Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation

Kori, Satomi; Ferry, Laure; Matano, Shohei; Jimenji, Tomohiro; Kodera, Noriyuki; Tsusaka, Takeshi; Matsumura, Rumie; Oda, Takashi; Sato, Mamoru; Dohmae, Naoshi; Ando, Toshio; Shinkai, Yoichi; Defossez, Pierre‐Antoine; Arita, Kyohei

doi:10.1016/j.str.2018.11.012

Cited by 44 publications

(52 citation statements)

References 57 publications

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“…Previous studies reported conflicting results regarding the mechanisms of UHRF1 recruitment to chromatin and the requirement of different UHRF1 domains for DNA maintenance methylation. For example, while several studies show that both functional TTD and/or PHD domains are required for chromatin binding, focal nuclear localization, and the DNA maintenance methylation function of human and mouse UHRF1 ( 7 , 28 , 30 ), it is still under debate which chromatin ligand is actually involved in UHRF1 recruitment: H3K9me2/3, TOP2A, LIG1 or others ( 7 , 8 , 31 , 58 ). Moreover, results obtained from other studies suggest that the SRA domain and hemimethylated DNA are the primary determinants for UHRF1 chromatin localization and DNA maintenance methylation ( 12 , 20 , 59–61 ).…”

Section: Resultsmentioning

confidence: 99%

“…This is illustrated by the delocalization of mUHRF1 V1 from H3K9me3 foci by the R298A mutation that does not open up the mTTD surface groove for H3 binding, but only disrupts synergy between mTTD and mPHD (Figures 6D and 7A ). The importance of the R-pocket on the surface of the TTD is further illustrated by its role in recognition of LIG1 and LIG1K126me ( 8 , 58 ).…”

Section: Discussionmentioning

confidence: 99%

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Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1

Tauber

Kreuz

Lemak

et al. 2020

Nucleic Acids Research

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Abstract UHRF1 is an important epigenetic regulator associated with apoptosis and tumour development. It is a multidomain protein that integrates readout of different histone modification states and DNA methylation with enzymatic histone ubiquitylation activity. Emerging evidence indicates that the chromatin-binding and enzymatic modules of UHRF1 do not act in isolation but interplay in a coordinated and regulated manner. Here, we compared two splicing variants (V1, V2) of murine UHRF1 (mUHRF1) with human UHRF1 (hUHRF1). We show that insertion of nine amino acids in a linker region connecting the different TTD and PHD histone modification-binding domains causes distinct H3K9me3-binding behaviour of mUHRF1 V1. Structural analysis suggests that in mUHRF1 V1, in contrast to V2 and hUHRF1, the linker is anchored in a surface groove of the TTD domain, resulting in creation of a coupled TTD-PHD module. This establishes multivalent, synergistic H3-tail binding causing distinct cellular localization and enhanced H3K9me3-nucleosome ubiquitylation activity. In contrast to hUHRF1, H3K9me3-binding of the murine proteins is not allosterically regulated by phosphatidylinositol 5-phosphate that interacts with a separate less-conserved polybasic linker region of the protein. Our results highlight the importance of flexible linkers in regulating multidomain chromatin binding proteins and point to divergent evolution of their regulation.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1

Tauber

Kreuz

Lemak

et al. 2020

Nucleic Acids Research

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“…An interaction between UHRF1 and DNA ligase 1 (LIG1, UniProtKB P18858) was first identified by tandem affinity purification of a UHRF1 transgene followed by mass spectrometry [ 11 ]. This interaction was recently shown to be methyllysine-dependent [ 21 , 22 ]. The UHRF1 tandem Tudor domain (TTD) binds lysine 9 di- and tri-methylation on histone H3 (H3K9me2/me3) and all three methylation states of lysine 126 on LIG1 (LIG1K126) [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

The histone and non-histone methyllysine reader activities of the UHRF1 tandem Tudor domain are dispensable for the propagation of aberrant DNA methylation patterning in cancer cells

Vaughan

Kupai

Foley

et al. 2020

Epigenetics & Chromatin

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The chromatin-binding E3 ubiquitin ligase ubiquitin-like with PHD and RING finger domains 1 (UHRF1) contributes to the maintenance of aberrant DNA methylation patterning in cancer cells through multivalent histone and DNA recognition. The tandem Tudor domain (TTD) of UHRF1 is well-characterized as a reader of lysine 9 di- and tri-methylation on histone H3 (H3K9me2/me3) and, more recently, lysine 126 di- and tri-methylation on DNA ligase 1 (LIG1K126me2/me3). However, the functional significance and selectivity of these interactions remain unclear. In this study, we used protein domain microarrays to search for additional readers of LIG1K126me2, the preferred methyl state bound by the UHRF1 TTD. We show that the UHRF1 TTD binds LIG1K126me2 with high affinity and selectivity compared to other known methyllysine readers. Notably, and unlike H3K9me2/me3, the UHRF1 plant homeodomain (PHD) and its N-terminal linker (L2) do not contribute to multivalent LIG1K126me2 recognition along with the TTD. To test the functional significance of this interaction, we designed a LIG1K126me2 cell-penetrating peptide (CPP). Consistent with LIG1 knockdown, uptake of the CPP had no significant effect on the propagation of DNA methylation patterning across the genomes of bulk populations from high-resolution analysis of several cancer cell lines. Further, we did not detect significant changes in DNA methylation patterning from bulk cell populations after chemical or genetic disruption of lysine methyltransferase activity associated with LIG1K126me2 and H3K9me2. Collectively, these studies identify UHRF1 as a selective reader of LIG1K126me2 in vitro and further implicate the histone and non-histone methyllysine reader activity of the UHRF1 TTD as a dispensable domain function for cancer cell DNA methylation maintenance.

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“…The former binds to hemi-methylated DNA, while the latter recognizes N-terminal 1 ARTK 4 residues and tri-methylated Lys9 of H3 (H3K9me3). The TTD domain also contributes to the interaction between UHRF1 and DNA ligase 1 15,16 . Furthermore, the E3 ubiquitin ligase activity of UHRF1 plays an essential role in DNMT1 recruitment to DNA methylation sites 17,18 , and is enhanced by association with hemi-methylated DNA and H3K9me3 19,20 .…”

mentioning

confidence: 99%

Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation

et al. 2020

Self Cite

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Stable inheritance of DNA methylation is critical for maintaining differentiated phenotypes in multicellular organisms. We have recently identified dual mono-ubiquitylation of histone H3 (H3Ub2) by UHRF1 as an essential mechanism to recruit DNMT1 to chromatin. Here, we show that PCNA-associated factor 15 (PAF15) undergoes UHRF1-dependent dual monoubiquitylation (PAF15Ub2) on chromatin in a DNA replication-coupled manner. This event will, in turn, recruit DNMT1. During early S-phase, UHRF1 preferentially ubiquitylates PAF15, whereas H3Ub2 predominates during late S-phase. H3Ub2 is enhanced under PAF15 compromised conditions, suggesting that H3Ub2 serves as a backup for PAF15Ub2. In mouse ES cells, loss of PAF15Ub2 results in DNA hypomethylation at early replicating domains. Together, our results suggest that there are two distinct mechanisms underlying replication timing-dependent recruitment of DNMT1 through PAF15Ub2 and H3Ub2, both of which are prerequisite for high fidelity DNA methylation inheritance.

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Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation

Cited by 44 publications

References 57 publications

Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1

Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1

The histone and non-histone methyllysine reader activities of the UHRF1 tandem Tudor domain are dispensable for the propagation of aberrant DNA methylation patterning in cancer cells

Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation

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