Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements

Abstract

BackgroundThe organisation of vertebrate genomes into topologically associating domains (TADs) is believed to facilitate the regulation of the genes located within them. A remaining question is whether TAD organisation is achieved through the interactions of the regulatory elements within them or if these interactions are favoured by the pre-existence of TADs. If the latter is true, the fusion of two independent TADs should result in the rewiring of the transcriptional landscape and the generation of ectopic contacts.ResultsWe show that interactions within the PAX3 and FOXO1 domains are restricted to their respective TADs in normal conditions, while in a patient-derived alveolar rhabdomyosarcoma cell line, harbouring the diagnostic t(2;13)(q35;q14) translocation that brings together the PAX3 and FOXO1 genes, the PAX3 promoter interacts ectopically with FOXO1 sequences. Using a combination of 4C-seq datasets, we have modelled the three-dimensional organisation of the fused landscape in alveolar rhabdomyosarcoma.ConclusionsThe chromosomal translocation that leads to alveolar rhabdomyosarcoma development generates a novel TAD that is likely to favour ectopic PAX3:FOXO1 oncogene activation in non-PAX3 territories. Rhabdomyosarcomas may therefore arise from cells which do not normally express PAX3. The borders of this novel TAD correspond to the original 5'- and 3'- borders of the PAX3 and FOXO1 TADs, respectively, suggesting that TAD organisation precedes the formation of regulatory long-range interactions. Our results demonstrate that, upon translocation, novel regulatory landscapes are formed allowing new intra-TAD interactions between the original loci involved.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1225-z) contains supplementary material, which is available to authorized users.

Miswired enhancer logic drives translocation positive rhabdomyosarcoma

“…1d). A previous study of 4C-seq in FP-RMS cell lines has shown similar interactions consistent with our results 15 , but here we provide the first ChIP-seq informed functional interpretation of these interactions as CTCF bounded enhancers that contain critical CR TFs. We hypothesize these newly juxtaposed enhancer elements keep the PAX3 promotor on the translocated allele active.…”

Topologically Associating Domains in Chromosome Architecture and Gene Regulatory Landscapes during Development, Disease, and Evolution

“…This suggests that disrupting TADs and cis-regulatory landscapes has been negatively selected during evolution. Accordingly, most-if not allexamples in the literature that report disruptions of TADs are associated with deleterious effects (Groschel et al 2014;Northcott et al 2014;Lupiáñez et al 2015;Flavahan et al 2016;Franke et al 2016;Hnisz et al 2016;Vicente-García et al 2017). Nevertheless, evolutionary changes can also happen within TADs, provided that gain or loss of regulatory elements do not strongly affect TAD structural organization (Acemel et al 2017)-in support of this, interaction domains in mouse and zebrafish seem to have conserved boundaries but quite different TAD lengths (Woltering et al 2014).…”

“…From an evolutionary perspective, as suggested by Gómez-Skarmeta and colleagues, this indicates that processes such as gene duplication and neofunctionalization (the process by which a gene acquires a new function upon a gene duplication event), classically thought to occur in a stepwise manner, can actually occur simultaneously with the formation of neo-TADs (Acemel et al 2017). Other chromosome mutations or rearrangements (such as deletions, inversion, and translocations) that split, fuse, or alter TADs in some way can also easily lead to gene expression changes (Groschel et al 2014;Northcott et al 2014;Lupiáñez et al 2015;Flavahan et al 2016;Franke et al 2016;Hnisz et al 2016;Vicente-García et al 2017). It has also been shown that alterations in a single CTCF site, affecting its orientation or binding of the protein, might be enough to reshape the organization of the TAD and the loops between cis-regulatory elements and their targets (de Wit et al 2015;Guo et al 2015;Sanborn et al 2015;Tang et al 2015).…”

An evolutionary perspective of regulatory landscape dynamics in development and disease

“…The translocation also fuses the regulatory landscapes of both genes, generating a novel TAD. This configuration leads to ectopic interaction of FOXO1 regulatory sequences with the PAX3 promoter, which likely results in ectopic expression of PAX3:FOXO1 in cell lineages associated with alveolar rhabdoymosarcomas [32]. Ectopic expression of PAX3 is also associated with limb malformations [33].…”