Eukaryotic Chromosome Organization — Lecture II

13-1

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Eukaryotic ChromosomeOrganization — Lecture II

Dr. Steven J. Pittler

VH 375BOffice 4-6744Cell 612-9720

Suggested Reading: Lewis 2nd Edition

Chapter on Chromosomes

13-2


Chromosomes

Structures that consists primarily of DNA and proteins that are duplicated and transmitted during mitosis or meiosisHeterochromatin stains dark and is mostly repetitive DNA sequencesEuchromatin stains lighter and contains protein encoding genes

13-3


13-4


Multiple Levelsof packing are

required to fit the DNA into the cell

nucleus

13-5


The basic unitof chromatin

is the nucleosome

13-6


The nucleosome consists of 146bp of DNA wrapped around a protein core of 8 histones

13-7


Histone H1 helps compact thenucleosomes into a 30nm fiber

13-8


The Histone tails are a

critical determinant of

chromatin structure

13-9


Specific modifications are associated with specific functions

13-10


The normal karyotype: 23 diploid chromosomes

Human somatic cells contain 46 chromosomes: paired homologs of chromosomes 1 to 22 and sex chromosomes (XX or XY)

• Diploid refers to the presence of two copies of each different chromosome.

• Gametes have one set of each chromosome and are called haploid.

• Cells missing a single chromosome or having an extra one are aneuploid

• Cells which contain a normal chromosome constitution are called euploid.

13-11


Karyotype analysisMetaphase chromosomes are squashed on a slide and stained with DNA binding dyes. Banding patterns help define different chromosomes.

Chromosomes were named in order of their size and centromere position that appear during mitotic metaphase.

13-12


“Histone Code” hypothesis

Modifications of the Histone tails act as marks that can be read by other proteins to control the expression or replication of chromosomal regions. The coding in the

histones may be heritable.

E.g. Generally, histone acetylation is associated with transcriptionally active genes

Deactylation is associated with inactive genes(= gene silencing)

13-13


EpigeneticsHeritable changes not caused by mutation

in the DNA

Can be due to stable changes in gene expressioncaused by changes in chromatin structure

13-14


Epigenetics and Disease:Genomic imprinting

Parent specific expression or repression of genes or chromosomes in offspring.

So… even though two copies of a given gene are inherited,one from each parent, only the maternal or paternal allele

is expressed.

The non-expressed allele is said to be “imprinted.”

13-15


Wilms Tumor-Childhood Tumor of the kidney (nephroblastoma)

Accounts for 7% of all childhood cancers

-Caused by a defect in imprinting of the Insulin-likeGrowth Factor 2 (IGF2) gene

- IGF2 is usually only expressed from the paternal locus, i.e. maternally imprinted

-Defects in imprinting that cause expression of the maternal locus lead to cancer

13-16


DNA methylation

Covalent modification of the DNA is also important for gene

silencing human cells

Most genes have GC rich areas of DNA in their promoter

regions. These are referred to as CpG islands.

Methylation of the C residues within the CpG islands leads

to gene silencing

13-17


Rett Syndrome: X-linked, neurodegenerative disorder

affects 1:10,000-15,000 (females only)Caused by a mutation in the gene

encodingMethyl-CpG-binding protein 2

(MeCP2), which in turn leads to loss of gene

silencing at many loci.

Epigenetics and Disease:DNA methylation

13-18


The karyotype shows the chromosome complement of a normal ________?

1. Male2. Female

13-19


Largest,Metacentric

Smallestacrocentric

Sex chromosomesXX (shown)

13-20


Anatomy of a chromosome

Chromosomes are categorized by the relative location of their centromere.

• At tip - telocentric (not found in humans)

• Close to tip - acrocentric• At midpoint - metacentric• Displaced from center -

submetacentric

13-21


Anatomy of a chromosome

The portion of the chromosome to each side of a centromere is called a chromosome arm.

shorter arm = p armlonger arm = q arm

13-22


Anatomy of a chromosomeTelomeres are:

• At the tips of chromosomes • Many repeats of the sequence TTAGGG• Subtelomeres have more varied short

repeats• These are the chromosomal parts between

protein-rich areas and the telomeres• These areas extend from 8,000 to 30,000

bases inward toward the centromere from the telomeres

13-23


SubtelomeresInclude some protein-encoding genes and bridge the gene-rich regions and the telomere repeatsWhen researchers compared subtelomeres to known gene sequences they found about 500 matches

13-24


Anatomy of a chromosomeCentromeres are the largest constriction of the chromosome • Site of attachment of spindle fibers• 171 base pair segment repeated 100,000

times, called alpha satellite sequences• Also include centromere-associated proteins

• Some are synthesized only when mitosis is imminent forming the kinetochore that emmanates from the centromere and connects the spindle fibers

• Appears during prophase and vanishes during telophase

13-25


13-26


Chromosomal shorthand

An ideogram represents a chromosome schematically.

