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Hox genes, a subset of homeobox genes, are a group of related genes that specify regions of the body plan of an embryo along the head-tail axis of animals. Hox proteins encode and specify the characteristics of 'position', ensuring that the correct structures form in the correct places of the body. For example, Hox genes in insects specify which appendages form on a segment (for example, legs, antennae, and wings in fruit flies), and Hox genes in vertebrates specify the types and shape of vertebrae that will form. In segmented animals, Hox proteins thus confer segmental or positional identity, but do not form the actual segments themselves. Studies on Hox genes in ciliated larvae have shown they are only expressed in future adult tissues. In larvae with gradual metamorphosis the Hox genes are activated in tissues of the larval body, generally in the trunk region, that will be maintained through metamorphosis. In larvae with complete metamorphosis the Hox genes are mainly expressed in

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Polycomb Recruitment and Targeting in Mammals

Patrick Schorderet

Polycomb- (PcG) and trithorax (trxG) group proteins are essential components in the regulation of multiple developmental regulators. In particular, during early stages, they act as chromatin modifiers in such a way as to set and maintain the transcriptional status of Hox genes. Little is known, in vertebrates, concerning the modalities of PcG binding to their target sites. One possibility is that they are recruited, in a synergistic manner, through their binding to specific DNA regulatory elements to control spatial and temporal restriction of Hox genes by trimethylating lysine 27 on histone 3 (H3K27me3). Whereas these DNA sequences, referred to as polycomb response elements (PREs), have been identified in Drosophila, their existence in mammals remains to be clearly demonstrated. In this work, we aim to decipher the means by which polycomb repressive complexes (PRCs) are recruited to PREs during early mouse development and focus on the HoxD cluster, a genomic segment that is amongst the most heavily covered by H3K27me3 marks in embryonic stem (ES) cells and where one of the few vertebrate PRE has been previously reporter. We describe relatively small DNA sequences lying within the HoxD locus that are necessary and sufficient for the tethering of polycomb to ectopic loci. These elements work synergistically to form a fully functional repressive domain. Moreover, we show that a sequence with high GC content, although not necessary for the initial recruitment of PRC per se, may stabilize the link between the complex and the underlying DNA. Finally, we propose a model for the evolution of polycomb targets and discuss the emergence of diverging recruitment mechanisms amongst Drosophila, mice and humans.

EPFL2013

Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

Denis Duboule, Marion Leleu, Daniël Noordermeer, Patrick Schorderet

Hox genes are essential regulators of embryonic development. Their step-wise transcriptional activation follows their genomic topology and the various states of activation are subsequently memorized into domains of progressively overlapping gene products. We have analyzed the 3D chromatin organization of Hox clusters during their early activation in vivo, using high-resolution circular chromosome conformation capture. Initially, Hox clusters are organized as single chromatin compartments containing all genes and bivalent chromatin marks. Transcriptional activation is associated with a dynamic bi-modal 3D organization, whereby the genes switch autonomously from an inactive to an active compartment. These local 3D dynamics occur within a framework of constitutive interactions within the surrounding Topological Associated Domains, indicating that this regulation process is mostly cluster intrinsic. The step-wise progression in time is fixed at various body levels and thus can account for the chromatin architectures previously described at a later stage for different anterior to posterior levels.DOI: http://dx.doi.org/10.7554/eLife.02557.001.

Elife Sciences Publications Ltd2014

Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells

Guillaume Andrey, Denis Duboule, Patrick Schorderet, Nayuta Yakushiji

During embryonic development, fields of progenitor cells form complex structures through dynamic interactions with external signaling molecules. How complex signaling inputs are integrated to yield appropriate gene expression responses is poorly understood. In the early limb bud, for instance, Sonic hedgehog (Shh) is expressed in the distal posterior mesenchyme, where it acts as a mediator of anterior to posterior (AP) patterning, whereas fibroblast growth factor 8 (Fgf8) is produced by the apical ectodermal ridge (AER) at the distal tip of the limb bud to direct outgrowth along the proximal to distal (PD) axis. Here we use cultured limb mesenchyme cells to assess the response of the target Hoxd genes to these two factors. We find that they act synergistically and that both factors are required to activate Hoxd13 in limb mesenchymal cells. However, the analysis of the enhancer landscapes flanking the HoxD cluster reveals that the bimodal regulatory switch observed in vivo is only partially achieved under these in vitro conditions, suggesting an additional requirement for other factors.

National Academy of Sciences2017

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