Structural basis of specific H2A K13/K15 ubiquitination by RNF168

Velten Horn, Michael Uckelmann, Heyi Zhang, Jelmer Eerland, Ivette Aarsman, Ulric B. le Paige, Chen Davidovich, Titia K. Sixma, Hugo van Ingen

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Ubiquitination of chromatin by modification of histone H2A is a critical step in both regulation of DNA repair and regulation of cell fate. These very different outcomes depend on the selective modification of distinct lysine residues in H2A, each by a specific E3 ligase. While polycomb PRC1 complexes modify K119, resulting in gene silencing, the E3 ligase RNF168 modifies K13/15, which is a key event in the response to DNA double-strand breaks. The molecular origin of ubiquitination site specificity by these related E3 enzymes is one of the open questions in the field. Using a combination of NMR spectroscopy, crosslinking mass-spectrometry, mutagenesis and data-driven modelling, here we show that RNF168 binds the acidic patch on the nucleosome surface, directing the E2 to the target lysine. The structural model highlights the role of E3 and nucleosome in promoting ubiquitination and provides a basis for understanding and engineering of chromatin ubiquitination specificity.
Original languageEnglish
Article number1751
Number of pages12
JournalNature Communications
Volume10
DOIs
Publication statusPublished - 15 Apr 2019

Keywords

  • histone post-translational modifications
  • ligases
  • molecular modelling
  • NMR spectroscopy
  • ubiquitylated proteins

Cite this

Horn, V., Uckelmann, M., Zhang, H., Eerland, J., Aarsman, I., le Paige, U. B., ... van Ingen, H. (2019). Structural basis of specific H2A K13/K15 ubiquitination by RNF168. Nature Communications, 10, [1751]. https://doi.org/10.1038/s41467-019-09756-z
Horn, Velten ; Uckelmann, Michael ; Zhang, Heyi ; Eerland, Jelmer ; Aarsman, Ivette ; le Paige, Ulric B. ; Davidovich, Chen ; Sixma, Titia K. ; van Ingen, Hugo. / Structural basis of specific H2A K13/K15 ubiquitination by RNF168. In: Nature Communications. 2019 ; Vol. 10.
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abstract = "Ubiquitination of chromatin by modification of histone H2A is a critical step in both regulation of DNA repair and regulation of cell fate. These very different outcomes depend on the selective modification of distinct lysine residues in H2A, each by a specific E3 ligase. While polycomb PRC1 complexes modify K119, resulting in gene silencing, the E3 ligase RNF168 modifies K13/15, which is a key event in the response to DNA double-strand breaks. The molecular origin of ubiquitination site specificity by these related E3 enzymes is one of the open questions in the field. Using a combination of NMR spectroscopy, crosslinking mass-spectrometry, mutagenesis and data-driven modelling, here we show that RNF168 binds the acidic patch on the nucleosome surface, directing the E2 to the target lysine. The structural model highlights the role of E3 and nucleosome in promoting ubiquitination and provides a basis for understanding and engineering of chromatin ubiquitination specificity.",
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Horn, V, Uckelmann, M, Zhang, H, Eerland, J, Aarsman, I, le Paige, UB, Davidovich, C, Sixma, TK & van Ingen, H 2019, 'Structural basis of specific H2A K13/K15 ubiquitination by RNF168' Nature Communications, vol. 10, 1751. https://doi.org/10.1038/s41467-019-09756-z

Structural basis of specific H2A K13/K15 ubiquitination by RNF168. / Horn, Velten ; Uckelmann, Michael; Zhang, Heyi; Eerland, Jelmer ; Aarsman, Ivette; le Paige, Ulric B.; Davidovich, Chen; Sixma, Titia K.; van Ingen, Hugo.

In: Nature Communications, Vol. 10, 1751, 15.04.2019.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Structural basis of specific H2A K13/K15 ubiquitination by RNF168

AU - Horn, Velten

AU - Uckelmann, Michael

AU - Zhang, Heyi

AU - Eerland, Jelmer

AU - Aarsman, Ivette

AU - le Paige, Ulric B.

AU - Davidovich, Chen

AU - Sixma, Titia K.

AU - van Ingen, Hugo

PY - 2019/4/15

Y1 - 2019/4/15

N2 - Ubiquitination of chromatin by modification of histone H2A is a critical step in both regulation of DNA repair and regulation of cell fate. These very different outcomes depend on the selective modification of distinct lysine residues in H2A, each by a specific E3 ligase. While polycomb PRC1 complexes modify K119, resulting in gene silencing, the E3 ligase RNF168 modifies K13/15, which is a key event in the response to DNA double-strand breaks. The molecular origin of ubiquitination site specificity by these related E3 enzymes is one of the open questions in the field. Using a combination of NMR spectroscopy, crosslinking mass-spectrometry, mutagenesis and data-driven modelling, here we show that RNF168 binds the acidic patch on the nucleosome surface, directing the E2 to the target lysine. The structural model highlights the role of E3 and nucleosome in promoting ubiquitination and provides a basis for understanding and engineering of chromatin ubiquitination specificity.

AB - Ubiquitination of chromatin by modification of histone H2A is a critical step in both regulation of DNA repair and regulation of cell fate. These very different outcomes depend on the selective modification of distinct lysine residues in H2A, each by a specific E3 ligase. While polycomb PRC1 complexes modify K119, resulting in gene silencing, the E3 ligase RNF168 modifies K13/15, which is a key event in the response to DNA double-strand breaks. The molecular origin of ubiquitination site specificity by these related E3 enzymes is one of the open questions in the field. Using a combination of NMR spectroscopy, crosslinking mass-spectrometry, mutagenesis and data-driven modelling, here we show that RNF168 binds the acidic patch on the nucleosome surface, directing the E2 to the target lysine. The structural model highlights the role of E3 and nucleosome in promoting ubiquitination and provides a basis for understanding and engineering of chromatin ubiquitination specificity.

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