title: Mapping the Shh long-range regulatory domain.
abstract: Coordinated gene expression controlled by long-distance enhancers is orchestrated by DNA regulatory sequences involving transcription factors and layers of control mechanisms. The Shh gene and well-established regulators are an example of genomic composition in which enhancers reside in a large desert extending into neighbouring genes to control the spatiotemporal pattern of expression. Exploiting the local hopping activity of the Sleeping Beauty transposon, the lacZ reporter gene was dispersed throughout the Shh region to systematically map the genomic features responsible for expression activity. We found that enhancer activities are retained inside a genomic region that corresponds to the topological associated domain (TAD) defined by Hi-C. This domain of approximately 900 kb is in an open conformation over its length and is generally susceptible to all Shh enhancers. Similar to the distal enhancers, an enhancer residing within the Shh second intron activates the reporter gene located at distances of hundreds of kilobases away, suggesting that both proximal and distal enhancers have the capacity to survey the Shh topological domain to recognise potential promoters. The widely expressed Rnf32 gene lying within the Shh domain evades enhancer activities by a process that may be common among other housekeeping genes that reside in large regulatory domains. Finally, the boundaries of the Shh TAD do not represent the absolute expression limits of enhancer activity, as expression activity is lost stepwise at a number of genomic positions at the verges of these domains.
authors.affiliation: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK.
authors.forename: Eve
authors.initials: E
authors.lastname: Anderson
authors.affiliation: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Devenney
authors.affiliation: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK bob.hill@igmm.ed.ac.uk.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Hill
authors.affiliation: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd, Edinburgh EH4 2XU, UK.
authors.forename: Laura A
authors.initials: LA
authors.lastname: Lettice
mesh_terms: D000818:Animals; D001755:Blastocyst / Q000166:cytology; D004251:DNA Transposable Elements; D004742:Enhancer Elements, Genetic; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D017930:Genes, Reporter; D005816:Genetic Complementation Test; D053823:Hedgehog Proteins / Q000235:genetics / Q000502:physiology*; D006579:Heterozygote; D007438:Introns; D051379:Mice; D008822:Mice, Transgenic; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D017434:Protein Structure, Tertiary; D019076:Transgenes
chemical_list: D004251:DNA Transposable Elements; D053823:Hedgehog Proteins; C465570:Shh protein, mouse
keywords: Enhancers; Long-range regulation; Mouse; Sleeping beauty transposon; Sonic hedgehog (Shh); Topological domains