Chapter 11 

  • Structure and function of Eukaryotic chromosome
    • Copy Cat (left) is clone of Rainbow (right)
    • all cells have identical DNA
    • each cat has many types of cells
    • cats are dissimilar in many phenotypes
  • Chromosomal DNA and proteins
    • chromosomes support packaging, replication, segregation, and expression of genetic information
    • chromatin: generic term for any complex of DNA and protein found in a nucleus of a cell; 1/3 DNA, 1/3 histones, 1/3 non-histone proteins
    • chromosomes: separate pieces of chromatin that behave as a unit during cell division
    • DNA interaction with histones and non-histone proteins produces sufficient level of compaction to fit into a cell nucleus
  • Different levels of chromosome compaction
    • if stretched out, total DNA in a single cell would be about 6 ft long
    • compaction allows DNA to fit in cell nucleus
    • Nucleosome: confirmed by crystal structure; condenses naked DNA 7-fold to a 100 A fiber
    • Supercoiling: hypothetical model (300 A fiber predicted has been seen); causes additional 6-fold compaction, achieving a 40- to 50-fold condensation relative to naked DNA
    • Redial loop-scaffold: hypothetical model (preliminary experimental support); through progressive compaction of 300 A fiber, condenses DNA to rodlike mitotic chromosomes that are 10,000 times more compact than naked DNA
  • Histone proteins
    • histones: small, positively charged, highly conserved; bind to and neutralize negatively charged DNA
    • ==5 types of histones: H1, H2A, H2B, H3, and H4==
    • core histones 2x (H2A, H2B, H3, and H4) make up the nucleosome
  • Non-histone proteins
    • hundreds of other proteins that make up chromatin and are not histones
    • 200-200,000 molecules of each kind of non-histone protein
    • functions of non-histone proteins: structural role (chromosome scaffold), chromosome replication, chromosome segregation, active in transcription
  • Nucleosome is the fundamental unit of chromosomal packaging
    • nucleosomes resemble beads on a string
    • spacing and structure of nucleosomes affect genetic function
    • accessibility for proteins that initiate transcription, replication, and further compaction
    • arrangement along chromatid is highly defined and varies in different cell types and under different conditions
  • Nucleosome core is an octamer of 2 of each of histones H2A, H2B, H3, and H4
    • 160 bp of DNA wraps twice around a nucleosome core
    • 40 bp of linker DNA connects adjacent nucleosomes
    • Histone H1 associates with linker DNA as it enters and leaves the nucleosome core
  • X-ray crystallography of a nucleosome
    • DNA bends sharply at several places as it wraps around the core histone octamer
    • base sequence dictates preferred nucleosome positions along the DNA
  • Nucleosome supercoiling model of higher-order packaging
    • 100 A nucleosomal chromatin is compacted into 300 A fiber by supercoiling
  • The radial loop-scaffold model for higher level of compaction
    • several non-histone proteins (NHPs) bind to chromatin every 60-100 kb and tether the 300 A fiber into structural loops
    • other NHPs gather several loops together into daisy-like rosettes
    • condensins may further condense chromosomes into a compact bundle for mitosis
  • The karyotype of a human female examined by a high-resolution G-banding
    • metaphase chromosomes stained with Giemsa stain have alternating bands of light and dark staining
    • each band contains many DNA loops and ranges from 1 to 10 Mb in length
    • banding patterns on each chromosome are highly reproducible
  • Locations of genes in relation to chromosomal bands
    • short arm: p arm
    • long arm: q arm
    • within each arm, light and dark bands are numbered consecutively
  • Fluorescent in situ hybridization (FISH) is used to characterize genomes
    • FISH depends on hybridization between metaphase chromosomes and a labeled DNA sequence
    • In FISH, chromosomes are spread on a glass slide and denatured to make them single stranded, a DNA sequence is labeled with a fluorescent tag to make a probe, and the probe hybridizes to chromosome at complementary region
  • Spectral karyotyping (SKY) is a variation of FISH
    • in SKY, probes specific for each chromosome are labeled with a different fluorescent dye
  • Chromosomal packaging and function
    • heterochromatin: highly condensed, usually inactive transcriptionally
    • darkly stained regions of chromosomes
    • constitutive: condensed in all cells
    • facultative: condensed in only some cells and relaxed in other cells
    • Euchromatin: relaxed, usually active transcriptionally
    • lightly stained regions of chromosomes
  • Transcription requires changes in chromatin structure
    • promoters of inactive genes are hidden in nucleosomes
    • to activate a gene, transcription factors bind to enhancers and recruit chromatin remodeling proteins
    • promoters are exposed by removing or repositioning nucleosomes
  • The four core histone tails can be modified with chemical groups
    • tails extend outward from nucleosome
    • enzymes can add chemical groups
    • modified tails can alter nucleosomes and bind chromatin modifier proteins
  • Histone tail modifications alter chromatin structure
    • methylation: histone methyltransferase adds methyl group to histone tails
    • methylation affect depends on specific amino acid modified
    • adding methyl group to H3 lysine 9 favors heterochromatin formation
    • methylation reversed by mehtyltransferases
    • Acetylation: histone acetyltransferase adds acetyl group to histone tails
    • Acetylation prevents close packing of nucleosomes
    • Acetylation favors expression of genes in euchromatin
    • Acetylation reversed by deacetylases
  • X-chromosome inactivation in female mammals occurs through heterochromatin formation
    • example of heterochromatin
    • dosage compensation in mammals so that X-linked genes in XX and XY individuals are expressed at same level
    • random inactivation of all except 1 X chromosome in each cell