An improved CUT&RUN method for regulation network reconstruction of low abundance transcription factor

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. •An improved CUT&RUN method can be used for detecting binding sites of low abundance transcription factor.•Bcl11b is a regulatory factor involved in breast cancer.•Bcl11b regulates Wnt signaling pathway in vitro and in vivo.