The major banding regions are indicated with numbers.

Sucrose intolerance is located at 3q.26 (chromosome 3, long arm, major band 26)

13-27


Chromosomes carry different genes

ideograms

13-28


Visualizing chromosomes• Obtain tissue from person

Fetal tissue: amniocentesis chorionic villi sampling fetal cell sorting Adult tissue: blood (white blood cells) cheek swab (buccal cells) skin cells tissue biopsy

• Prepare cells on slide to remove rest of cell matter• Stain DNA with dyes or DNA probes (is a labeled piece

of DNA that binds to its complimentary sequence on a particular chromosome) to visualize DNA

• Evaluate chromosomes in comparison to known information

13-29


FISHing

• Conventional chromosome stains have one drawback- they are not specific to a particular chromosome

• FISH uses DNA probes that are complimentary to specific base sequences, and if those sequences are unique to a particular chromosome the technique can identify it

13-30


FISH: fluorescence in situ hybridizationDNA probes labelled with fluorescing dye bind complementary DNA

13-31


Cytogenetics

the subdiscipline within genetics that focuses on chromosome variations.

Abnormal number of copies of genes or chromosomes can lead to genetic abnormalities.

13-32


Mutation at the Chromosome Level Abnormal numbers of genes or chromosomes Range from the single-base changes to missing or extra pieces

of chromosomes A mutation is a chromosomal aberration if it is large enough to

see with a light microscope using stains and/or fluorescent tags Generally, excess genetic material has a milder effect on human

health when compared to a deficit of genetic material Most chromosomal abnormalities are so severe that prenatal

development ceases in the embryo 0.65 percent of all newborns have chromosomal aberrations An additional 0.20 percent have chromosomal rearrangements

that do not produce symptoms

13-33


Chromosomal Abnormalities

• Down syndrome-extra chromosome 21• Turner syndrome- XO- a female with only one

X chromosome• Klinefelter syndrome- XXY, a male with an

extra X chromosome– Before this women who were XO were thought to

be genetic males because they lack Barr bodies and XXY were thought to be genetic females because their cells have Barr bodies

13-34


Chromosome anomaliesmay cause phenotype abnormalities.

A chromosome karyotype revealed she carries three copies of chromosome 21, a condition called trisomy 21.

This young girl has Down syndrome.

13-35


Extra AutosomesChromosomes 13, 18, and 21 are the most

frequently seen extra autosomes and they have the lowest gene densities- they carry considerably fewer protein-encoding genes

13-36


Chromosomal shorthandAbbreviation What it means46, XY Normal male46, XX Normal female45, X Turner syndrome female47, XXY Klinefelter syndrome male47, XYY Jacobs syndrome male46, XY del (7q) Male missing part of long arm of

chromosome 747, XX+21 Female with trisomy 2146, XY t (7;9) (p21.1;q34.1)

Male with translocation between short arm of chromosome 7 at band 21.1 and long arm of chromosome 9 at band 34.1

13-37


Chromosome Abnormalities

PolyploidyAneuploidy monosomy trisomyDeletionDuplicationInversionTranslocation

Iso chromosomeRing chromosome

Extra chromosome setExtra or missing chromosome one chromosome absent one chromosome extraPart of a chromosome missingPart of a chromosome present twiceSegment of chromosome reversedTwo chromosome arms exchanged in part or entirelyA chromosome with identical armsA chromosome that forms a ring due to deletions in telomeres, which cause ends to adhere

13-38


Polyploidy

Individuals with three copies of each chromosome are triploid, or an extra set

•Polyploidy accounts for 17% of all spontaneous abortions and 3% of stillbirths/newborn deaths.

Result of:•Two sperm fertilize one egg.•Haploid sperm fertilizes diploid egg.

13-39


Aneuploidy

• Most autosomal aneuploids are spontaneously aborted

• Mental retardation is common in an individual who survives aneuploidy

• Sex chromosome aneuploidy have milder symptoms• Children born with the wrong number of chromosomes

have an extra chromosome- trisomy• Rather than missing a chromosome- monosomy

• Down syndrome can result from trisomy 21 or from translocation• Translocation Down syndrome accounts for 4% of

cases, has a much higher risk of recurrence than trisomy 21

13-40


Aneuploidy

• Nondisjunction is a common cause of aneuploidy resulting in a gamete with one extra chromosome and another gamete with one missing chromosome.

