosomal changes can be detected by metaphase or interphase FISH.