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Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1.

Zhao F, Liu Y, Su X, Lee JE, Song Y, Wang D, Ge K, Gao J, Zhang MQ, Li H
J Biol Chem 295 16877-16887 (2020)
Cited: 10 times
EuropePMC logo PMID: 32994220

Abstract

Histone recognition by "reader" modules serves as a fundamental mechanism in epigenetic regulation. Previous studies have shown that Spindlin1 is a reader of histone H3K4me3 as well as "K4me3-R8me2a" and promotes transcription of rDNA or Wnt/TCF4 target genes. Here we show that Spindlin1 also acts as a potent reader of histone H3 "K4me3-K9me3/2" bivalent methylation pattern. Calorimetric titration revealed a binding affinity of 16 nm between Spindlin1 and H3 "K4me3-K9me3" peptide, which is one to three orders of magnitude stronger than most other histone readout events at peptide level. Structural studies revealed concurrent recognition of H3K4me3 and H3K9me3/2 by aromatic pockets 2 and 1 of Spindlin1, respectively. Epigenomic profiling studies showed that Spindlin1 colocalizes with both H3K4me3 and H3K9me3 peaks in a subset of genes enriched in biological processes of transcription and its regulation. Moreover, the distribution of Spindlin1 peaks is primarily associated with H3K4me3 but not H3K9me3, which suggests that Spindlin1 is a downstream effector of H3K4me3 generated in heterochromatic regions. Collectively, our work calls attention to an intriguing function of Spindlin1 as a potent H3 "K4me3-K9me3/2" bivalent mark reader, thereby balancing gene expression and silencing in H3K9me3/2-enriched regions.

Articles - 7bqz mentioned but not cited (2)

  1. Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1. Zhao F, Liu Y, Su X, Lee JE, Song Y, Wang D, Ge K, Gao J, Zhang MQ, Li H. J Biol Chem 295 16877-16887 (2020)
  2. Molecular insights into Spindlin1-HBx interplay and its impact on HBV transcription from cccDNA minichromosome. Liu W, Yao Q, Su X, Deng Y, Yang M, Peng B, Zhao F, Du C, Zhang X, Zhu J, Wang D, Li W, Li H. Nat Commun 14 4663 (2023)


Reviews citing this publication (2)

  1. The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes. Beacon TH, Delcuve GP, López C, Nardocci G, Kovalchuk I, van Wijnen AJ, Davie JR. Clin Epigenetics 13 138 (2021)
  2. Bivalent Genes Targeting of Glioma Heterogeneity and Plasticity. Markouli M, Strepkos D, Papavassiliou KA, Papavassiliou AG, Piperi C. Int J Mol Sci 22 E540 (2021)

Articles citing this publication (6)

  1. The Spin1 interactor, Spindoc, is dispensable for meiotic division, but essential for haploid spermatid development in mice. Jiang X, Zhu X, Cheng Y, Azhar M, Xing X, Li W, Cao Y, Shi Q, Bao J. Reprod Biol Endocrinol 19 144 (2021)
  2. SPINDOC binds PARP1 to facilitate PARylation. Yang F, Chen J, Liu B, Gao G, Sebastian M, Jeter C, Shen J, Person MD, Bedford MT. Nat Commun 12 6362 (2021)
  3. Structure-Based Design, Docking and Binding Free Energy Calculations of A366 Derivatives as Spindlin1 Inhibitors. Luise C, Robaa D, Regenass P, Maurer D, Ostrovskyi D, Seifert L, Bacher J, Burgahn T, Wagner T, Seitz J, Greschik H, Park KS, Xiong Y, Jin J, Schüle R, Breit B, Jung M, Sippl W. Int J Mol Sci 22 5910 (2021)
  4. Exploring aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction: an in silico study. Luise C, Robaa D, Sippl W. J Comput Aided Mol Des 35 695-706 (2021)
  5. Recognition of Dimethylarginine Analogues by Tandem Tudor Domain Protein Spindlin1. Porzberg MRB, Moesgaard L, Johansson C, Oppermann U, Kongsted J, Mecinović J. Molecules 27 983 (2022)
  6. The TUDOR domain of SMN is an H3K79me1 histone mark reader. Binda O, Kimenyi Ishimwe AB, Galloy M, Jacquet K, Corpet A, Fradet-Turcotte A, Côté J, Lomonte P. Life Sci Alliance 6 e202201752 (2023)


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