Significance Mammalian chromatin is compartmentalized in topologically associating domains (TADs), genomic regions within which sequences preferentially contact each other. This organization has been ...proposed to be essential to organize the regulatory information contained in mammalian genomes. We show that Six homeobox genes, essential developmental regulators organized in gene clusters across different animal phyla, share a deeply conserved chromatin organization formed by two abutting TADs that predates the Cambrian explosion. This organization is required to generate separate regulatory landscapes for neighboring genes within the cluster, resulting in very different gene expression patterns. Finally, we show that this extremely conserved 3D architecture is associated with a characteristic arrangement of CCCTC-binding factor (CTCF) binding sites in diverging orientations, revealing a genome-wide conserved signature for TAD borders.
Increasing evidence in the last years indicates that the vast amount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin structures. However, the impact of this spatial chromatin organization on gene expression and its degree of evolutionary conservation is still poorly understood. The Six homeobox genes are essential developmental regulators organized in gene clusters conserved during evolution. Here, we reveal that the Six clusters share a deeply evolutionarily conserved 3D chromatin organization that predates the Cambrian explosion. This chromatin architecture generates two largely independent regulatory landscapes (RLs) contained in two adjacent topological associating domains (TADs). By disrupting the conserved TAD border in one of the zebrafish Six clusters, we demonstrate that this border is critical for preventing competition between promoters and enhancers located in separated RLs, thereby generating different expression patterns in genes located in close genomic proximity. Moreover, evolutionary comparison of Six-associated TAD borders reveals the presence of CCCTC-binding factor (CTCF) sites with diverging orientations in all studied deuterostomes. Genome-wide examination of mammalian HiC data reveals that this conserved CTCF configuration is a general signature of TAD borders, underscoring that common organizational principles underlie TAD compartmentalization in deuterostome evolution.
During formation of the Hedgehog (Hh) signaling proteins, cooperative activities of the Hedgehog INTein (Hint) fold and Sterol Recognition Region (SRR) couple autoproteolysis to cholesterol ligation. ...The cholesteroylated Hh morphogens play essential roles in embryogenesis, tissue regeneration, and tumorigenesis. Despite the centrality of cholesterol in Hh function, the full structure of the Hint-SRR ("Hog") domain that attaches cholesterol to the last residue of the active Hh morphogen remains enigmatic. In this work, we combine molecular dynamics simulations, photoaffinity crosslinking, and mutagenesis assays to model cholesterolysis intermediates in the human Sonic Hedgehog (hSHH) protein. Our results provide evidence for a hydrophobic Hint-SRR interface that forms a dynamic, non-covalent cholesterol-Hog complex. Using these models, we suggest a unified mechanism by which Hh proteins can recruit, sequester, and orient cholesterol, and offer a molecular basis for the effects of disease-causing hSHH mutations.
Gene expression in different spatial domains is often controlled by separate cis-regulatory modules (CRMs), but regulatory states determining CRM activity are not only distinct in space, they also ...change continuously during developmental time. Here, we systematically analyzed the regulatory sequences controlling hox11/13b expression and identified a single CRM required throughout embryonic gut development. We show that within this CRM, distinct sets of binding sites recognizing Ets, Tcf, and homeodomain transcription factors control the dynamic spatial expression of hox11/13b in each developmental phase. Several binding sites execute multiple, sometimes contradictory, regulatory functions, depending on the temporal and spatial regulatory context. In addition, we identified a nearby second CRM operating in inter-modular AND logic with the first CRM to control hox11/13b expression in hindgut endoderm. Our results suggest a mechanism for continuous gene expression in response to changing developmental network functions that depends on sequential combinatorial regulation of individual CRMs.
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•A cis-regulatory module controls hox11/13b expression throughout gut organogenesis•This cis-regulatory module responds to developmentally changing regulatory inputs•Alternative use of binding sites provides context-specific gene regulation•Combination of two juxtaposed modules is necessary for expression in the hindgut
Gene expression is controlled by developmentally changing regulatory states. Cui et al. now find that the dynamic patterns of hox11/13b expression in response to distinct regulatory states during sea urchin endoderm development are controlled by sequentially operating transcription factor binding sites within an intronic cis-regulatory module.
Nature provides a number of mechanisms to encode dynamic information in biomolecules. In metazoans, there exist rare chemical modifications that occur in entirely unique regimes. One such example ...occurs in the Hedgehog (Hh) morphogens, proteins singular across all domains of life for the nature of their covalent ligation to cholesterol. The isoform- and context-specific efficiency of this ligation profoundly impacts the activity of Hh morphogens and represents an unexplored facet of Hh ligand-dependent cancers. To elucidate the chemical mechanism of this modification, we have defined roles of the uncharacterized sterol recognition region (SRR) in Hh proteins. We use a combination of sequence conservation, directed mutagenesis, and biochemical assays to specify residues of the SRR participate in cellular and biochemical aspects of Hh cholesterolysis. Our investigations offer a functional portrait of this region, providing opportunities to identify parallel reactivity in nature and a template to design tools in chemical biology.
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The Hedgehog (Hh) signaling pathway plays an essential role during embryogenesis and when dysregulated, can lead to human cancer (basal cell carcinomas) and the most lethal form of ...juvenile medulloblastoma. Binding of the Hh ligand to its receptor Patched (Ptch) relieves inhibition of the GPCR protein Smoothened (Smo) leading to activation of the Gli transcription factors and changes in target gene expression. The Hh ligand is decorated with two covalent modifications, N‐terminal palmitoylation and C‐terminal cholesterolyation. Hh proteins are synthesized as approximately 45 kDa full‐length species, whereupon a unique process yields the mature morphogen: an autocatalytic cleavage that splits the protein in two and attaches cholesterol to the newly formed C‐terminus. Of the two approximately equal molecular weight cleavage products, the dually lipidated N‐terminal fragment (Hh‐N/“Hog” domain) constitutes the classical Hh morphogen, whereas the C‐terminus (Hh‐C/“Hint”) is responsible for the cleavage reaction.
In order to elucidate the chemical mechanism of cholesterolyation, we have determined the roles of the previously uncharacterized sterol recognition region (SRR) in Hh proteins. Using bioinformatics, alanine scanning, and biochemical assays we have identified key motifs and specified residues of the SRR that are required for biochemical processing of Hh. These results provide a first in detail insights into the role of this unique small region of the Hh protein that is capable of cellular targeting and engaging cholesterol to generate an active Hh ligand.
Support or Funding Information
This work was supported by the Margaret E. Early Medical Research Trust.
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