Chromatin conformation capture (4C-seq) of lncRNAs CTD-2566J3.1

This study focused on the antisense lncRNA CTD-2566J3.1, located at the RAD51B locus, which shows enhancer-associated epigenetic marks such as H3K27ac and H3K4me1.

Using 4C-seq on BT-474 and T47D luminal breast cancer cells cultured under both 2D and 3D conditions, we identified frequent physical interactions between CTD-2566J3.1 enhancer regions and three target genes: RAD51B, MAP3K9, and ACTN1 in 3D cultures. These regions were also enriched with estrogen-related transcription factors ESR1 and FOXA1, suggesting hormonal regulation. These findings indicate that CTD-2566J3.1 acts as a multifunctional lncRNA regulating key oncogenic pathways in breast cancer through chromatin interactions and gene expression control, emphasizing the importance of 3D culture models to uncover context-dependent regulatory mechanisms.