45. Bienz M (2006) The PHD finger, a nuclear protein-interaction domain. Trends Biochem Sci
31(1):35–40. https://doi.org/10.1016/j.tibs.2005.11.001
46. Teske KA, Hadden MK (2017) Methyllysine binding domains: structural insight and
small molecule probe development. Eur J Med Chem 136:14–35. https://doi.org/10.1016/j.
ejmech.2017.04.047
47. Bhushan B, Erdmann A, Zhang Y, Belle R, Johannson C, Oppermann U, Hopkinson RJ,
Schofield CJ, Kawamura A (2018) Investigations on small molecule inhibitors targeting the
histone H3K4 tri-methyllysine binding PHD-finger of JmjC histone demethylases. Bioorg
Med Chem 26(11):2984–2991. https://doi.org/10.1016/j.bmc.2018.03.030
48. Polakis P (2012) Wnt signaling in cancer. Cold Spring Harb Perspect Biol 4(5):a008052.
https://doi.org/10.1101/cshperspect.a008052
49. Daniels DL, Eklof Spink K, Weis WI (2001) Beta-catenin: molecular plasticity and drug design.
Trends Biochem Sci 26(11):672–678. https://doi.org/10.1016/S0968-0004(01)01952-1
50. Miller TC, Rutherford TJ, Johnson CM, Fiedler M, Bienz M (2010) Allosteric remodelling
of the histone H3 binding pocket in the Pygo2 PHD finger triggered by its binding to the
B9L/BCL9 co-factor. J Mol Biol 401(5):969–984. https://doi.org/10.1016/j.jmb.2010.07.007
51. Miller TC, Rutherford TJ, Birchall K, Chugh J, Fiedler M, Bienz M (2014) Competitive
binding of a benzimidazole to the histone-binding pocket of the Pygo PHD finger. ACS Chem
Biol 9(12):2864–2874. https://doi.org/10.1021/cb500585s
52. Amato A, Lucas X, Bortoluzzi A, Wright D, Ciulli A (2018) Targeting ligandable pockets
on plant homeodomain (PHD) zinc finger domains by a fragment-based approach. ACS Chem
Biol 13(4):915–921. https://doi.org/10.1021/acschembio.7b01093
53. Maurer-Stroh S, Dickens NJ, Hughes-Davies L, Kouzarides T, Eisenhaber F, Ponting CP
(2003) The Tudor domain ‘Royal Family’: tudor, plant Agenet, chromo, PWWP and MBT
domains. Trends Biochem Sci 28(2):69–74. https://doi.org/10.1016/S0968-0004(03)00004-5
54. Lu R, Wang GG (2013) Tudor: a versatile family of histone methylation ‘readers’. Trends
Biochem Sci 38(11):546–555. https://doi.org/10.1016/j.tibs.2013.08.002
55. Golumbeski GS, Bardsley A, Tax F, Boswell RE (1991) Tudor, a posterior-group gene
of Drosophila melanogaster, encodes a novel protein and an mRNA localized during
mid-oogenesis. Genes Dev 5(11):2060–2070. https://doi.org/10.1101/gad.5.11.2060
56. Lee KK, Workman JL (2007) Histone acetyltransferase complexes: one size doesn’t fit all.
Nat Rev Mol Cell Biol 8(4):284–295. https://doi.org/10.1038/nrm2145
57. Bian C, Xu C, Ruan J, Lee KK, Burke TL, Tempel W, Barsyte D, Li J, Wu M, Zhou BO,
Fleharty BE, Paulson A, Allali-Hassani A, Zhou JQ, Mer G, Grant PA, Workman JL, Zang J,
Min J (2011) Sgf29 binds histone H3K4me2/3 and is required for SAGA complex
recruitment and histone H3 acetylation. EMBO J 30(14):2829–2842. https://doi.org/10.
1038/emboj.2011.193
58. Selenko P, Sprangers R, Stier G, Buhler D, Fischer U, Sattler M (2001) SMN tudor domain
structure and its interaction with the Sm proteins. Nat Struct Biol 8(1):27–31. https://doi.org/
10.1038/83014
59. Friesen WJ, Massenet S, Paushkin S, Wyce A, Dreyfuss G (2001) SMN, the product of the
spinal muscular atrophy gene, binds preferentially to dimethylarginine-containing protein
targets. Mol Cell 7(5):1111–1117. https://doi.org/10.1016/S1097-2765(01)00244-1
60. Corsini L, Sattler M (2007) Tudor hooks up with DNA repair. Nat Struct Mol Biol 14
(2):98–99. https://doi.org/10.1038/nsmb0207-98
61. Eissenberg JC (2012) Structural biology of the chromodomain: form and function. Gene
496(2):69–78. https://doi.org/10.1016/j.gene.2012.01.003
62. Hughes RM, Wiggins KR, Khorasanizadeh S, Waters ML (2007) Recognition of
trimethyllysine by a chromodomain is not driven by the hydrophobic effect. Proc Natl Acad
Sci U S A 104(27):11184–11188. https://doi.org/10.1073/pnas.0610850104
63. Riemen AJ, Waters ML (2009) Design of highly stabilized beta-hairpin peptides through
cation-pi interactions of lysine and n-methyllysine with an aromatic pocket. Biochemistry
48(7):1525–1531. https://doi.org/10.1021/bi801706k
386
G. Sbardella
31(1):35–40. https://doi.org/10.1016/j.tibs.2005.11.001
46. Teske KA, Hadden MK (2017) Methyllysine binding domains: structural insight and
small molecule probe development. Eur J Med Chem 136:14–35. https://doi.org/10.1016/j.
