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This article is part of the supplement: Epigenetics and Chromatin: Interactions and processes

Open Access Poster presentation

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

Sivakanthan Kasinathan12* and Steven Henikoff13

  • * Corresponding author: Sivakanthan Kasinathan

Author Affiliations

1 Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA

2 Medical Scientist Training Program and Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA

3 Howard Hughes Medical Institute, Seattle, WA 98109, USA

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Epigenetics & Chromatin 2013, 6(Suppl 1):P114  doi:10.1186/1756-8935-6-S1-P114


The electronic version of this article is the complete one and can be found online at: http://www.epigeneticsandchromatin.com/content/6/S1/P114


Published:8 April 2013

© 2013 Kasinathan and Henikoff; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Poster presentation

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.