Eukaryotic Chromosome

A mammalian chromosome is massive, with tens to hundreds of megabases of DNA. The entire haploid human genome contains about 3 billion base pairs of DNA. Only about 5% of this encodes functional RNAs or Proteins or controls their production. Eukaryotic chromosomes are bound to structural proteins to form chromatin. During metaphase, chromatin is highly condensed into the recognizable structure seen at left. During interphase, chromatin is highly decondensed so that regulatory proteins can access the DNA.

During evolution large rearrangements can occur in the size and number of chromosomes. A syntenic region contains genes that are found in the same order in different species, although not always on the same chromosome. For example, the Indian Muntjac has three large chromosomes and a tiny X chromosome; the very similar Reeves Muntjac has just as much DNA — and often in the same sequence — but divided among 23 chromosomes. These chromosomal rearrangements are rare, but are extremely important for speciation because they make productive mating impossible. The number, sizes and shapes of metaphase chromosomes constitute the karyotype (distinctive for each species). During metaphase, chromosomes are distringuished by banding patterns and chromosome painting.

Chromosome Structure at Different Stages of the Cell Cycle

Interphase	During interphase, chromosomes are highly decondensed in most regions, allowing access of regulatory proteins for transcription and replication. Within the nucleus, individual chromosomes are found within diffuse but non-overlapping domains.
M Phase	During mitosis, duplicated chromosomes condense into defined sister chromatids to allow their segregation at cytokinesis. After chromosome condensation, the nuclear envelope breaks down in a process controlled by the nuclear lamina so that the chromosomes can segregate to opposite ends. At metaphase, chromosomes are aligned along the metaphase plate and sister chromatids are split at the centromere to segregate to opposite poles of the dividing cell.

Interphase

During interphase, chromosomes are highly decondensed in most regions, allowing access of regulatory proteins for transcription and replication. Within the nucleus, individual chromosomes are found within diffuse but non-overlapping domains.

M Phase

During mitosis, duplicated chromosomes condense into defined sister chromatids to allow their segregation at cytokinesis. After chromosome condensation, the nuclear envelope breaks down in a process controlled by the nuclear lamina so that the chromosomes can segregate to opposite ends. At metaphase, chromosomes are aligned along the metaphase plate and sister chromatids are split at the centromere to segregate to opposite poles of the dividing cell.

Sister Chromatids and the Centromere

The region of the chromosome where the sister chromatids are held together is called the centromere. This assembles a structure called the kinetochore that is required for attachment to microtubules during alignment at the metaphase plate, splitting of the sister chromatids, and movement to the spindle poles. Because of the nature of DNA replication, a linear chromosome requires special sequences at the ends called Telomeres. DNA replication requires an RNA primer to initiate synthesis, which is degraded after priming. The loss of these primers on the lagging strand of the chromosome ends will result in a loss of information with each round of replication.

Telomerase is a special enzyme that uses its own RNA template to add telomeric repetitive DNA to chromosome ends. The three critical elements of a eukaryotic chromosome required for normal chromosome replication and mitotic segregation are: a replication origin (ARS), centromere and telomeres. These were identified using yeast: Adding telomeric DNA to a DNA containing an ARS and Centromere allows its maintenance as a linear chromosome. Yeast artificial chromosomes containing ARS, Cen, and Tel elements allowed the cloning of large fragments of human chromosomes.

		Progeny of Transfected Cell
Plasmid	Recipient	Growth	Mitotic Segregation	Observation
LEU⁺ Circular	LEU^- Yeast	None		Transfection with a LEU⁺ plasmid does not alone restore LEU to a LEU^- cell.
LEU⁺ ARS⁺ Circular	LEU^- Yeast	Some	Poor	Replication occurs, but poor segregation means only ~10% of progeny carry the plasmid.
LEU⁺ ARS⁺ CEN⁺ Circular	LEU^- Yeast	Yes	Good	A centromeric (CEN) genome fragment is needed for strong segregation.
LEU⁺ ARS⁺ CEN⁺ Linear	LEU^- Yeast	None		Linearization (via restriction enzymes) of a TEL^- circular plasmid makes it unstable.
LEU⁺ ARS⁺ CEN⁺ TEL⁺ Linear	LEU^- Yeast	Yes	Good	Linear plasmids must carry the telomeric (TEL) gene fragment at each each end to remain stable in progeny cells.