Transcript DNA content, chromosome numbers, genomes, ploidy

Mammalian Cytogenetics
Chromosome structure & karyotype
Gene 405: Mammalian Genetics
Fall 2002
17 September, 2002
What is cytogenetics?
Cyto:
Genetics:
Study of ………… component of the cell?
And that component named as:
What sort of answers does/can it provide?
Your feed-back!
1.
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Diploid numbers of some commonly studied organisms
(as well as a few extreme examples)
Homo sapiens (human)
46
Mus musculus (house mouse)
40
Zea mays(corn or maize)
20
Drosophila melanogaster (fruit fly)
8
Xenopus laevis (South African clawed frog)
36
Caenorhabditis elegans (microscopic roundworm)
12
Equisetum arvense (field horsetail, a plant)
216
Saccharomyces cerevisiae (budding yeast)
32
Canis familiaris (domestic dog)
78
Arabidopsis thaliana (plant in the mustard family)
10
Myrmecia pilosula (an ant)
2
Parascaris equorum var. univalens (parasitic
roundworm)
2
Cambarus clarkii (a crayfish)
200
Diploid numbers of some commonly studied animals
Common
Name
Genus and
Species
Diploid
Chromosome
Number
Buffalo
Bison bison
60
Cat
Felis catus
38
Cattle
Bos taurus, B.
indicus
60
Dog
Canis
familiaris
78
Donkey
E. asinus
62
Goat
Capra hircus
60
Horse
Equus
caballus
64
Human
Homo sapiens
46
Pig
Sus scrofa
38
Sheep
Ovis aries
54
Recorded maximum number of chromosomes:
Ophioglossum reticulatum
This fern has roughly 630 pairs of chromosomes or 1260
chromosomes per cell.
Polyploidy is a common in these plants
Remarkable!!
The cells can accurately segregate these enormous numbers of
chromosomes during mitosis.
Recorded minimum number of chromosomes : ant subspecies
Myrmecia pilosula
Females have a single pair of chromosomes.
Males of this group of ants have a single chromosome
Reproduces by a process called haplodiploidy
fertilized eggs (diploid) become females
unfertilized eggs (haploid) develop into males.
Chromosome
Three clues to tell chromosomes apart:
1. Chromosome size
2. Position of the centromeres (see also below)
3. Characteristic banding patterns
(caused by staining the chromosomes with dyes)
MOSTLY
chromosomes are too
elongated and tenuous
Before
cell division
each chromosome is duplicated
When first seen
Duplicates are held together
at the centromere.
Human centromeres
contains over 3 million base pairs of DNA.
Most of this is repetitive DNA: short sequences
(e.g., 171 bp) tandemly repeated
duplicated chromosomes are called dyads
Duplicated chromosomes sister chromatids,
Kinetochore
Arms
complex of proteins that forms
at the centromere
(11 in budding yeast)
Shorter of the two
Longer
p-arm
q-arm
Primary constriction
• The centromere is visible as the primary
of the chromosome
constriction
• necessary for correct segregation during cell division
• site of spindle attachment to the kinetochore and
• the site of sister chromatid association
Metacentric
Sub-metacentric
acrocentric
Secondary constriction
Nucleolar organizer region (NOR)
A chromosomal segment containing genes that encode ribosomal RNA
Located at the secondary constriction of some chromosomes
Chromatin not visible at these sites
NOR bearing chromosomes often bear ‘satellite region’;
SATELLITE CHROMOSOMES
Length dependent on stage of cell cycle
Typically visible from prometaphas through interphase
Common cause of erroneous counting of chromosomes
Nucleus
Cellular DNA
Cytoplasm
How to get the best estimate of the size of haploid nuclear genome?
