Supplementary Figures, Tables and Materials and Methods from RAIN Is a Novel Enhancer-Associated lncRNA That Controls RUNX2 Expression and Promotes Breast and Thyroid Cancer

Rossi, Teresa; Pistoni, Mariaelena; Sancisi, Valentina; Gobbi, Giulia; Torricelli, Federica; Donati, Benedetta; Ribisi, Salvatore; Gugnoni, Mila; Ciarrocchi, Alessia

doi:10.1158/1541-7786.22512853.v1

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Supplementary Figures, Tables and Materials and Methods from RAIN Is a Novel Enhancer-Associated lncRNA That Controls RUNX2 Expression and Promotes Breast and Thyroid Cancer

journal contribution

posted on 2023-04-03, 16:44 authored by Teresa Rossi, Mariaelena Pistoni, Valentina Sancisi, Giulia Gobbi, Federica Torricelli, Benedetta Donati, Salvatore Ribisi, Mila Gugnoni, Alessia Ciarrocchi

S1. Schematic representation of the central hypervariable region of RAIN S2. qRT-PCR analysis of SUPT3H expression in the indicated cell lines. S3. qRT-PCR analysis of RUNX2 and RAIN expression in TPC1 cells treated with 1 μM JQ1 or mock (DMSO). S4. Schematic representation of the distribution of the biotin 3'-end TEG probes on the 3'-end long RAIN region used for ChIRP. S5. ChIP analysis of RUNX2 ENHs (ENH3, ENH10, ENH11 and ENH13) with anti-WDR5. S6. Scratch wound healing assay in TPC1 and MDA-MB231 cells transfected with l-RAIN or scramble oligos in presence of mitomycin C. S7. MA plot. S8. RUNX2-RAIN neighboring genes.

Funding

Assumption University of Thailand

History

ARTICLE ABSTRACT

Enhancer (ENH)-associated long noncoding RNAs (lncRNA) are a peculiar class of RNAs produced by transcriptionally active ENHs, owning potential gene-regulatory function. Here, we characterized RAIN, a novel ENH-associated lncRNA. Analysis of RAIN expression in a retrospective cohort of human thyroid cancers showed that the expression of this lncRNA is restricted to cancer cells and strongly correlates with the expression of the cancer-promoting transcription factor RUNX2. We showed that RAIN, serving as a cis-regulatory element, promotes RUNX2 expression by two mechanisms. Binding WDR5 and facilitating its localization on the RUNX2 promoter, RAIN modifies the transcriptional status of the RUNX2 locus facilitating transcription initiation. In parallel, RAIN acts as decoy for negative elongation factor complex, restraining its inhibitory function on transcription elongation. In both thyroid and breast cancer cells, RAIN promotes oncogenic features. Using RNA-sequencing profiling, we showed that RAIN orchestrates the expression of a network of cancer-promoting transcription regulators, suggesting that RAIN affects cancer cell phenotype by coordinating the expression of a complex transcriptional network. Our data contribute to understand lncRNA function in gene regulation and to consolidate their role in cancer.