1. Structural Biology and Molecular Biophysics

Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19

  1. Cheng Dong
  2. Reiko Nakagawa
  3. Kyohei Oyama
  4. Yusuke Yamamoto
  5. Weilian Zhang
  6. Aiping Dong
  7. Yanjun Li
  8. Yuriko Yoshimura
  9. Hiroyuki Kamiya
  10. Jun-ichi Nakayama
  11. Jun Ueda
  12. Jinrong Min  Is a corresponding author
  1. Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, China
  2. Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Japan
  3. Department of Cardiac Surgery, Asahikawa Medical University, Japan
  4. Structural Genomics Consortium, University of Toronto, Canada
  5. Division of Chromatin Regulation, National Institute for Basic Biology, Japan
  6. Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Japan
  7. Centre for Advanced Research and Education, Asahikawa Medical University, Japan
  8. Department of Physiology, University of Toronto, Canada
https://doi.org/10.7554/eLife.58675
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Cite this article
  1. Cheng Dong
  2. Reiko Nakagawa
  3. Kyohei Oyama
  4. Yusuke Yamamoto
  5. Weilian Zhang
  6. Aiping Dong
  7. Yanjun Li
  8. Yuriko Yoshimura
  9. Hiroyuki Kamiya
  10. Jun-ichi Nakayama
  11. Jun Ueda
  12. Jinrong Min
(2020)
Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19
eLife 9:e58675.
https://doi.org/10.7554/eLife.58675
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7 figures, 3 tables and 2 additional files

Figures

Figure 1
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Tudor domains of PHF1 and PHF19 preferentially recognize H3K36me3 and H3tK27me3.

(A) Schematic representation of domain structures of PHF1, MTF2, and PHF19. PHD: plant homeodomain finger. EH: extended homologous domain. (B) Peptide sequences of H3K36me3, H3K27me3, and H3tK27me3. …

Figure 2
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PHF1 is associated with the H3t in vivo.

(A) Expression levels of PHF1 in different mouse tissues using the RT-qPCR analysis. (B) Immunostaining of testis sections by antibodies against H3t (green) and PHF1 (red). Seminiferous tubules at …

Figure 3
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PHF1-Tudor could enrich H3t peptides.

(A, B) In vitro GST pull-down assays using GST-tagged PHF1-Tudor proteins and histones prepared from H3t-expressed HEK293T cells. GST proteins from input, bound, and unbound flow-through (FT) …

Figure 4
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Crystal structures of PHF1/19-Tudor domain in complex with H3tK27me3.

(A) Overall structure of PHF1-Tudor in complex with H3tK27me3. PHF1-Tudor is shown in cartoon representation and colored in green. The H3tK27me3 peptide is colored in salmon and shown as sticks. (B) …

Figure 5
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H3tK27me3 and H3K36me3 peptides bound to PHF1/19 within the same binding grooves but in reverse directions.

(A) Superposition of the complex structures of PHF1-H3tK27me3 and PHF1-H3K36me3 (PDB: 4HCZ). The PHF1-Tudor is shown in a gray surface representation. The H3tK27me3 and H3K36me3 peptides are shown …

Figure 6
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V24 of H3t is an optimal residue for the H3t recognition by the Tudor domain of PHF1/19.

(A) Binding affinities of PHF1 and PHF19 Tudor domain with various peptides determined using ITC. (B) The crystal structure of PHF1 in complex with H3K36me3H39V. The mutant H3K36me3H39V peptide is …

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Tables

Table 1
Binding affinities of PHF1/MTF2 mutants with the H3tK27me3 peptide.
PHF1ITC (µM)
W41ANB
Y47ANB
F65ANB
F71A192 ± 18
L38A125 ± 9
L45A178 ± 9
L46A127 ± 8
L46Y50 ± 5
L48A81 ± 2
L38A, L45A, L46A, L48A>500
E66A>200
MTF2ITC (µM)
S86F91 ± 21
S86Y110 ± 11

