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Synthetic genome readers target clustered binding sites across diverse chromatin states

Significance Targeting specific genomic loci with synthetic molecules remains a major goal in chemistry, biology, and precision medicine. Identifying how synthetic genome readers bind the chromatinized genome in cells would facilitate their development, but doing so remains a formidable challenge. We map the genome-wide binding patterns for two structurally distinct synthetic molecules. To achieve this goal, we couple our cross-linking of small molecules to isolate chromatin approach to next-generation sequencing. In addition to binding high-affinity sites, these molecules, surprisingly, bind clustered low-affinity sites. The data also show that these genome readers target sites in both open and closed chromatin. Our findings highlight the importance of genome-guided design for molecules that will serve as precision-targeted therapeutics. Targeting the genome with sequence-specific DNA-binding molecules is a major goal at the interface of chemistry, biology, and precision medicine. Polyamides, composed of N-methylpyrrole and N-methylimidazole monomers, are a class of synthetic molecules that can be rationally designed to “read” specific DNA sequences. However, the impact of different chromatin states on polyamide binding in live cells remains an unresolved question that impedes their deployment in vivo. Here, we use cross-linking of small molecules to isolate chromatin coupled to sequencing to map the binding of two bioactive and structurally distinct polyamides to genomes directly within live H1 human embryonic stem cells. This genome-wide view from live cells reveals that polyamide-based synthetic genome readers bind cognate sites that span a range of binding affinities. Polyamides can access cognate sites within repressive heterochromatin. The occupancy patterns suggest that polyamides could be harnessed to target loci within regions of the genome that are inaccessible to other DNA-targeting molecules.