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High-resolution mapping of transcription factor binding sites on native chromatin

Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. Formaldehyde cross-linking and sonication followed by chromatin immunoprecipitation and sequencing (X-ChIP-seq) is the most widely used technique for genome-wide profiling of protein binding sites. However, there are many issues associated with X-ChIP including low resolution and poor specificity and sensitivity. Here, we implement native (i.e., without cross-linking) ChIP of micrococcal nuclease-digested chromatin followed by paired-end sequencing (N-ChIP-seq) for mapping binding sites of the structurally distinct budding yeast TFs Abf1 and Reb1. N-ChIP-seq reproducibly recovers Abf1 and Reb1 binding sites with higher specificity and sensitivity than other profiling methods and identifies both previously characterized and novel sites. Altering N-ChIP-seq conditions allows flexibility in modulating specificity and sensitivity of binding site detection. Further, unlike X-ChIP methods, N-ChIP-seq is not biased toward identifying sites in accessible chromatin. Taken together, these results suggest that N-ChIP-seq outperforms current X-ChIP methodologies for genome-wide profiling of TF binding sites.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Kasinathan, S., Henikoff, S. High-resolution mapping of transcription factor binding sites on native chromatin. Epigenetics & Chromatin 6 (Suppl 1), P114 (2013).

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