Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.
In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA–protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation.
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Acknowledgments
The experimental part of this work was performed at EMBL and technically supported by the EMBL Genomics Core Facilities. C.D.C. was supported by a Ph.D. fellowship from the Boehringer Ingelheim Fonds. S.H.A. was supported by an EIPOD Marie Curie/COFUND postdoctoral fellowship. The experimental part of the study was supported by grants from the National Institutes of Health, Deutsche Forschungsgemeinschaft and European Research Council Advanced Investigator Grant (to L.M.S.). Research at VP laboratory is supported by a SciLifeLab Fellowship from the Science for Life Laboratory (SFO Karolinska Institutet), a Starting Grant from the Swedish Research Council (Vetenskapsrådet), a Swedish Foundation’s Starting Grant (Ragnar Söderberg Foundation), and a Wallenberg Academy Fellowship (Knut and Alice Wallenberg Foundation). Christophe D. Chabbert and Sophie H. Adjalley contributed equally to this work.
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Chabbert, C.D., Adjalley, S.H., Steinmetz, L.M., Pelechano, V. (2018). Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis. In: Visa, N., Jordán-Pla, A. (eds) Chromatin Immunoprecipitation. Methods in Molecular Biology, vol 1689. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7380-4_16
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DOI: https://doi.org/10.1007/978-1-4939-7380-4_16
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