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

Cristina Vicente-García,Peter W J Rigby,Damien P Devos,Jaime J Carvajal,Ibai Irastorza-Azcárate,Juan J Tena,Silvia Naranjo,Barbara Villarejo-Balcells,Jose L Gómez-Skarmeta,Rafael D Acemel

doi:10.1186/s13059-017-1225-z

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.

Highlights

The organisation of vertebrate genomes into topologically associating domains (TADs) is believed to facilitate the regulation of the genes located within them
Loss of synteny analyses place the 5' boundary of the FOXO1/FoxO1 locus in close proximity to its promoter One of the major unknowns in the study of alveolar rhabdomyosarcoma (ARMS) is the nature of the cell that originally suffered the PAX3:FOXO1 chromosomal translocation leading to tumour development
Analysis of evolutionarily conserved regions (ECRs) upstream of mouse FoxO1 shows that a conserved region 47 kb upstream of the gene maps immediately upstream of the human MAML3 gene on Chr4, while another ECR, located 17 kb upstream of mouse FoxO1 maps upstream of the human FOXO1 gene on Chr 13 (Additional file 1: Figure S2)

Summary

Introduction

The organisation of vertebrate genomes into topologically associating domains (TADs) is believed to facilitate the regulation of the genes located within them. From an evolutionary point of view, it has been shown that ancestral recombinations leading to loss of synteny occur at TAD borders [10], maintaining their structures and indicating that TADs are under positive selective forces, most likely because the disruption of a TAD has deleterious effects on the regulation of the genes within it. It is still not clear if TADs originate from interactions between enhancers and promoters within the domain or if it is this compartmentalisation that permits and restricts enhancer-promoter contacts [11,12,13]. The directionality of the CTCF binding sites seems to be predictive of their loop-forming activity as deletion or inversion of these sites results in the generation of inappropriate enhancerpromoter contacts [15, 16]

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Conclusion