Biochemical analysis of nucleosome targeting by Tn5 transposase

Shoko Sato, Yasuhiro Arimura, Tomoya Kujirai, Akihito Harada, Kazumitsu Maehara, Jumpei Nogami, Yasuyuki Ohkawa, Hitoshi Kurumizaka

Research output: Contribution to journalArticle

Abstract

Tn5 transposase is a bacterial enzyme that integrates a DNA fragment into genomic DNA, and is used as a tool for detecting nucleosome-free regions of genomic DNA in eukaryotes. However, in chromatin, the DNA targeting by Tn5 transposase has remained unclear. In the present study, we reconstituted well-positioned 601 dinucleosomes, in which two nucleosomes are connected with a linker DNA, and studied the DNA integration sites in the dinucleosomes by Tn5 transposase in vitro. We found that Tn5 transposase preferentially targets near the entry–exit DNA regions within the nucleosome. Tn5 transposase minimally cleaved the dinucleosome without a linker DNA, indicating that the linker DNA between two nucleosomes is important for the Tn5 transposase activity. In the presence of a 30 base-pair linker DNA, Tn5 transposase targets the middle of the linker DNA, in addition to the entry–exit sites of the nucleosome. Intriguingly, this Tn5-targeting characteristic is conserved in a dinucleosome substrate with a different DNA sequence from the 601 sequence. Therefore, the Tn5-targeting preference in the nucleosomal templates reported here provides important information for the interpretation of Tn5 transposase-based genomics methods, such as ATAC-seq.

Original languageEnglish
Article number190116
JournalOpen Biology
Volume9
Issue number8
DOIs
Publication statusPublished - Aug 1 2019

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Nucleosomes
DNA
Tn5 transposase
DNA sequences
Genomics
Eukaryota
Base Pairing
Chromatin

All Science Journal Classification (ASJC) codes

  • Neuroscience(all)
  • Immunology
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Sato, S., Arimura, Y., Kujirai, T., Harada, A., Maehara, K., Nogami, J., ... Kurumizaka, H. (2019). Biochemical analysis of nucleosome targeting by Tn5 transposase. Open Biology, 9(8), [190116]. https://doi.org/10.1098/rsob.190116

Biochemical analysis of nucleosome targeting by Tn5 transposase. / Sato, Shoko; Arimura, Yasuhiro; Kujirai, Tomoya; Harada, Akihito; Maehara, Kazumitsu; Nogami, Jumpei; Ohkawa, Yasuyuki; Kurumizaka, Hitoshi.

In: Open Biology, Vol. 9, No. 8, 190116, 01.08.2019.

Research output: Contribution to journalArticle

Sato, Shoko ; Arimura, Yasuhiro ; Kujirai, Tomoya ; Harada, Akihito ; Maehara, Kazumitsu ; Nogami, Jumpei ; Ohkawa, Yasuyuki ; Kurumizaka, Hitoshi. / Biochemical analysis of nucleosome targeting by Tn5 transposase. In: Open Biology. 2019 ; Vol. 9, No. 8.
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