A SNAI2/CTCF Interaction is Required for NOTCH1 Expression in Rhabdomyosarcoma

• Published in: Molecular and cellular biology Vol. 43; no. 11; pp. 547 - 565
• Main Authors: Sreenivas, Prethish, Wang, Long, Wang, Meng, Challa, Anil, Modi, Paulomi, Hensch, Nicole Rae, Gryder, Berkley, Chou, Hsien-Chao, Zhao, Xiang R, Sunkel, Benjamin, Moreno-Campos, Rodrigo, Khan, Javed, Stanton, Benjamin Z, Ignatius, Myron S
• Format: Journal Article
• Language: English
• Published: United States Taylor & Francis 2023
• Subjects: CCCTC-Binding Factor - metabolism; Child; Chromatin; Genetics and Molecular Biology; Humans; Receptor, Notch1 - genetics; Receptor, Notch1 - metabolism; Rhabdomyosarcoma - genetics; RNA, Small Interfering - genetics; Snail Family Transcription Factors - genetics; Snail Family Transcription Factors - metabolism; Chromatin; HiC; NOTCH1; CRISPR/Cas9; gene regulation; Notch; Rhabdomyosarcoma; ChIP-seq; SNAI2; CTCF
• ISSN: 1098-5549; 0270-7306; 1098-5549
• DOI: 10.1080/10985549.2023.2256640

Rhabdomyosarcoma (RMS) is a pediatric malignancy of the muscle with characteristics of cells blocked in differentiation. is an oncogene that promotes self-renewal and blocks differentiation in the fusion negative-RMS sub-type. However, how expression is transcriptionally maintained in tumors is unknown. Analyses of SNAI2 and CTCF chromatin binding and HiC analyses revealed a conserved SNAI2/CTCF overlapping peak downstream of the locus marking a sub-topologically associating domain (TAD) boundary. Deletion of the SNAI2-CTCF peak showed that it is essential for expression and viability of FN-RMS cells. Reintroducing constitutively activated -ΔE in cells with the SNAI2-CTCF peak deleted restored cell-viability. Ablation of SNAI2 using CRISPR/Cas9 reagents resulted in the loss of majority of RD and SMS-CTR FN-RMS cells. However, the few surviving clones that repopulate cultures have recovered . Cells that re-establish expression after SNAI2 ablation are unable to differentiate robustly as SNAI2 shRNA knockdown cells; yet, -ablated cells continued to be exquisitely sensitive to ionizing radiation. Thus, we have uncovered a novel mechanism by which SNAI2 and CTCF maintenance of a sub-TAD boundary promotes rather than represses expression. Further, we demonstrate that SNAI2 suppression of apoptosis post-radiation is independent of / effects on self-renewal and differentiation.