Nuclear organization and genome function

Abstract

Long-range interactions between transcription regulatory elements play an important role in gene activation, epigenetic silencing, and chromatin organization. Transcriptional activation or repression of developmentally regulated genes is often accomplished through tissue-specific chromatin architecture and dynamic localization between active transcription factories and repressive Polycomb bodies. However, the mechanisms underlying the structural organization of chromatin and the coordination of physical interactions are not fully understood. Insulators and Polycomb group proteins form highly conserved multiprotein complexes that mediate functional long-range interactions and have proposed roles in nuclear organization. In this review, we explore recent findings that have broadened our understanding of the function of these proteins and provide an integrative model for the roles of insulators in nuclear organization.

Figure 1

Diagram showing the structure of different vertebrate and Drosophila insulators. A. Structure of the vertebrate CTCF and TFIIIC insulators. Indicated are factors associated with CTCF such as cohesin, CHD8 and YY1, and with TFIIIC. B. Each Drosophila insulator subclass contains a different binding protein that may define the specific function of the corresponding subclass. All insulators share the common protein CP190, although the role of this protein in the function of the GAGA insulator has not been demonstrated experimentally. In addition, all subclasses may also have one Mod(mdg4) isoform. The gypsy/Su(Hw) insulator contains Mod(mdg4)2.2. The dCTCF and BEAF insulators lack this isoform but contain a different variant of Mod(mdg4). GAGA has been shown to interact with Mod(mdg4)2.2.

Figure 2

Structure of some of the domains created by interactions between CTCF insulators in mouse embryonic stem cells. Actively transcribed genes are represented by a green arrow and silenced genes by a red line; nucleosomes and the histone tails are represented in grey, with active histone modifications indicated as green spheres and repressive modifications as red spheres. DNA is represented in black and CTCF as blue ovals. A. CTCF forms a loop to separate a domain containing active histone modifications and transcribed genes from repressive marks and silenced genes. B. CTCF forms a loop to separate a domain containing repressive histone modifications and silenced genes from active marks and transcribed genes. C. CTCF forms a loop containing nucleosomes enriched in mono and dimethylated H3K4, and trimethylated H3K4 at the boundaries of the loops, whereas the active transcription modification H3K36me3 and repressive H3K27me3 mark are observed outside the loops on opposite sides.

Figure 3

Comprehensive model for the highly conserved role of insulators in nuclear organization. Insulators in yeast (TFIIIC – orange), Drosophila (dCTCF, Su(Hw), BEAF – green, CP190, Mod(mdg4) – yellow), and mammals (CTCF – olive green, TFIIIC - orange) mediate long-range inter- and intra-chromosomal interactions important for gene regulation, and cluster into subnuclear foci called insulator bodies. Insulators underlie interactions necessary for Pc body repression (blue) and localize with general transcription factors (pink) to transcription factories. Insulators localize to subnuclear structures, including the nuclear lamina (red) where they are enriched at the borders of Lamina-associated domains (LAD), and the nucleolus (grey). CTCF insulator activity in mammals requires cohesin (red), and TFIIIC insulator sites are associated with both cohesin and condensin (red). Insulator activity in Drosophila relies on recruitment of fly-specific proteins CP190 and Mod(mdg4).