The interaction landscape between transcription factors and the nucleosome

Fangjie Zhu, Lucas Farnung, Eevi Kaasinen, Biswajyoti Sahu, Yimeng Yin, Bei Wei, Svetlana O. Dodonova, Kazuhiro R. Nitta, Ekaterina Morgunova, Minna Taipale, Patrick Cramer and Jussi Taipale ()
Additional contact information
Fangjie Zhu: University of Cambridge
Lucas Farnung: Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology
Eevi Kaasinen: Karolinska Institutet
Biswajyoti Sahu: University of Helsinki
Yimeng Yin: Karolinska Institutet
Bei Wei: Karolinska Institutet
Svetlana O. Dodonova: Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology
Kazuhiro R. Nitta: Karolinska Institutet
Ekaterina Morgunova: Karolinska Institutet
Minna Taipale: University of Cambridge
Patrick Cramer: Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology
Jussi Taipale: University of Cambridge

Nature, 2018, vol. 562, issue 7725, 76-81

Abstract: Abstract Nucleosomes cover most of the genome and are thought to be displaced by transcription factors in regions that direct gene expression. However, the modes of interaction between transcription factors and nucleosomal DNA remain largely unknown. Here we systematically explore interactions between the nucleosome and 220 transcription factors representing diverse structural families. Consistent with earlier observations, we find that the majority of the studied transcription factors have less access to nucleosomal DNA than to free DNA. The motifs recovered from transcription factors bound to nucleosomal and free DNA are generally similar. However, steric hindrance and scaffolding by the nucleosome result in specific positioning and orientation of the motifs. Many transcription factors preferentially bind close to the end of nucleosomal DNA, or to periodic positions on the solvent-exposed side of the DNA. In addition, several transcription factors usually bind to nucleosomal DNA in a particular orientation. Some transcription factors specifically interact with DNA located at the dyad position at which only one DNA gyre is wound, whereas other transcription factors prefer sites spanning two DNA gyres and bind specifically to each of them. Our work reveals notable differences in the binding of transcription factors to free and nucleosomal DNA, and uncovers a diverse interaction landscape between transcription factors and the nucleosome.

Keywords: Interactive Landscape; Studied Transcription Factors; Dyad Positions; Dyad Region; Nucleosome Occupancy (search for similar items in EconPapers)
Date: 2018
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Citations: View citations in EconPapers (10)

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DOI: 10.1038/s41586-018-0549-5

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