ejmech.2017.04.047
47. Bhushan B, Erdmann A, Zhang Y, Belle R, Johannson C, Oppermann U, Hopkinson RJ,
Schofield CJ, Kawamura A (2018) Investigations on small molecule inhibitors targeting the
histone H3K4 tri-methyllysine binding PHD-finger of JmjC histone demethylases. Bioorg
Med Chem 26(11):2984–2991. https://doi.org/10.1016/j.bmc.2018.03.030
48. Polakis P (2012) Wnt signaling in cancer. Cold Spring Harb Perspect Biol 4(5):a008052.
https://doi.org/10.1101/cshperspect.a008052
49. Daniels DL, Eklof Spink K, Weis WI (2001) Beta-catenin: molecular plasticity and drug design.
Trends Biochem Sci 26(11):672–678. https://doi.org/10.1016/S0968-0004(01)01952-1
50. Miller TC, Rutherford TJ, Johnson CM, Fiedler M, Bienz M (2010) Allosteric remodelling
of the histone H3 binding pocket in the Pygo2 PHD finger triggered by its binding to the
B9L/BCL9 co-factor. J Mol Biol 401(5):969–984. https://doi.org/10.1016/j.jmb.2010.07.007
51. Miller TC, Rutherford TJ, Birchall K, Chugh J, Fiedler M, Bienz M (2014) Competitive
binding of a benzimidazole to the histone-binding pocket of the Pygo PHD finger. ACS Chem
Biol 9(12):2864–2874. https://doi.org/10.1021/cb500585s
52. Amato A, Lucas X, Bortoluzzi A, Wright D, Ciulli A (2018) Targeting ligandable pockets
on plant homeodomain (PHD) zinc finger domains by a fragment-based approach. ACS Chem
Biol 13(4):915–921. https://doi.org/10.1021/acschembio.7b01093
53. Maurer-Stroh S, Dickens NJ, Hughes-Davies L, Kouzarides T, Eisenhaber F, Ponting CP
(2003) The Tudor domain ‘Royal Family’: tudor, plant Agenet, chromo, PWWP and MBT
domains. Trends Biochem Sci 28(2):69–74. https://doi.org/10.1016/S0968-0004(03)00004-5
54. Lu R, Wang GG (2013) Tudor: a versatile family of histone methylation ‘readers’. Trends
Biochem Sci 38(11):546–555. https://doi.org/10.1016/j.tibs.2013.08.002
55. Golumbeski GS, Bardsley A, Tax F, Boswell RE (1991) Tudor, a posterior-group gene
of Drosophila melanogaster, encodes a novel protein and an mRNA localized during
mid-oogenesis. Genes Dev 5(11):2060–2070. https://doi.org/10.1101/gad.5.11.2060
56. Lee KK, Workman JL (2007) Histone acetyltransferase complexes: one size doesn’t fit all.
Nat Rev Mol Cell Biol 8(4):284–295. https://doi.org/10.1038/nrm2145
57. Bian C, Xu C, Ruan J, Lee KK, Burke TL, Tempel W, Barsyte D, Li J, Wu M, Zhou BO,
Fleharty BE, Paulson A, Allali-Hassani A, Zhou JQ, Mer G, Grant PA, Workman JL, Zang J,
Min J (2011) Sgf29 binds histone H3K4me2/3 and is required for SAGA complex
recruitment and histone H3 acetylation. EMBO J 30(14):2829–2842. https://doi.org/10.
1038/emboj.2011.193
58. Selenko P, Sprangers R, Stier G, Buhler D, Fischer U, Sattler M (2001) SMN tudor domain
structure and its interaction with the Sm proteins. Nat Struct Biol 8(1):27–31. https://doi.org/
10.1038/83014
59. Friesen WJ, Massenet S, Paushkin S, Wyce A, Dreyfuss G (2001) SMN, the product of the
spinal muscular atrophy gene, binds preferentially to dimethylarginine-containing protein
targets. Mol Cell 7(5):1111–1117. https://doi.org/10.1016/S1097-2765(01)00244-1
60. Corsini L, Sattler M (2007) Tudor hooks up with DNA repair. Nat Struct Mol Biol 14
(2):98–99. https://doi.org/10.1038/nsmb0207-98
61. Eissenberg JC (2012) Structural biology of the chromodomain: form and function. Gene
496(2):69–78. https://doi.org/10.1016/j.gene.2012.01.003
62. Hughes RM, Wiggins KR, Khorasanizadeh S, Waters ML (2007) Recognition of
trimethyllysine by a chromodomain is not driven by the hydrophobic effect. Proc Natl Acad
Sci U S A 104(27):11184–11188. https://doi.org/10.1073/pnas.0610850104
63. Riemen AJ, Waters ML (2009) Design of highly stabilized beta-hairpin peptides through
cation-pi interactions of lysine and n-methyllysine with an aromatic pocket. Biochemistry
48(7):1525–1531. https://doi.org/10.1021/bi801706k
386
G. Sbardella