Mitotic chromosomes are differentiated longitudinally into regions of euchromatin and heterochromatin. Euchromatin is the gene-rich portion of the genome that decondenses after mitosis. Heterochromatin exists in a relatively condensed state throughout the mitotic cell cycle (17-19,52), generally replicates late in the S-phase after euchromatin (53), contains few genes (e.g., refs. 54-57), and consists of mainly satellite DNAs and transposable elements (e.g., refs. 46,48,58-67). In D. melanogaster, approximately one-third of the male and approximately one-fourth of the female genomes are heterochromatic (68), including the entire Y chromosome, the proximal approximately one-third of the X chromosome, the middle 20% (i.e., the pericentric regions) of chromosomes 2 and 3, and roughly three-quarters of chromosome 4. In addition, the telomeric regions of all chromosomes are heterochromatic (69).
At the molecular level, heterochromatin domains are associated with his-tone H3 methylated at conserved residue lysine 9, a modification catalyzed by SU(VAR)3-9 methyltransferase in Drosophila and by its homologs in other multicellular eukaryotes (e.g., refs. 70,71). This modification creates a binding site on histone H3 for heterochromatin protein 1 [HP1; encoded by
Su(var)2-5], which in turn may recruit other heterochromatin-associated proteins to form higher-order chromatin complexes.
In polytene chromosomes, heterochromatin-associated DNAs usually show reduced polyteny compared to euchromatic sequences, and they coalesce into a nuclear structure termed a chromocenter (see Subheading 4.3.). Another type of chromatin, "intercalary heterochromatin," is associated with polytene chromosomes and is discussed in Subheading 4.4.
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