A mechanistic understanding of how cis-regulatory sequences are decoded relies on high-resolution transcription factor binding footprints. Since the function of enhancers can only be assayed in the cell type in which they are active, this task ultimately requires the analysis of a wide variety of different cell types, many of which are hard to isolate in large numbers. To map transcription factor binding in specific cell types in vivo, it is therefore vital to improve the efficiency of current ChIP-seq protocols, ideally also with increased resolution. Nucleotide resolution can be achieved through a ChIP-exo protocol, which uses a lambda exonuclease digestion step to precisely locate the boundary at which the cross-linked protein is bound to DNA. To apply ChIP-exo to Drosophila embryos, we recently developed a new technique termed ChIP-nexus (ChIP with nucleotide resolution through exonuclease, unique barcode and single ligation). ChIP-nexus introduces a novel library preparation protocol that relies on self-circularization and thus improves the efficiency by which DNA fragments are incorporated into the library. ChIP-nexus outperforms existing ChIP protocols in resolution and specificity and pinpoints relevant binding sites within enhancers containing multiple binding motifs. We are currently working on additional modifications to the protocol to further increase the efficiency, allowing lower amounts of starting material. This will enable the precise mapping of transcription factor binding in cell types of low abundance, facilitating the application of ChIP-seq to samples that were previously not accessible to such an analysis..