  1. NB indicates no detectable binding.

Table 2
Data collection and refinement statistics.
PHF1-H3tK27me3PHF19-H3tK27me3PHF1-H3K36me3-H39V
PDB ID6WAU6WAT6WAV
Data collection
Space groupP21P32C2
Cell (a,b,c (Å))
(α, β, γ (°))		32.8, 286.8, 123.5
90, 90.7, 90		111.5, 111.5, 34.4
90, 90, 120		153.0, 65.6, 29.0
90, 97.1, 90
Resolution (Å)47.80–1.80
(1.83–1.80)		55.74–1.71
(1.74–1.71)		40.07–1.70
(1.73–1.70)
Rmerge overall0.071 (0.939)0.048 (1.314)0.048 (0.416)
Rmeas overall0.082 (1.117)0.054 (1.608)0.056 (0.487)
No. reflections207862 (9809)51838 (2547)29381 (1501)
Mean I/sigma10.5 (1.3)21.6 (0.7)16.4 (3.1)
CChalf0.999 (0.706)1.000 (0.190)0.998 (0.810)
Completeness (%)99.2 (93.7)99.4 (92.1)93.8 (90.9)
Multiplicity3.8 (3.3)5.4 (2.9)3.7 (3.6)
Model refinement
Resolution (Å)40.76–1.8048.27–1.7532.80–1.70
Reflections/free395473/1994948195/224229359/1455
Rwork/Rfree0.215/0.2600.209/0.2510.198/0.242
All (No. atoms/mean B (Å2))33004/39.03137/30.02348/20.8
Tudor27847/38.72697/29.61878/19.5
Peptide4169/42.0383/32.2306/26.0
Water953/36.547/30.7132/25.1
Others35/31.910/26.732/27.4
rmsd bonds (Å)/angles (°)0.011/1.10.012/1.90.011/1.7

  1. Values in parentheses are for the highest-resolution shell.

Key resources table
Reagent type (species)
or resource		DesignationSource or referenceIdentifiersAdditional
information
Gene (Mus musculus)H3.4 histone (H3t)GenBank382523
Gene (Homo sapiens)PHF1GenBank5252
Strain, strain background (Escherichia coli)BL21(DE3)Thermo FisherC600003
Cell line (Homo sapiens)293T/17ATCCCRL-11268
AntibodyAnti-histone H3 (rabbit polyclonal)abcamab1791WB (1:2000)
AntibodyAnti-histone H3t (mouse monoclonal)This paper Ueda et al., 2017WB (1:1000)
IF (1:1000)
AntibodyAnti-PHF1 (rabbit polyclonal)AbcamCat# ab80042IF (1:500)
AntibodyAnti-SCP3 (mouse monoclonal)Abcam10G11/7
Cat# ab97672		IF (1:1000)
AntibodyAnti-γ H2A.X (mouse monoclonal)Merck MilliporeCat# #05–636IF (1:1000)
AntibodyLectin PNA tagged with Alexa Fluor 488Thermo FisherCat# L21409IF (1:1000)
Sequence-based reagentEef1a1–FwUeda et al., 2017PCR primersCTCTGACTACCCTCCACTTGGTCG
Sequence-based reagentEef1a1–RevUeda et al., 2017PCR primersATTAAGACTGGGGTGGCAGGTGTT
Sequence-based reagentPhf1–FwThis paperPCR primersTGAGAAGTGTCGCCATGCTTA
Sequence-based reagentPhf1–RevThis paperPCR primersCATAGGGACCTTTCTTCAGTGC
Recombinant DNA reagentpET28-MHLSGC, Toronto26096 (Genbank accession number: EF456735)Expression of the Tudor domains of PHF1, MTF2 and PHF19, and their mutants
Software, algorithmOrigin 6.1, Origin 7.0OriginLabhttp://www.originlab.com/For ITC curve fitting and calculation of Kd values
Software, algorithmXDSPMID:20124692http://xds.mpimf-heidelberg.mpg.de/Processing of X-ray diffraction data
Software, algorithmPymolDeLano Scientific LLChttp://www.pymol.org/Drawing structure figures
Software, algorithmCootPMID:15572765http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/Structure model building
Software, algorithmCCP4PMID:21460441https://www.ccp4.ac.uk/Structure determination and refinement
Software, algorithmMASCOT programMatrix ScienceVersion 2.6
Software, algorithmProteome discoverer 2.2Thermo Fisher
OtherHoechst 33342Thermo FisherCat# H3570IF (1:5000)

Additional files

Supplementary file 1

Summary of H3K27 residue containing H3/H3t peptides detected in the input fraction.

https://cdn.elifesciences.org/articles/58675/elife-58675-supp1-v3.xlsx
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https://cdn.elifesciences.org/articles/58675/elife-58675-transrepform-v3.docx

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