The Dynamic Architecture of Hox Gene Clusters

Abstract

The spatial and temporal control of Hox gene transcription is essential for patterning the vertebrate body axis. Although this process involves changes in histone posttranslational modifications, the existence of particular three-dimensional (3D) architectures remained to be assessed in vivo. Using high-resolution chromatin conformation capture methodology, we examined the spatial configuration of Hox clusters in embryonic mouse tissues where different Hox genes are active. When the cluster is transcriptionally inactive, Hox genes associate into a single 3D structure delimited from flanking regions. Once transcription starts, Hox clusters switch to a bimodal 3D organization where newly activated genes progressively cluster into a transcriptionally active compartment. This transition in spatial configurations coincides with the dynamics of chromatin marks, which label the progression of the gene clusters from a negative to a positive transcription status. This spatial compartmentalization may be key to process the colinear activation of these compact gene clusters.

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

“…4C). Hox genes have been shown to be regulated by antisense transcription as well as the topological organization of the locus and the contact to remote enhancers (22,23), but so far only for the HOXA cluster has a role cohesin and CTCF at the barrier element been shown (24). Among genes that are differentially expressed after CTCF depletion, we observed a clear enrichment of CTCF-binding at their promoters (Fig.…”

Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding

“…Because chromatin reorganization accompanies down-regulation of transcription within Dppa2/4 and Rex1 domains, we considered the possibility that changes in transcriptional activity could be driving chromatin reorganization of these domains, as suggested for gene-rich regions on the X chromosome (21) and homeobox (Hox) genes (23,24). To test this, we analyzed chromatin organization in domains either expressing or not expressing Dppa2 or Rex1 using RNA/DNA-FISH.…”

High-resolution analysis of cis -acting regulatory networks at the α-globin locus

“…Its average fragment size is 433 bp, improving resolution compared with using 6-cutter enzymes [13][14][15]. Circles containing relatively short fragments can be efficiently amplified in subsequent PCR reactions (see below).…”

“…The 4C approach allows analysis of chromosome conformation, in an unbiased way, without prior knowledge, to identify all sequences (in cis and trans) that interact with a genomic element of interest, and, therefore, is of considerable value in identifying the comprehensive network of regulatory elements controlling individual genes [13][14][15]. This addresses a common and timely problem in genome annotation, and solves the issue of assigning the functional effects of a particular sequence or structural variant (e.g.…”

“…Such methods ( [8,9,[11][12][13][14][15]; referred to as circularized 3C, or circular chromosome conformation capture (4C)) are based on the assumption that, as a result of cross-linking, cutting and ligating regions of interacting chromatin, circular molecules containing various combinations of associated segments of DNA will be formed (figure 1). Using inverse PCR primers located near the ends of a chosen fragment of interest (the 'bait'), the amplified 4C library should capture all sequences (within a population of cells) that interact with the bait.…”