Histone chaperone Nap1 dismantles an H2A/H2B dimer from a partially unwrapped nucleosome

1. Luger,K., Ma¨ der,A.W., Richmond,R.K., Sargent,D.F. and

Richmond,T.J. (1997) Crystal structure of the nucleosome core

˚ resolution. Nature, 389, 251–260.

particle at 2.8 A

2. Lai,W.K.M. and Pugh,B.F. (2017) Understanding nucleosome

dynamics and their links to gene expression and DNA replication.

Nat. Rev. Mol. Cell Biol., 18, 548–562.

3. Venkatesh,S. and Workman,J.L. (2015) Histone exchange, chromatin

structure and the regulation of transcription. Nat. Rev. Mol. Cell

Biol., 16, 178–189.

4. Nagae,F., Brandani,G.B., Takada,S. and Terakawa,T. (2021) The

lane-switch mechanism for nucleosome repositioning by DNA

translocase. Nucleic Acids Res., 49, 9066–9076.

5. Hammond,C.M., Strømme,C.B., Huang,H., Patel,D.J. and Groth,A.

(2017) Histone chaperone networks shaping chromatin function. Nat.

Rev. Mol. Cell Biol., 18, 141–158.

6. Toth,K.F.,

Mazurkiewicz,J. and Rippe,K. (2005) Association states

of nucleosome assembly protein 1 and its complexes with histones. J.

Biol. Chem., 280, 15690–15699.

7. Park,Y.-J. and Luger,K. (2006) The structure of nucleosome assembly

protein 1. Proc. Natl Acad. Sci. USA, 103, 1248–1253.

8. Andrews,A.J., Downing,G., Brown,K., Park,Y.-J. and Luger,K.

(2008) A thermodynamic model for Nap1–histone interactions. J.

Biol. Chem., 283, 32412–32418.

9. Fujii-Nakata,T., Ishimi,Y., Okuda,A. and Kikuchi,A. (1992)

Functional analysis of nucleosome assembly protein, NAP-1. J. Biol.

Chem., 267, 20980–20986.

10. Park,Y.-J., Chodaparambil,J.V., Bao,Y., McBryant,S.J. and Luger,K.

(2005) Nucleosome assembly protein 1 exchanges histone H2A–H2B

dimers and assists nucleosome sliding. J. Biol. Chem., 280, 1817–1825.

Downloaded from https://academic.oup.com/nar/article/51/11/5351/7161535 by Library of Research Reactor Institute, Kyoto University user on 05 October 2023

ingly, these proteins commonly contain a disordered tail

with many acidic residues. For example, residues 929–971

of the SPT16 subunit in the human FACT complex are in

the intrinsically disordered C-terminal tail, and 55% are

acidic residues (glutamate or aspartate) (47). In the case

of the FACT complex, the previous study showed that the

tails are required for FACT to dismantle H2A/H2B dimers

from a destabilized nucleosome (48,49), as shown for Nap1

(72% of residues from 366 to 417 in the tail are acidic

residues) in the current study. Further studies are necessary

to confirm if the penetrating fuzzy binding mechanism applies to the cases of FACT, SET/TAF I␤, NPM and other

chaperones.

Our previous in vitro studies suggested that the collision between a model translocase, T7 RNAP, and a nucleosome induces downstream nucleosome repositioning by the

lane-switch mechanism (4). In that study, we also showed

that repositioning occurs after nucleosomal DNA is unwrapped up to –18 bp away from the dyad. The current

study showed that a histone chaperone Nap1 dismantles an

H2A/H2B dimer before nucleosomal DNA is unwrapped

up to –31 bp away from the dyad. Therefore, the dismantling may precede and prevent downstream repositioning.

While T7 RNAP, which we used in the current study, is believed not to specifically interact with a nucleosome, a eukaryotic translocase can possibly accomplish the (temporal)

H2A/H2B dismantling via its own specific interactions with

histones as the translocase proceeds through a nucleosome.