• Nondisjunction during the first meiotic anaphase division results in a copy of each homolog in the gamete and two cells do not have any copies.

• Nondisjunction during the second meiotic anaphase division results in both sister chromatids in one gamete, one with no copy, and two normal cells.

13-41


Nondisjunctionin meiosis I Anaphase INondisjunctionin meiosis I

Anaphase II

Nondisjunctionin meiosis II

Gametes

Abnormal gametes Abnormal gametes Normal gametes

Nondisjunction causes aneuploidy

13-42


Trisomies and MonosomiesOne extra or one missing chromosome results in extra or

missing copies of all of the genes on that chromosome.

Most trisomies and monosomies produce inviable embryos.

Some fetuses with trisomy of smaller autosomes survive to birth with syndromic conditions:

trisomy (syndrome) Incidence at birth

% conceptions that survive >1 year

13 (Patau) 1/12,500 to 1/21,700 < 5 %

18 (Edward) 1/6,000 to 1/10,000 < 5%

21 (Down) 1/800 to 1/826 85%

13-43


Autosomal Aneuploids

• Most autosomal aneuploids are lethal• Trisomy 21 Down syndrome

– Most common– Extra folds in the eyelids called epicanthal folds

and a flat face– Termed mongoloid by Sir John Langdon Haydon in

1866– In 1961, researchers identified a mosaic Down

syndrome• Affected girl with all the physical signs but normal

intelligence

13-44



• Trisomy 21 cont’d• Usually short and has straight, sparse hair, and a

thick tongue protruding through the lips• Hands have abnormal pattern of creases, loose joints,

and poor reflexes and muscle tone give a floppy appearance

• Intelligence varies• Physical problems are common

– Heart and kidney defects, and hearing and vision loss– Suppressed immune system– Digestive system problems– Down syndrome 15 is more likely to develop leukemia

13-45



• Trisomy 18- Edward Syndrome• Only 1 in 6,000 -10,000 newborns have trisomy 18• Most do not survive birth• Great physical and mental disabilities, with

developmental skills stalled at the six-month level• Major abnormalities

– Heart defects, displaced liver, growth retardation, and oddly clenched fists

– Overlapping placement of fingers, narrow and flat skull, abnormally shaped and low-set ears, small mouth and face, unusual or absent fingerprints, short large toes with fused second or third toes, and “rocker-bottom” feet

– Most cases are attributed to non-disjunction in meiosis II of the oocyte

13-46


Oddly clenched

fist

13-47



• Trisomy 13- Patau Syndrome• Most do not survive birth• Most striking but quite rare is fusion of the developing

eyes, so that the fetus has one large eyelike structure in the center of the face

• More common is a small or absent eye• Major abnormalities

– Heart defects, kidneys, brain, face, and limbs– The nose is malformed, and cleft lip and/or present in a

small head– Extra fingers and toes– Extra spleen, abnormal liver, rotated intestines, and an

abnormal pancreas

13-48


Sex Chromosome AneuploidySituation Oocyte Sperm ConsequenceNormal X Y 46, XY normal male

X X 46, XX normal femaleFemale Nondisjunction

XX Y 47, XXY Klinefelter syndromeXX X 47, XXX triplo-X

Y 45, Y nonviableX 45, X Turner syndrome

Male Nondisjunction (meiosis I)

X 45, X Turner syndromeX XX 47, XXX triplo-X

Male nondisjunction (meiosis II)

X YY 47, XYY Jacobs syndromeX 45, X Turner syndrome

13-49


Turner syndrome45, X

1 in 2,000 female births 99% of Turner die in utero

• Absence of Y leads to development as a female.

• Absence of two copies of X-linked genes in a female results in Turner syndrome.

Phenotypes include short stature, webbing at back of neck, incomplete sexual development, hearing impairment, malformed eyebrows.

