Mammalian Cytogenetics Chromosome structure karyotype Gene 405 Mammalian

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. 2. 3. 4. 5. 6. 7.

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 constriction of the chromosome • 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 H 1 Structure evolutionarily H 2 A H 2 B Highly conserved among eukaryotes H 3 H 4 High mobility group proteins Insoluble scaffold proteins 5% of total chromosome mass Chromosome core

9 fold compaction 5 fold compaction linker H 1 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 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 1 p 32 1 q 12 1 q 31 -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