Indeed, recent studies using cryogenic electron microscopy

revealed that a collision between a eukaryotic RNA polymerase II and a nucleosome causes the loss of an H2A/H2B

dimer (13,14). This prevention of downstream repositioning

may underlie the molecular mechanism of maintaining the

nucleosome positioning in transcription, histone recycling

and nucleosomal DNA repair.

In a previous study, a spooling mechanism was experimentally proposed in which the upstream DNA reassociation with the region on the histone core complex exposed

by unwrapping leads to repositioning of the histone core

complex to the upstream DNA (50). In the current study,

we truncated upstream DNA to reduce computational cost

and focus on H2A/H2B dissociation instead of repositioning. Therefore, it is impossible to reproduce the spooling

mechanism by the current simulation setup. Also, detailed

structural modeling of polymerase and bent DNA inside it

may be required to reproduce the spooling mechanism. Simulations using such a model will be tried in the future.

In the current study, we performed coarse-grained molecular dynamics simulations to obtain insight into the structural dynamics of H2A/H2B dismantling from a partially

unwrapped nucleosome by Nap1. Although the model parameters have been carefully tuned for the intranucleosome

interactions (26), only electrostatic and excluded volume interactions were applied to the interactions between Nap1

and a nucleosome. This simple treatment boosted the calculation speed with compromised accuracy. The binding interface and affinity between Nap1 and H2A/H2B globular domains were reasonably well reproduced, although they can

be improved by additionally considering hydrophobic interactions. Despite the margin for improvement, the molecular

dynamics simulation technique is one of the powerful ap-

Nucleic Acids Research, 2023, Vol. 51, No. 11 5363

32. Kumar,S., Rosenberg,J.M., Bouzida,D., Swendsen,R.H. and

Kollman,P.A. (1992) The weighted histogram analysis method for

free-energy calculations on biomolecules. I. The method. J. Comput.

Chem., 13, 1011–1021.

33. Kirov,N., Tsaneva,I., Einbinder,E. and Tsanev,R. (1992) In vitro

transcription through nucleosomes by T7 RNA polymerase. EMBO

J., 11, 1941–1947.

34. Rando,O.J. (2010) Genome-wide mapping of nucleosomes in yeast.

Methods Enzymol., 470, 105–118.

35. Arimura,Y., Tachiwana,H., Oda,T., Sato,M. and Kurumizaka,H.

(2012) Structural analysis of the hexasome, lacking one histone

H2A/H2B dimer from the conventional nucleosome. Biochemistry,

51, 3302–3309.

36. Takada,S., Kanada,R., Tan,C., Terakawa,T., Li,W. and Kenzaki,H.

(2015) Modeling structural dynamics of biomolecular complexes by

coarse-grained molecular simulations. Acc. Chem. Res., 48,

3026–3035.

37. D’Arcy,S., Martin,K.W., Panchenko,T., Chen,X., Bergeron,S.,

Stargell,L.A., Black,B.E. and Luger,K. (2013) Chaperone Nap1

shields histone surfaces used in a nucleosome and can put H2A–H2B

in an unconventional tetrameric form. Mol. Cell, 51, 662–677.

38. Doudou,S., Burton,N.A. and Henchman,R.H. (2009) Standard free

energy of binding from a one-dimensional potential of mean force. J.

Chem. Theory Comput., 5, 909–918.

39. Doose,S., Neuweiler,H. and Sauer,M. (2009) Fluorescence quenching

by photoinduced electron transfer: a reporter for conformational

dynamics of macromolecules. ChemPhysChem, 10, 1389–1398.

40. Ohtomo,H., Akashi,S., Moriwaki,Y., Okuwaki,M., Osakabe,A.,

Nagata,K., Kurumizaka,H. and Nishimura,Y. (2016) C-terminal

acidic domain of histone chaperone human NAP1 is an efficient

binding assistant for histone H2A–H2B, but not H3–H4. Genes Cells,

21, 252–263.

41. Sarkar,P., Zhang,N., Bhattacharyya,S., Salvador,K. and D’Arcy,S.

(2019) Characterization of Caenorhabditis elegans nucleosome

assembly protein 1 uncovers the role of acidic tails in histone binding.

