Multiple Enhancers Regulate Hoxd Genes and the Hotdog LncRNA during Cecum Budding

Abstract

Hox genes are required for the development of the intestinal cecum, a major organ of plant-eating species. We have analyzed the transcriptional regulation of Hoxd genes in cecal buds and show that they are controlled by a series of enhancers located in a gene desert flanking the HoxD cluster. The start site of two opposite long noncoding RNAs (lncRNAs), Hotdog and Twin of Hotdog, selectively contacts the expressed Hoxd genes in the framework of a topological domain, coinciding with robust transcription of these genes during cecum budding. Both lncRNAs are specifically transcribed in the cecum, albeit bearing no detectable function in trans. Hedgehogs have kept this regulatory potential despite the absence of the cecum, suggesting that these mechanisms are used in other developmental situations. In this context, we discuss the implementation of a common "budding toolkit" between the cecum and the limbs.

Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape

“…TgBAC HoxD regulatory elements controlling Hoxd gene expression both in the proximal limb buds and the intestinal cecum (17,18). This DNA segment also contains the transcriptional start sites of Hog and Tog, two lncRNAs coregulated with selected Hoxd genes in the developing cecum (18), and whose transcription was also slightly enriched in E13.5 MBs compared with the surrounding control tissue (Fig.…”

“…Consequently, specific subgroups of Hox genes, at least within the HoxA and HoxD clusters, are controlled by the same series of global enhancers; hence, they are coregulated in different contexts, which provide the system with both quantitative and qualitative modulations. This regulation has been well documented for the HoxD cluster, which contains a range of long-acting enhancers of different specificities within its two large flanking gene deserts (17)(18)(19)(20).…”

“…This DNA segment also contains the transcriptional start sites of Hog and Tog, two lncRNAs coregulated with selected Hoxd genes in the developing cecum (18), and whose transcription was also slightly enriched in E13.5 MBs compared with the surrounding control tissue (Fig. 5B).…”

“…5A). Within the T-DOM, series of enhancers are found, which regulate groups of genes lying in the central part of the cluster, as if the regulatory sequences would contact a chromatin pocket encompassing Hoxd8 to Hoxd11 (18). These large and apparently constitutive chromosome domains (TADs) may facilitate the required regulatory switches at important developmental loci, and were also proposed to have triggered the evolution of pleiotropy by providing the regulatory context for evolving novel enhancers (16,19).…”

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states

“…Recently, this gene cluster, similar to its HoxA relative (14,15), was shown to reside at a boundary between two TADs (located ca. between Hoxd11 and Hoxd12), with each TAD containing enhancers required to regulate different subgroups of genes in developing organs or structures (9,16,19) such as distal limbs, proximal limbs, genitals, or the cecum. Interestingly, all enhancers sharing a particular specificity are found within the same TAD, and thus far, no cell type or tissue was reported where these two opposite regulatory landscapes would operate concomitantly (8,16,17,19), suggesting a functional switch occurs between these two TADs in their capacity to regulate subsets of target Hoxd genes.…”