CHROMATIN - avidly staining nuclear body
Each chromosome:
• DNA
2/3
• Histones
1/3
• Non-histones
Low mol. weight proteins
High binding affinity to DNA
H1
Structure evolutionarily
H2A
H2B
Highly conserved among
eukaryotes
H3
H4
High mobility group proteins
Insoluble scaffold proteins
5% of total chromosome mass
Chromosome core
9 fold compaction
5 fold compaction
linker
H1
5 fold compaction
Numerical description of chromosome shape
Chromosome parameters
Each chromosome:
Characteristic length
Typical centromere position
Conserved size of short (p: petite) & long arm (q)
• Relative length
• Centromeric index
• Arm ratio
• Descriptors used to group/classify chromosomes
• Useful in karyotype development
All chromosomes in a
metaphase spread are not of the same size
Sizing chromosome in relation
to each other
Measuring length of entire compliment
Finding fraction/percentage for each
Relative
length
(RL)
=
100
x
length of a chromosome
length of haploid compliment for that spread
• Estimated for several spreads
• Species standard worked out (used as guidelines)
Chromosome
# Genes
# of Bases
Chromosome 1
2968
279 million bases
Chromosome 2
2288
251 million bases
Chromosome 3
2032
221 million bases
Chromosome 4
1297
197 million bases
Chromosome 5
1643
198 million bases
Chromosome 6
1963
176 million bases
Chromosome 7
1443
163 million bases
Chromosome 8
1127
148 million bases
Chromosome 9
1299
140 million bases
Chromosome 10
1440
143 million bases
Chromosome 11
2093
148 million bases
Chromosome 12
1652
142 million bases
Chromosome 13
748
118 million bases
Chromosome 14
1098
107 million bases
Chromosome 15
1122
100 million bases
Chromosome 16
1098
104 million bases
Chromosome 17
1576
88 million bases
Chromosome 18
766
86 million bases
Chromosome 19
1454
72 million bases
Chromosome 20
927
66 million bases
Chromosome 21
303
45 million bases
Chromosome 22
288
48 million bases
Chromosome X
1184
163 million bases
Chromosome Y
231
51 million bases
CENTROMERE INDEX
Indicative of where the centromere is located
Metacentric chromosomes
approx. 50
Sub-metacentric chromosomes
< 50
Centromeric
index =
(CI)
Arm ratio
(AR)
100
x
length of short arm
total chromosome length
=
length of long arm
length of short arm
If both arms equal:
If submetacentric:
AR is 1
AR is > 1
Karyotype
The complete set of chromosomes in the cells of an organism is its karyotype.
Karyotype of the human female
22 pairs of autosomes
1 pair of X chromosomes
Karyotype of the human male
the same 22 pairs of autosomes
one X chromosome
one Y chromosome
From banding
to schematic representation
to idiogram
Chromosome
number
arm
region
band
1
p
3
2
1p32
1q12
1q31-42
Human idiogram
Resolution
Idiogram Album: Human copyright © 1994 David Adler
Different types of banding
R-banded metaphase spread
C-banding
Q-banding
M-FISH METAPHASE SPREAD AND
KARYOTYPE
How to define a karyotype?
Traditional definition
Arrangement of all the chromosomes of a cell
- according to an internationally agreed system
of arrangement for the species
- based on size, shape and centromeric position
- homologous chromosomes arranged together
Refined definition:
- accurate identification of homologues (banding)
- following international nomenclature
Types of chromosomal aberrations
Numerical
Euploids
Aneuploids
Structural
Human trisomies
Trisomies involving:
21
13
18
X
16
1?
survive
Longterm survival
Fertility a problem
low survival
rate
?
What do these trisomies share with each other?
A number of abnormal characteristics
Mental retardation
Retarded growth
Cardiac defects
Defects/deformities involving different organs/tissues
Physical deformities
Structural aberrations
Relatively frequent
Humans & other mammals
Somatic line
What if breakage is in
Germ line
Where can chromosomes break?
When can chromosomes break?
Deletions
Translocations
Duplications
Inversions
Structural aberrations
Deletion
Inversion
Duplication
Reciprocal Translocation
Clinical significance of chromosome aberrations
- Viability ?
- Early embryonic death
- Spontaneous abortions
- Prenatal death
- Post natal death (low survivability)
- Congenital defects or deformities
- Reduced life expectancy
- fertility
- Abnormalities in offspring
abnormal gamete formation
Polytene Chromosomes
• Giant chromosomes - dipteran
• Begin as normal chromosomes
• Repeated rounds of DNA replication
(endoreplication); & no cell division
Become large banded chromosomes
• Centromere – no endoreplication
• Bundle in a mass - chromocenter
• Found in larvae - allow faster growth
• Bands unique to each chromosome
• Allow high resolution mapping