The redundancy of the mammalian heterochromatic compartment

Abstract

Two chromatin compartments are present in most mammalian cells; the first contains primarily euchromatic, early replicating chromatin and the second, primarily late-replicating heterochromatin, which is the subject of this review. Heterochromatin is concentrated in three intranuclear regions: the nuclear periphery, the perinucleolar space and in pericentromeric bodies. We review recent evidence demonstrating that the heterochromatic compartment is critically involved in global nuclear organization and the maintenance of genome stability, and discuss models regarding how this compartment is formed and maintained. We also evaluate our understanding of how heterochromatic sequences (herein named heterochromatic associated regions (HADs)) might be tethered within these regions and review experiments that reveal the stochastic nature of individual HAD positioning within the compartment. These investigations suggest a substantial level of functional redundancy within the heterochromatic compartment.

Figure 1. A–B. Heterochromatin distribution in mammalian cell

Murine embryonic fibroblast stained with A) DAPI (blue) plus antibodies to fibrillarin (red) to mark nucleoli and B) antibodies to H3K9me3 (green) and fibrillarin (red). PH = peripheral heterochromatin. PNH = perinucleolar heterochromatin. PCH = pericentromeric heterochromatin. From [2]. C–D. Heterochromatin changes during erythropoiesis. Electron micrographs of C) murine proerythroblast and D) late erythroblast showing change in heterochromatin distribution (arrows) during differentiation. From [6] with permission from Nature Publishing Group. E–F. Heterochromatin changes during early development. E) Single confocal section of mouse preimplantation embryo at early 2 cell and F) 16 cell stage showing distribution of pericentromeric (red) and centromeric chromatin (green). DNA is grey, bars = 5 μm. From [9].

Figure 2. The redundancy of the heterochromatic compartment

A) Redistribution of mother LADs (left, green) in daughter cell (left, green). DAPI staining of chromatin is blue. The unstained areas in the nucleus on the left are nucleoli. Adapted from the graphical abstract in [65], with permission from Elsevier. B) Venn diagrams depict the overlapping association of two late and one early replicating region with the PH, PCH and PNH in human lymphoblastoid nucleus. The size and overlap of the ellipses is proportional to the percent association of the region with each compartment as determined by DNA FISH. From [68]. C) Cartoon overlaid on DAPI-stained nucleus to represent redundant association sites of late replicating DNA regions (yellow dots) in the PH (blue nuclear outline), PCH (red) and PNH (green). Regions can relocalize from PNH to PH after mitosis or upon the loss of nucleoli (arrow with check mark). Shuttling between the PCH and PH or the PNH and PCH has not been studied directly (bidirectional arrows with question marks). From [68]. D) 3D reconstruction and rendering of chromosome paint images from primary B cells from three different mouse strains showing how the presence or absence of an NOR affects chromosome 12 (cyan) and chromosome 15 (yellow) territory position. When NORs are on both chromosomes (C57), territories tend to associate with the nucleolus (orange), if no NOR is present, the territory associates more often with the periphery (CBA: no NOR on chromosome 12; 129P3: no NOR on chromosome 15). DAPI stain is shown in gray. Scale bar = 1 μm. From [72].

Figure 3. Model depicting redundant distribution of HADs within heterochromatic compartment

Red dashed arrows indicate that most heterochromatic associated domains (HADs) can be found in any of the three heterochromatic regions in different cells or after mitosis. PH: peripheral heterochromatin. PNH: perinucleolar heterochromatin. PCH: pericentromeric heterochromatin. RNAs: RNA adaptors (yellow) transcribed from HADs. PH RNA adaptors have not yet been identified (yellow “?”). Differently colored balls: tethering proteins, some of which are unique to a region (blue and green) and may tether some HADs specifically, and some of which are present in multiple regions (Lamin A, orange). White regions: DAPI staining. Underlying image is midplane of HeLa nucleus acquired using structured illumination microscopy from [74]. Reproduced with permission from Springer. PCH is not obvious in DAPI-stained HeLa nuclei and is labeled here only for illustrative purposes.