Phase separation drives aberrant chromatin looping and cancer development

• Published in: Nature (London) Vol. 595; no. 7868; pp. 591 - 595
• Main Authors: Ahn, Jeong Hyun, Davis, Eric S., Daugird, Timothy A., Zhao, Shuai, Quiroga, Ivana Yoseli, Uryu, Hidetaka, Li, Jie, Storey, Aaron J., Tsai, Yi-Hsuan, Keeley, Daniel P., Mackintosh, Samuel G., Edmondson, Ricky D., Byrum, Stephanie D., Cai, Ling, Tackett, Alan J., Zheng, Deyou, Legant, Wesley R., Phanstiel, Douglas H., Wang, Gang Greg
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22.07.2021; Nature Publishing Group
• Subjects: 14/63; 38/15; 38/91; 631/208/68/2486; 631/337/100/101; 631/67/1990/283/1897; Abnormalities; Animals; Binding; Cancer; Carcinogenesis; Chimeras; Chromatin; Chromatin - genetics; Chromosome translocations; Development and progression; Ewings sarcoma; Female; Genes; Genetic abnormalities; Genetic aspects; Genetic transformation; Genomes; Glycine; Health aspects; HEK293 Cells; HeLa Cells; Homeobox; Homeodomain Proteins - genetics; Humanities and Social Sciences; Humans; Intrinsically Disordered Proteins - genetics; Leukemia; Liquid phases; Mice; Mice, Inbred BALB C; Molecular structure; multidisciplinary; Mutation; Neoplasms - genetics; Neoplasms - pathology; Nuclear Pore Complex Proteins - genetics; Occupancy; Oncogene Proteins, Fusion - genetics; Phase separation; Phenylalanine; Proteins; Proto-oncogenes; Science; Science (multidisciplinary); Transcription activation; Transcription factors; Transcription Factors - genetics; Transcriptional Activation; Translocation; Translocation, Genetic; Tumorigenesis; United States
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-021-03662-5

The development of cancer is intimately associated with genetic abnormalities that target proteins with intrinsically disordered regions (IDRs). In human haematological malignancies, recurrent chromosomal translocation of nucleoporin (NUP98 or NUP214) generates an aberrant chimera that invariably retains the nucleoporin IDR—tandemly dispersed repeats of phenylalanine and glycine residues 1 , 2 . However, how unstructured IDRs contribute to oncogenesis remains unclear. Here we show that IDRs contained within NUP98–HOXA9, a homeodomain-containing transcription factor chimera recurrently detected in leukaemias 1 , 2 , are essential for establishing liquid–liquid phase separation (LLPS) puncta of chimera and for inducing leukaemic transformation. Notably, LLPS of NUP98–HOXA9 not only promotes chromatin occupancy of chimera transcription factors, but also is required for the formation of a broad ‘super-enhancer’-like binding pattern typically seen at leukaemogenic genes, which potentiates transcriptional activation. An artificial HOX chimera, created by replacing the phenylalanine and glycine repeats of NUP98 with an unrelated LLPS-forming IDR of the FUS protein 3 , 4 , had similar enhancing effects on the genome-wide binding and target gene activation of the chimera. Deeply sequenced Hi-C revealed that phase-separated NUP98–HOXA9 induces CTCF-independent chromatin loops that are enriched at proto-oncogenes. Together, this report describes a proof-of-principle example in which cancer acquires mutation to establish oncogenic transcription factor condensates via phase separation, which simultaneously enhances their genomic targeting and induces organization of aberrant three-dimensional chromatin structure during tumourous transformation. As LLPS-competent molecules are frequently implicated in diseases 1 , 2 , 4 – 7 , this mechanism can potentially be generalized to many malignant and pathological settings. The NUP98–HOXA9 oncogenic fusion protein found in leukaemia undergoes phase separation in the nucleus, which helps to promote activation of leukaemic genes and to establish aberrant chromatin looping.