DNA Organization in Eukaryotic Chromosomes

Chapter 12: Section 12.4

Chapter 12: Organization in Chromosomes

Eukaryotic chromosomal organization

Many eukaryotes are diploid (2N) The amount of DNA that eukaryotes have varies; the amount of DNA is not necessarily related to the complexity (Amoeba proteus has a larger amount of DNA than Homo sapiens) Eukaryotic chromosomes are integrated with proteins that help it fold (protein + DNA = chromatin) Chromosomes become visible during cell division DNA of a human cell is 2.3 m (7.5 ft) in length if placed end to end while the nucleus is a few micrometers; packaging/folding of DNA is necessary

Chapter 12: Organization in Chromosomes

Eukaryotic chromosomal organization

2 main groups of proteins involved in folding/packaging eukaryotic chromosomes

 Histones = positively charged proteins filled with amino acids lysine and arginine that bond  Nonhistones = less positive

Chapter 12: Organization in Chromosomes

Model for Chromatin Structure

Chromatin is linked together every 200 bps (nuclease digestion) Chromatin arranged like beads on a string (electron microscope) 8 histones in each nucleosome 147 bps per nucleosome core particle with 53 bps for linker DNA (H1) Left-handed superhelix
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Eukaryotic chromosomal organization

Histone proteins
 Abundant  Histone protein sequence is highly conserved among eukaryotesconserved function  Provide the first level of packaging for the chromosome; compact the chromosome by a factor of approximately 7  DNA is wound around histone proteins to produce nucleosomes; stretch of unwound DNA between each nucleosome

Chapter 12: Organization in Chromosomes

Eukaryotic chromosomal organization

Nonhistone proteins
 Other proteins that are associated with the chromosomes  Many different types in a cell; highly variable in cell types, organisms, and at different times in the same cell type  Amount of nonhistone protein varies  May have role in compaction or be involved in other functions requiring interaction with the DNA  Many are acidic and negatively charged; bind to the histones; binding may be transient
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Eukaryotic chromosomal organization

Histone proteins
 5 main types
H1attached to the nucleosome and involved in further compaction of the DNA (conversion of 10 nm chromatin to 30 nm chromatin) H2A Two copies in each nucleosome H2B histone octomer; DNA wraps H3 around this structure1.75 times H4

 This structure produces 10nm chromatin

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Fig. 8.17 A possible nucleosome structure

Chapter 12: Organization in Chromosomes Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.

Fig. 8.18 Nucleosomes connected together by linker DNA and H1 histone to produce the beads-on-a-string extended form of chromatin

H1

Histone octomer

Linker DNA 10 nm chromatin is produced in the first level of packaging.

Chapter 12: Organization in Chromosomes Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings. 9

Eukaryotic chromosomal organization

Histone proteins
 DNA is further compacted when the DNA nucleosomes associate with one another to produce 30 nm chromatin  Mechanism of compaction is not understood, but H1 plays a role (if H1 is absent, then chromatin cannot be converted from 10 to 30 nm)  DNA is condensed to 1/6th its unfolded size
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Fig. 8.20b Packaging of nucleosomes into the 30-nm chromatin fiber

Chapter 12: Organization in Chromosomes Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.

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Eukaryotic chromosomal organization

Compaction continues by forming looped domains from the 30 nm chromatin, which seems to compact the DNA to 300 nm chromatin Human chromosomes contain about 2000 looped domains 30 nm chromatin is looped and attached to a nonhistone protein scaffolding DNA in looped domains are attached to the nuclear matrix via DNA sequences called MARs (matrix attachment regions)
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Fig. 8.21 Model for the organization of 30-nm chromatin fiber into looped domains that are anchored to a nonhistone protein chromosome scaffold

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Eukaryotic chromosomal organization

MARs are known to be near regions of the DNA that are actively expressed Loops are arranged so that the DNA condensation can be independently controlled for gene expression

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Fig. 8.22 The many different orders of chromatin packing that give rise to the highly condensed metaphase chromosome

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DNA compaction
Level of DNA compaction changes throughout the cell cycle; most compact during M (see fig 8.22 bottom) and least compact during S 2 types of chromatin; related to the level of gene expression
 Euchromatindefined originally as areas that stained lightly  Heterochromatindefined originally as areas that stained darkly
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DNA compaction
Euchromatinchromosomes or regions therein that exhibit normal patterns of condensation and relaxation during the cell cycle
 Most areas of chromosomes in active cells  Usually areas where gene expression is occurring

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DNA compaction
Heterochromatinchromosomes or regions therein that are condensed throughout the cell cycle Provided first clue that parts of eukaryotic chromosomes do not always encode proteins.

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DNA Cell Cycle

 At the G1/S, G2/M, and M checkpoints, cells decide whether to proceed to the next stage of the cell cycle. Regulation of cell cycle progress is mediated by cyclins and cyclin-dependent kinases (CDKs) that regulate synthesis and destruction of cyclin proteins.

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