Biochemistry, 58, 108–113.

42. Liu,Y., Xu,L., Xie,C., Hong,J., Li,F., Ruan,K., Chen,J., Wu,J. and

Shi,Y. (2019) Structural insights into ceNAP1 chaperoning activity

toward ceH2A–H2B. Structure, 27, 1798–1810.

43. Mazurkiewicz,J., Kepert,J.F. and Rippe,K. (2006) On the mechanism

of nucleosome assembly by histone chaperone NAP1. J. Biol. Chem.,

281, 16462–16472.

44. Andrews,A.J., Chen,X., Zevin,A., Stargell,L.A. and Luger,K. (2010)

The histone chaperone Nap1 promotes nucleosome assembly by

eliminating nonnucleosomal histone DNA interactions. Mol. Cell, 37,

834–842.

45. Buzon,P.,

Vela´ zquez-Cruz,A., Gonza´ lez-Arzola,K.,

D´ıaz-Quintana,A., D´ıaz-Moreno,I. and Roos,W.H. (2022) Histone

chaperones exhibit conserved functionality in nucleosome remodeling

biophysics. bioRxiv doi: https://doi.org/10.1101/2022.01.13.476140,

13 January 2022, preprint: not peer reviewed.

46. Chen,P., Dong,L., Hu,M., Wang,Y.-Z., Xiao,X., Zhao,Z., Yan,J.,

Wang,P.-Y., Reinberg,D., Li,M. et al. (2018) Functions of FACT in

breaking the nucleosome and maintaining its integrity at the

single-nucleosome level. Mol. Cell, 71, 284–293.

47. Formosa,T. and Winston,F. (2020) The role of FACT in managing

chromatin: disruption, assembly, or repair?Nucleic Acids Res., 48,

11929–11941.

48. Safaric,B., Chacin,E., Scherr,M.J., Rajappa,L., Gebhardt,C.,

Kurat,C.F., Cordes,T. and Duderstadt,K.E. (2022) The fork

protection complex recruits FACT to reorganize nucleosomes during

replication. Nucleic Acids Res., 50, 1317–1334.

49. Sivkina,A.L., Karlova,M.G., Valieva,M.E., McCullough,L.L.,

Formosa,T., Shaytan,A.K., Feofanov,A.V., Kirpichnikov,M.P.,

Sokolova,O.S. and Studitsky,V.M. (2022) Electron microscopy

analysis of ATP-independent nucleosome unfolding by FACT.

Commun Biol, 5, 2.

50. Studitsky,V.M., Clark,D.J. and Felsenfeld,G. (1995) Overcoming a

nucleosomal barrier to transcription. Cell, 83, 19–27.

Downloaded from https://academic.oup.com/nar/article/51/11/5351/7161535 by Library of Research Reactor Institute, Kyoto University user on 05 October 2023

11. Levchenko,V., Jackson,B. and Jackson,V. (2005) Histone release

during transcription: displacement of the two H2A−H2B dimers in

the nucleosome is dependent on different levels of

transcription-induced positive stress. Biochemistry, 44, 5357–5372.

12. Lorch,Y., Maier-Davis,B. and Kornberg,R.D. (2006) Chromatin

remodeling by nucleosome disassembly in vitro. Proc. Natl Acad. Sci.

USA, 103, 3090–3093.

13. Ehara,H., Kujirai,T., Shirouzu,M., Kurumizaka,H. and Sekine,S.

(2022) Structural basis of nucleosome disassembly and reassembly by

RNAPII elongation complex with FACT. Science, 377, eabp9466.

14. Farnung,L., Ochmann,M., Garg,G., Vos,S.M. and Cramer,P. (2022)

Structure of a backtracked hexasomal intermediate of nucleosome

transcription. Mol. Cell, 82, 3126–3134.

