Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions

Abstract

Accumulating evidence converges on the possibility that chromosomes interact with each other to regulate transcription in trans. To systematically explore the epigenetic dimension of such interactions, we devised a strategy termed circular chromosome conformation capture (4C). This approach involves a circularization step that enables high-throughput screening of physical interactions between chromosomes without a preconceived idea of the interacting partners. Here we identify 114 unique sequences from all autosomes, several of which interact primarily with the maternally inherited H19 imprinting control region. Imprinted domains were strongly overrepresented in the library of 4C sequences, further highlighting the epigenetic nature of these interactions. Moreover, we found that the direct interaction between differentially methylated regions was linked to epigenetic regulation of transcription in trans. Finally, the patterns of interactions specific to the maternal H19 imprinting control region underwent reprogramming during in vitro maturation of embryonic stem cells. These observations shed new light on development, cancer epigenetics and the evolution of imprinting.

Characterization of multi-locus imprinting disturbances and underlying genetic defects in patients with chromosome 11p15.5 related imprinting disorders

“…Since both pathogenic mutations and isolated epimutations at this iDMR have never been reported [33], it is conceivable a different mechanism of pathogenicity, possibly mediated by a cross-talk between MEST and ICR1. According, recent advances sustain an interplay among ICR1 and other iDMRs (our unpublished data) and chromatin interactions between H19 and portions of chromosome 7 [34]. MEST methylation may also be part of an imprinting gene network (IGN), involving the trans -acting functions of H19 lncRNA [35,36].…”

Repeated elements coordinate the spatial organization of the yeast genome

“…the region spanning ETS2-NTS1, which comprises part of the enhancer and replication fork barrier (RFB); henceforth called the ETS2 domain; Figure 1A) using 4C ( Figure 1B, C) (Simonis et al, 2006;Zhao et al, 2006); 108 MspI-flanked genomic regions reproducibly interact with the ETS2 domain (Figure 2A; see also Supporting information, Figure S1, Spreadsheet S1). Intra-chromosomal interactions within chromosome XII formed the largest single group (25%), as previously observed (Molnar and Kleckner, 2008;Simonis et al, 2006).…”

“…4C was performed using a method derived from previously published methods (Simonis et al, 2006;Zhao et al, 2006). Chromatin was crosslinked in whole cells through the addition of formaldehyde (2% v/v final) for 10 min at room temperature.…”

“…It is clear that the spatial arrangement of the genome into subcompartments is important for the regulation of developmental and cellular processes (Chakalova et al, 2005;Dostie et al, 2006;Foster and Bridger, 2005;Lanctot et al, 2007;Ling et al, 2006;Spilianakis et al, 2005;Zhao et al, 2006). However, we currently do not know how nuclear subcompartments are formed.…”

“…This potential is exemplified by the fact that the interacting DNA sequences are often not linearly arranged or even on the same chromosome (Dostie et al, 2006;Ling et al, 2006;O'Sullivan et al, 2004;Simonis et al, 2006;Spilianakis et al, 2005;Zhao et al, 2006). Therefore, the formation of intra-or interchromosomal interactions specifies the relative positions of chromosomal sequences, due to the contiguous nature of the chromosome(s).…”