Antibody-Free and Fast Profiling of Transcription Factor Binding Sites Using Aptamer-Guided Chromatin Cleavage with Sequencing (AptaChC-seq)

A large number of transcription factors are enriched at specific DNA sites in the nuclear, playing an important role in the regulation of gene expression. Chromatin immunoprecipitation sequencing (ChIP seq) is the classic method for the detection of chromatin transcription factor landscape. This method is limited by the complexity of steps, low signal to noise ratio, large number of cells required, high cost, and heavy reliance on high-purity high-performance antibodies. In recent years, based on MNase and Tn5 transposase, CUT&RUN, CUT&Tag, ChIL-seq, itChIP-seq have been developed and widely used, but they still rely on antibodies and take a long time. Here, we develop an antibody-free and fast method for profiling transcription factor binding sites, called Aptamer-Guided Chromatin Cleavage with Sequencing (AptaChC-seq). AptaChC-seq has the advantages of high signal to noise ratio, low cost, good reproducibility. The Transcription Factor Binding Sites of human FOXM1 was detected by AptaChC-seq and CUT&Tag in HEK293FT cells. ATAC-seq was also conducted for comparation. AptaChC-seq of human FOXM1 was further tested in human MCF-7 and MCF-10A cells. AptaChC-seq of human RELA and RBPJ was also tested in HEK293FT cells.