High Sensitivity Profiling of Chromatin Structure by MNase-SSP.
| Autor: | Ramani V; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA. Electronic address: vijay.ramani@ucsf.edu., Qiu R; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Shendure J; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA. Electronic address: shendure@uw.edu. |
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| Jazyk: | angličtina |
| Zdroj: | Cell reports [Cell Rep] 2019 Feb 26; Vol. 26 (9), pp. 2465-2476.e4. |
| DOI: | 10.1016/j.celrep.2019.02.007 |
| Abstrakt: | A complete view of eukaryotic gene regulation requires that we accurately delineate how transcription factors (TFs) and nucleosomes are arranged along linear DNA in a sensitive, unbiased manner. Here we introduce MNase-SSP, a single-stranded sequencing library preparation method for nuclease-digested chromatin that enables simultaneous mapping of TF and nucleosome positions. As a proof of concept, we apply MNase-SSP toward the genome-wide, high-resolution mapping of nucleosome and TF occupancy in murine embryonic stem cells (mESCs). Compared with existing MNase-seq protocols, MNase-SSP markedly enriches for short DNA fragments, enabling detection of binding by subnucleosomal particles and TFs, in addition to nucleosomes. From these same data, we identify multiple, sequence-dependent binding modes of the architectural TF Ctcf and extend this analysis to the TF Nrsf/Rest. Looking forward, we anticipate that single stranded protocol (SSP) adaptations of any protein-DNA interaction mapping technique (e.g., ChIP-exo and CUT&RUN) will enhance the information content of the resulting data. (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.) |
| Databáze: | MEDLINE |
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