Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

Abstract

The spatial organization of genes in the interphase nucleus plays an important role in establishment and regulation of gene expression. Contradicting results have been reported to date, with little consensus about the dynamics of nuclear organization and the features of the contact loci. In this study, we investigated the properties and dynamics of genomic loci that are in contact with glucocorticoid receptor (GR)-responsive loci. We took a systematic approach, combining genome-wide interaction profiling by the chromosome conformation capture on chip (4C) technology with expression, protein occupancy, and chromatin accessibility profiles. This approach allowed a comprehensive analysis of how distinct features of the linear genome are organized in the three-dimensional nuclear space in the context of rapid gene regulation. We found that the transcriptional response to GR occurs without dramatic nuclear reorganization. Moreover, contrary to the view of transcription-driven organization, even genes with opposite transcriptional responses colocalize. Regions contacting GR-regulated genes are not particularly enriched for GR-regulated loci or for any functional group of genes, suggesting that these subnuclear environments are not organized to respond to a specific factor. The contact regions are, however, highly enriched for DNase I-hypersensitive sites that comprehensively mark cell-type -specific regulatory sites. These findings indicate that the nucleus is pre-organized in a conformation allowing rapid transcriptional reprogramming, and this organization is significantly correlated with cell-type-specific chromatin sites accessible to regulatory factors. Numerous open chromatin loci may be arranged in nuclear domains that are poised to respond to diverse signals in general and to permit efficient gene regulation.

Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing

“…GR binding also coincides with hypersensitive sites (John et al 2008Grøntved et al 2013), and it was previously demonstrated that the majority of long-range genomic contacts involve hypersensitive sites (Hakim et al 2011). Considering the dynamics in chromatin accessibility observed here, we hypothesized that it could play a role in gene transcription regulation from a distance.…”

Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories

“…Note however that genes positioned within 1 μm of each other in a fixed cell will occasionally be much closer in live cells due to the diffusion of chromatin, which is known to occur in the submicron to micron range [51]. Indeed, it has been shown that interaction signals measured by 4C robustly correlated with distances of up to 1 μm as measured by 3D DNa-FISh [52].…”

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

“…Similarly, epigenetic modifications encompassing large domains of the genome have been described to participate in gene silencing and, more recently, gene activation during the process of malignant transformation (Hon et al 2012). Previous studies on the spatial organization of glucocorticoid response in murine cells showed that the hormonal response was facilitated by a preorganized conformation of the nucleus, particularly by cell type-specific chromatin sites accessible to regulatory factors (Hakim et al 2011). We postulate that the initial organization of TADs could act as topological constraint for changes in gene expression in response to external cues.…”

“…These genes, which can be located on different chromosomes, are organized in spatial clusters and preferentially transcribed in the same ''factories'' (Osborne et al 2004(Osborne et al , 2007Cavalli 2007). Whether such mechanisms participate in transient modifications of the transcription rate in differentiated cells responding to external cues is still unclear (Fullwood et al 2009;Kocanova et al 2010;Hakim et al 2011). Transient regulation of gene expression at the transcription level depends on the establishment of regulatory Ó 2014 Le Dily et al This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genesdev.cshlp.org/site/misc/terms.xhtml).…”