15. McBryant,S.J., Park,Y.-J., Abernathy,S.M., Laybourn,P.J.,

Nyborg,J.K. and Luger,K. (2003) Preferential binding of the histone

(H3–H4)2 tetramer by NAP1 is mediated by the amino-terminal

histone tails. J. Biol. Chem., 278, 44574–44583.

16. Aguilar-Gurrieri,C., Larabi,A., Vinayachandran,V., Patel,N.A.,

Yen,K., Reja,R., Ebong,I., Schoehn,G., Robinson,C.V., Pugh,B.F.

et al. (2016) Structural evidence for Nap1-dependent H2A–H2B

deposition and nucleosome assembly. EMBO J., 35, 1465–1482.

17. Fuxreiter,M. (2018) Fuzziness in protein interactions––a historical

perspective. J. Mol. Biol., 430, 2278–2287.

18. Mashanov,G.I. and Batters,C. (2011) In: Single Molecule

Enzymology. Methods and Protocols. Humana Press, Totowa, NJ.

19. Crickard,J.B., Moevus,C.J., Kwon,Y., Sung,P. and Greene,E.C. (2020)

Rad54 drives ATP hydrolysis-dependent DNA sequence alignment

during homologous recombination. Cell, 181, 1380–1394.

20. Abra` moff,M.D., Magalhaes,P.J. and Ram,S.J. (2004) Image

processing with Image. J. Biophotonics, 7, 36–42.

21. Li,W., Wang,W. and Takada,S. (2014) Energy landscape views for

interplays among folding, binding, and allostery of calmodulin

domains. Proc. Natl Acad. Sci. USA, 111, 10550–10555.

22. Terakawa,T. and Takada,S. (2011) Multiscale ensemble modeling of

intrinsically disordered proteins: p53 N-terminal domain. Biophys. J.,

101, 1450–1458.

23. Freeman,G.S., Hinckley,D.M., Lequieu,J.P., Whitmer,J.K. and de

Pablo,J.J. (2014) Coarse-grained modeling of DNA curvature. J.

Chem. Phys., 141, 165103.

24. Niina,T., Brandani,G.B., Tan,C. and Takada,S. (2017)

Sequence-dependent nucleosome sliding in rotation-coupled and

uncoupled modes revealed by molecular simulations. PLoS Comput.

Biol., 13, e1005880.

25. Terakawa,T. and Takada,S. (2014) RESPAC: method to determine

partial charges in coarse-grained protein model and its application to

DNA-binding proteins. J. Chem. Theory Comput., 10, 711–721.

26. Brandani,G.B., Tan,C. and Takada,S. (2021) The kinetic landscape of

nucleosome assembly: a coarse-grained molecular dynamics study.

PLoS Comput. Biol., 17, e1009253.

27. Gansen,A., Felekyan,S., Kuhnemuth,R.,

Lehmann,K., Toth,K.,

Seidel,C.A.M. and Langowski,J. (2018) High precision FRET studies

reveal reversible transitions in nucleosomes between microseconds

and minutes. Nat. Commun., 9, 4628.

28. Kenzaki,H., Koga,N., Hori,N., Kanada,R., Li,W., Okazaki,K.,

Yao,X.-Q. and Takada,S. (2011) CafeMol: a coarse-grained

biomolecular simulator for simulating proteins at work. J. Chem.

Theory Comput., 7, 1979–1989.

29. Davey,C.A., Sargent,D.F., Luger,K., Maeder,A.W. and

Richmond,T.J. (2002) Solvent mediated interactions in the structure

˚ resolution. J. Mol. Biol., 319,

of the nucleosome core particle at 1.9 A

1097–1113.

30. Vasudevan,D., Chua,E.Y.D. and Davey,C.A. (2010) Crystal

structures of nucleosome core particles containing the ‘601’ strong

positioning sequence. J. Mol. Biol., 403, 1–10.

31. Park,Y.-J., McBryant,S.J. and Luger,K. (2008) A ␤-hairpin

comprising the nuclear localization sequence sustains the

self-associated states of nucleosome assembly protein 1. J. Mol. Biol.,

375, 1076–1085.

...