Heterochromatin and Euchromatin

Abstract

Eukaryotes are characterised by the extensive packaging of their genomes, initially in a nucleosomal array, and further into higher order domains. Differential packaging is used as a mechanism of gene regulation, with stable silencing of large domains achieved by packaging the deoxyribonucleic acid (DNA) into a heterochromatic structure. Chromosome rearrangements and transgene insertions that misplace euchromatic genes near or within the heterochromatin result in silencing of the euchromatic genes, testifying to a distinct heterochromatin assembly that can antagonise transcription. Most heterochromatic regions are rich in repetitious sequences, frequently derived from transposable elements, and such packaging helps to silence such elements. Domains of heterochromatin and euchromatin are defined by specific covalent modifications of histones and, in some cases, DNA, as well as by associations with a specific subset of nonhistone chromosomal proteins. Chromosomal domains may be targeted for heterochromatin formation by specific noncoding ribonucleic acids (RNAs).

Key Concepts:

  • The chromatin of eukaryotes is differentially packaged into domains of euchromatin and heterochromatin.

  • Displacing a euchromatic gene to near or within the heterochromatin often results in silencing of the euchromatic gene in some of the cells in which it should be active, resulting in a variegating phenotype.

  • Euchromatin and heterochromatin are distinguishable biochemically by different covalent modifications of histones (and in some cases DNA) and by distinct nonhistone proteins.

  • Members of the HP1a chromo domain protein family bind methylated histone H3 and interact with the H3K9 histone methyltransferase to organise transcriptionally repressive heterochromatin.

  • The piRNA pathway is implicated in targeting transposon silencing through local heterochromatin formation.

Keywords: euchromatin; heterochromatin; histone acetylation; HP1a; position‐effect variegation; SIR2

Figure 1.

(a) Schematic illustration of white variegation in a Drosophila X‐chromosome inversion. The white locus (w+) is located in the distal euchromatin (thin line) of the wild‐type X‐chromosome. It provides a function essential to normal pigmentation of the fly's eye. An inversion induced by X‐rays, with one breakpoint in the pericentric heterochromatin and one breakpoint close to the white gene, places the white gene within several kilobases of the pericentric heterochromatin (thick line). Heterochromatic proteins (geometric forms), which normally assemble only in heterochromatic regions, may now spread across the breakpoint in some cells, potentially packaging the gene in a heterochromatic form, resulting in silencing (white facet) in those cells. Although a barrier is postulated between heterochromatin and euchromatin, no functional barrier element has been detected in flies. (b) Given a variegating phenotype, second‐site mutations that result in a loss of silencing can be recovered; such mutations (suppressors of position effect) usually identify genes that encode proteins that contribute to the heterochromatin structure or participate in its assembly. Similarly, second‐site mutations that result in increased silencing (enhancers of position effect) often identify genes that contribute to the active state.

Figure 2.

(a) Packaging of budding yeast (S. cerevisiae) telomeres. Binding of RAP1 may be a key nucleating event in the assembly of these complexes. Complexes of Sir3 and Sir4 proteins bind to the hypoacetylated, hypomethylated histones, extending along the DNA; Sir2 is also critical for stable maintenance of the silenced state. (b) Packaging of euchromatin and heterochromatin in fission yeast (S. pombe) and metazoans. Methylation (Me) of histone H3 at lysine 9 (H3K9) by a histone H3K9 methyltransferase (H3K9 HMT) creates a binding site for a subset of heterochromatin protein 1 (HP1) family proteins, which then interact with one another and other nonhistone proteins to remodel nucleosomes (yellow) into a heterochromatic configuration. Acetylation (Ac) of H3K9 and other histone sites maintains a euchromatic structure. Modified from http://www.rikenresearch.riken.jp/images/figures/hi_4122.jpg. © RIKEN.

Figure 3.

Distribution of nonhistone chromosomal proteins in the polytene chromosomes of D. melanogaster shown using immunofluorescence. Left: phase‐contrast picture. Note that the extended, euchromatic arms are fused in a common heterochromatic chromocentre. Middle: distribution of GAGA factor (green), a protein that plays a role in gene activation. Right: distribution of HP1 (red), a protein primarily associated with heterochromatin that plays a role in gene silencing. Photo courtesy of C. Craig. © C. Craig.

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Eissenberg, Joel C, and Elgin, Sarah CR(Feb 2014) Heterochromatin and Euchromatin. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001164.pub3]