Chromatin loops, gene positioning, and gene expression

Abstract

Technological developments and intense research over the last years have led to a better understanding of the 3D structure of the genome and its influence on genome function inside the cell nucleus. We will summarize topological studies performed on four model gene loci: the α- and β-globin gene loci, the antigen receptor loci, the imprinted H19-Igf2 locus and the Hox gene clusters. Collectively, these studies show that regulatory DNA sequences physically contact genes to control their transcription. Proteins set up the 3D configuration of the genome and we will discuss the roles of the key structural organizers CTCF and cohesin, the nuclear lamina and the transcription machinery. Finally, genes adopt non-random positions in the nuclear interior. We will review studies on gene positioning and propose that cell-specific genome conformations can juxtapose a regulatory sequence on one chromosome to a responsive gene on another chromosome to cause altered gene expression in subpopulations of cells.

Keywords: chromatin domains; gene expression; genome structure; nuclear organization; nuclear periphery.

FIGURE 1

Long-range transcriptional regulation at model gene loci. (A) At the active β-globin locus, LCR–gene contacts and interactions between flanking CTCF sites set up an active chromatin hub (ACH). (B) The IGCR1 contacts the 3′ regulatory region and the intronic enhancer of the IgH locus in pro-B cells. Inclusion of the distal V genes is influenced by the presence of the IGCR1. (C) CTCF blocks the interaction of the Igf2/H19 enhancer with the Igf2 gene on the maternal allele. Methylation of the ICR prevents CTCF binding and enables Igf2 expression from the paternal allele. (D) A “regulatory archipelago” controls the expression of the hoxd13–hoxd10 genes over distance in limb extremities.

FIGURE 2

Topological boundaries can act as barriers for spreading of heterochromatin. The 2D heat map shows the Hi-C interaction frequency in human ES cells. Underneath is indicated the directionality index (DI) in hESCs and IMR90 cells. The DI is a Hi-C measure showing a site’s preference to engage in unidirectional contacts with downstream (red) or upstream (green) sequences. Borders of the topological domains are defined by a change in the directionality of interactions (transition from green to red). The UCSC Genome Browser shots show the distribution of H3K9me3, a measure for heterochromatin formation. Note that in IMR90 cells heterochromatin stops at the topological boundaries. Reprinted by permission from Macmillan Publishers Ltd (Dixon et al., 2012), copyright (2012).

FIGURE 3

CTCF flanks chromatin marked by specific histone modifications. (A) Linear representation of a chromosomal region with active and inactive genes, CTCF binding sites and an enhancer (for explanation of symbols, see bottom figure). (B) ChIA-PET reveals different chromatin loops formed by CTCF (Handoko et al., 2011): CTCF loops demarcate regions (1) with active chromatin marks, (2) with inactive chromatin marks, (3) with enhancers and promoters, and (4) with undefined chromatin surrounded by regions with opposing chromatin signatures.