The chromatin factor ROW cooperates with BEAF‐32 in regulating long‐range inducible genes

Insulator proteins located at the boundaries of topological associated domains (TAD) are involved in higher‐order chromatin organization and transcription regulation. However, it is still not clear how long‐range contacts contribute to transcriptional regulation. Here, we show that relative‐of‐WOC (ROW) is essential for the long‐range transcription regulation mediated by the boundary element‐associated factor of 32kD (BEAF‐32). We find that ROW physically interacts with heterochromatin proteins (HP1b and HP1c) and the insulator protein (BEAF‐32). These proteins interact at TAD boundaries where ROW, through its AT‐hook motifs, binds AT‐rich sequences flanked by BEAF‐32‐binding sites and motifs. Knockdown of row downregulates genes that are long‐range targets of BEAF‐32 and bound indirectly by ROW (without binding motif). Analyses of high‐throughput chromosome conformation capture (Hi‐C) data reveal long‐range interactions between promoters of housekeeping genes bound directly by ROW and promoters of developmental genes bound indirectly by ROW. Thus, our results show cooperation between BEAF‐32 and the ROW complex, including HP1 proteins, to regulate the transcription of developmental and inducible genes through long‐range interactions.