lncRNA MANCR Isoforms Selectively Contribute to Epigenomic and p53-Responsive Transcriptional Control in Triple-Negative Breast Cancer

Background: Long noncoding RNAs (lncRNAs) are important regulators of gene expression and are frequently dysregulated in cancer. The mitotically associated lncRNA MANCR is highly expressed in aggressive cancers and contributes to genomic instability in triple-negative breast cancer (TNBC), but the molecular mechanisms underlying its activity remain poorly defined. Methods: Here we integrated computational and experimental approaches to examine the structure and regulatory interactions of MANCR isoforms. RNA-sequencing was performed in MDA-MB-231 and MCF10A cells and integrated with publicly available breast cancer transcriptomic datasets. MANCR-associated chromatin was characterized by ChIRP-seq in MDA-MB-231 cells. Computational analyses of patient data, sequence motifs, and molecular modeling suggested an interaction between MANCR and p53, which was investigated using RNA immunoprecipitation sequencing (RIP-seq) and a p53-responsive luciferase reporter assay. Results: Analysis of transcriptomic datasets revealed tumor-type-specific expression patterns for seven MANCR isoforms in breast cancer cell lines. Computational prediction of RNA secondary structures identified conserved structural features across isoforms, suggesting potential functional specialization. We identify p53 as a MANCR-associated protein through computational docking and RNA immunoprecipitation sequencing (RIP-seq) and demonstrate that MANCR depletion reduces p53-dependent transcriptional activity. Chromatin isolation by RNA purification sequencing (ChIRP-seq) revealed 1250 genomic regions associated with MANCR, including enrichment of p53 consensus motifs and GC-rich sequence elements. Motif analysis further identified candidate sequence features associated with MANCR-occupied chromatin regions. Conclusions: Together, these results suggest that MANCR may contribute to transcriptional regulation in TNBC in an isoform-specific manner through interactions with chromatin and p53 signaling pathways.