Compartmentalization of the nucleus

Abstract

The nucleus is a spatially organized compartment. The most obvious way in which this is achieved is at the level of chromosomes. The positioning of chromosomes with respect to nuclear landmarks and with respect to each other is both non-random and cell-type specific. This suggests that cells possess molecular mechanisms to influence the folding and disposition of chromosomes within the nucleus. The localization of many proteins is also heterogeneous within the nucleus. Therefore, chromosome folding and the localization of proteins leads to a model in which individual genes are positioned in distinct protein environments that can affect their transcriptional state. We focus here on the spatial organization of the nucleus and how it impacts upon gene expression.

Figure 1. The nucleus has spatial organization

Cartoon depicting the arrangement of chromosomes into discrete territories. (A) Expanded view of Lamin-associated chromatin enriched for dense heterochromatin (hatched pattern). (B) Gene kissing at RNA polymerase II factory consisting of clusters of active genes from different chromosomes in association with RNA polymerase II (gray). (C) Intra-chromosomal loop mediated by CTCF (grey ovals) in association with cohesin (purple ring).

Figure 2. Protein heterogeneities form in the nucleus

(A) Chromosomes looping out from their respective territories upon activation to interact with a stable protein body (blue cloud) enriched for RNA polymerase II (grey). (B) de novo formation of a nuclear body is induced by mRNA (red) production at active sites of transcription. (C) Gene targeting to a nuclear pore complex, which serves as an organizing surface to concentrate proteins (blue) and RNA polymerase II (gray).