Long-range chromosomal interactions and gene regulation

Abstract

Over the last few years important new insights into the process of long-range gene regulation have been obtained. Gene regulatory elements are found to engage in direct physical interactions with distant target genes and with loci on other chromosomes to modulate transcription. An overview of recently discovered long-range chromosomal interactions is presented, and a network approach is proposed to unravel gene-element relationships. Gene expression is controlled by regulatory elements that can be located far away along the chromosome or in some cases even on other chromosomes. Genes and regulatory elements physically associate with each other resulting in complex genome-wide networks of chromosomal interactions. Here we describe several well-characterized cases of long-range interactions involved in the activation and repression of transcription. We speculate on how these interactions may affect gene expression and outline possible mechanisms that may facilitate encounters between distant elements. Finally, we propose that a genome-wide network analysis may provide new insights into the logic of long-range gene regulation.

Figure 1

An overview of a 260 kb region on human chromosome 5 containing the T_H2 locus encompassing the IL5, RAD50, IL4 and IL13 genes reveal that many putative elements are located far from any promoter. The image is a typical screenshot of the UCSC human genome browser (http://genome.cse.ucsc.edu/cgi-bin/hgGateway). Indicated are the positions of genes (UCSC gene predictions), conserved elements found in 28 vertebrates [determined using the Phastcons program described by Siepel et al. 102], DNaseI Hypersensitive sites [data from 32] and the locations of Histone H3 monomethylation at Lysine 4 [data from 32, 103]. All these features are marks for putative regulatory elements. The DNaseI hypersensitive sites located at the 3′ end of the RAD50 gene represent the Locus Control Region that regulates IL5, IL4 and IL13 expression (see the section of T_H2 regulation in the main text).

Figure 2

Representation of chromosome conformation capture (3C) technology. Cells are treated with formaldehyde to induce crosslinks between interacting chromatin fragments (center oval). Chromatin is then digested with a restriction enzyme and ligated at dilute DNA concentrations to induce intramolecular ligation. Crosslinks are reversed and ligation products are then quantified by PCR (arrows indicate PCR primers).

Figure 3

Long-range interactions involved in activation of transcription. A. Depicted is the linear organization of the human Beta-globin locus. The locus control region (LCR) and 3′ hypersensitive (3′HS1) site are depicted in gray. The ε, Gγ- and Aγ-, δ-, β-globin genes are indicated in red, blue, orange, green, and peach, respectively. The LCR and 3′HS1 are found to associate with the γ-globin genes upon its activation resulting in the depicted loop structure. B. Depicted is the linear organization of the T helper type 2 cytokine locus. Il5, RAD50 (whose 3′ region contains the locus control region), Il13, and Il4 are indicated in red, gray, blue, and green, respectively. The promoter regions of Il5, Il13, and Il4 are found to interact with each other as well as with the LCR region.

Figure 4

Long-range interactions involved in repression of transcription. A. Depicted is the linear organization of the locus containing the Drosophila mutation, brown^Dominant (bw^D) gene (shown in gray). The bw^D is found associated with the centromeric heterochromatin (depicted as a solid oval). B. Depicted is the linear organization of a hypothetical locus containing two polycomb response elements (PRE) (shown as gray boxes) near a gene (green arrow). The gene is repressed when the PREs localize at PcG bodies (depicted as red circles) resulting in a chromatin loop.

Figure 5

Network analysis of chromosomal interactions in the T_H2 locus. Top panel: depicted is a linear organization of T_H2 locus. Arrows indicate long-range interactions between genes and elements as detected in naïve T-cells , . Lower panel: long-range interactions can be conveniently presented as a network of interacting nodes.