By improving the previous method of CUT&RUN, we developed D-CUT&RUN (DSP fixed CUT&RUN) for under-expressed transcription factor. High-quality data could be obtained for low expressed transcription factors using chemical crosslinkers (DSP) and reducing agent (DTT). We applied our D-CUT&RUN to detection of Bcl11b and Mycn binding sites in mammary epithelial progenitor cells. Pathway enrichment analysis results of Bcl11b target genes showed that Bcl11b was a regulatory factor involved in breast cancer and it could negatively regulate Wnt signaling pathway. Furthermore, the role of Bcl11b in breast cancer was mediated by catabolic process and stress-related pathway. Our research suggested that D-CUT&RUN could be used for low abundance transcription factor binding sites detection and Bcl11b could be a target for breast cancer treatment in the future.
Keywords: Bcl11b; Breast Cancer; CUT&RUN; Mycn; Wnt signaling pathway.
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