13-50


Turner syndrome• A chromosomal imbalance causes the hormone

deficit• 1954 P.E. Polani discovered cells from Turner

syndrome patients lack a Barr body (inactive X)• 50% are XO, the rest have partial deletions or are

mosaics, with only some cells affected• Like autosomal aneuploidy this syndrome is more

frequent among spontaneously aborted fetus than newborns

• Two X chromosomes are necessary for normal sexual development

13-51


Triplo-X aneuploidy47, XXX

1 in 1,000 female birthsExtra copy of every X-linked gene Few modest effects on phenotype include

tallness, menstrual irregularities and slight impact on intelligence- less intelligent than their siblings

X-inactivation of two X chromosomes occurs while third remains active seems to compensate for presence of extra X

13-52


Klinefelter syndrome47, XXY

1 in 1,000 male birthsExtra copy of each X-linked gene• Phenotypes include incomplete sexual

development (rudimentary testes and prostate), long limbs, large hands and feet, some breast tissue development, and they are infertile.

• Some cases are not diagnosed until fertility problems arise or remain undiagnosed.

Look at readingon page 256

13-53


XYY syndrome47, XYY (Jacobs Syndrome)1 in 1,000 male birthsExtra Y chromosome

96% phenotypically normal• Modest phenotypes may include great

height, acne and minor speech and reading problems.

• Studies suggesting some increase in aggressive behaviors remain controversial.

13-54


Chromosome structural abnormalities

Chromosomal deletions or duplications result in extra or missing copies of genes in the involved segment.

13-55


Chromosome Deletions

• Is missing genetic material– Cri-du-chat syndrome

• Caused by deletion of part of the short arm of chromosome 5 (5p- syndrome)• High-pitch cry that resembles mewing of a cat• Pinched facial features, developmentally delayed, and mentally retarded• Removes the gene for telomerase reverse transcriptase• Shortened lifespan• Low birth weight, poor muscle tone, small head, and impaired language skills• Reading page 258

13-56


Duplication

• Is a region of a chromosome where genes are repeated

• Causes symptoms if they are extensive

13-57


Larger duplications lead to more severe phenotype

13-58


TranslocationDifferent nonhomologous chromosome exchange portions of chromosomes or combined parts

Two major types:Robertsonian translocation •Two nonhomologous acrocentric chromosomes break at the centromere and long arms fuse. The short arms are often lost. •5% of Down syndrome results from a Robertsonian translocation between chr 21 and chr 14 .

Reciprocal translocation •Two nonhomologous chromosomes exchange a portion of their chromosome arms.

13-59


Reciprocal translocationExchange of material from one chromosome arm to another is called a reciprocal translocation.

Rearrangement of the genetic material results in an individual who carries a translocation but is not missing any genetic material unless a translocation breakpoint interrupts a gene.

13-60


Reciprocal translocation

13-61


Reciprocal Translocations

• Translocation between chromosome 2 and 20 causes Alagile syndrome– The exchange disrupts a gene on chr 20 that causes the

condition– Produces a characteristic face, absence of bile ducts in

the liver, abnormalities of the eyes and ribs, heart defects, and severe itching

• Translocation between chromosomes 12 and 22– Language delay, mild mental retardation, loose joints,

minor facial anomalies, and a narrow, long head: matched those of 22q13.3 deletion syndrome

– Caused by the absence of ProSAP2 because the translocation cuts the gene

13-62


Reciprocal Translocation 2:20

13-63


Inversions

Inverted chromosomes have a region flipped in orientation compared to wild type chromosomes.

• 5-10% cause health problems probably due to disruption of genes at the breakpoints.

• Crossing over within the inverted segments leads to genetically imbalanced gametes.

Two types of inversions occur:Paracentric - inverted region does NOT include

centromerePericentric - inverted region includes centromere

13-64


Segregation of a paracentric inversion

13-65


Segregation of a pericentric inversion

13-66


Isochromosomes

Chromosomes with identical arms form when centromeres divide along the incorrect plane during meiosis.

13-67


Ring chromosomes

• Chromosomes shaped like a ring occur in 1 of 25,000 conceptions.

• May arise when telomeres are lost and sticky chromosome ends fuse.

• Ring chromosomes have phenotypes associated with the loss or addition of genetic material.

13-68


Causes of chromosomal abnormalitiesPolyploidy Error in cell division in which all chromatids fail

to separate at anaphase. Multiple fertilizations.Aneuploidy Nondisjunction leading to extra or lost

chromosomesDeletions and

duplicationsTranslocations.Crossover between a pericentric inversion and normal homologue

Translocation Recombination between nonhomologous chromosomes

Inversion Breakage and reunion with wrong orientation

Dicentric or acentric fragments

Crossover between paracentric inversion and normal homologue.

Isochromosome Division of centromeres on wrong plane

Ring chromosome Loss of telomeres and fusion of ends

Documents

Eukaryotic Chromosome Organization — Lecture II