Science - USA (2019-02-15)

REFERENCES AND NOTES

1. P. Cramer, D. A. Bushnell, R. D. Kornberg,Science 292 ,
   1863 – 1876 (2001).


2. K. Luger, A. W. Mäder, R. K. Richmond, D. F. Sargent,
   T. J. Richmond,Nature 389 , 251–260 (1997).


3. O. I. Kulaeva, F. K. Hsieh, H. W. Chang, D. S. Luse,
   V. M. Studitsky,Biochim. Biophys. Acta 1829 ,76–83 (2013).


4. L. Bintuet al.,Cell 151 , 738–749 (2012).


5. C. M. Weber, S. Ramachandran, S. Henikoff,Mol. Cell 53 ,
   819 – 830 (2014).


6. T. Kujiraiet al.,Science 362 , 595–598 (2018).


7. S. J. Petesch, J. T. Lis,Trends Genet. 28 , 285–294 (2012).


8. B. Li, M. Carey, J. L. Workman,Cell 128 , 707–719 (2007).


9. G. A. Hartzog, J. L. Speer, D. L. Lindstrom,Biochim. Biophys.
   Acta 1577 , 276–286 (2002).


10. G.A.Hartzog,J.Fu,Biochim. Biophys. Acta 1829 ,105–115 (2013).


11. A. Mayeret al.,Nat. Struct. Mol. Biol. 17 , 1272–1278 (2010).


12. H. Eharaet al.,Science 357 , 921–924 (2017).
    13. C. Bernecky, J. M. Plitzko, P. Cramer,Nat. Struct. Mol. Biol. 24 ,
    809 – 815 (2017).
    14. F. Werner,J. Mol. Biol. 417 ,13–27 (2012).
    15. T. Wadaet al.,Genes Dev. 12 , 343 – 356 (1998).
    16. A. Hirtreiteret al.,Nucleic Acids Res. 38 , 4040–4051 (2010).
    17. G. Bar-Nahumet al.,Cell 120 , 183–193 (2005).
    18. J. B. Crickard, J. Lee, T. H. Lee, J. C. Reese,Nucleic Acids Res.
    45 , 6362–6374 (2017).
    19. J.P.Daniels,S.Kelly,B.Wickstead,K.Gull,Biol. Direct 4 ,24(2009).
    20. D. Prather, N. J. Krogan, A. Emili, J. F. Greenblatt, F. Winston,
    Mol. Cell. Biol. 25 , 10122–10135 (2005).
    21. M. S. Swanson, F. Winston,Genetics 132 , 325–336 (1992).
    22. H. Kettenberger, K. J. Armache, P. Cramer,Cell 114 , 347– 357
    (2003).
    23. D. Wanget al.,Science 324 , 1203–1206 (2009).
    24. B. Kastneret al.,Nat. Methods 5 ,53–55 (2008).
    25. C. Plaschkaet al.,Nature 533 , 353–358 (2016).
    26. Y. Heet al.,Nature 533 , 359–365 (2016).
    27. Y. Tsunaka, Y. Fujiwara, T. Oyama, S. Hirose, K. Morikawa,
    Genes Dev. 30 , 673–686 (2016).
    28. L. Farnung, S. M. Vos, P. Cramer,Nat. Commun. 9 ,5432(2018).
    29. H.Kwak,N.J.Fuda,L.J.Core,J.T.Lis,Science 339 ,950–953 (2013).
    30. S. M. Vos, L. Farnung, H. Urlaub, P. Cramer,Nature 560 ,
    601 – 606 (2018).

ACKNOWLEDGMENTS

We thank K. Katsura, M. Aoki, R. Akasaka (RIKEN), and T. Osanai

for assistance with the yeast fermentation, mutagenesis, and the

computing environment and Y. Iikura (The University of Tokyo) for her

assistance.Funding:This work was supported in part by the RIKEN

Dynamic Structural Biology project (to M.S., S.S., and H.K.); Japan

Society for the Promotion of Science KAKENHI grants JP18H05534 (to

H.K.), JP25116002 (to H.K.), and JP15H04344 (to S.S.); Japan Science

and Technology Agency Core Research for Evolutional Science and

Technology, Japan Science and Technology Agency grant JPMJCR16G1

(to H.K.); and the Platform Project for Supporting Drug Discovery

and Life Science Research (BINDS) from the Agency for Medical

Research and Development under grants JP18am0101076 (to H.K.) and

JP18am0101082 (to M.S.).Author contributions:H.E. prepared

elongation factors and RNAPII. T.K. and Y.F. prepared the RNAPII-

nucleosome complexes and performed biochemical analyses. H.E., T.K.,

M.S., and S.S. performed cryo-EM analyses. S.S. and H.K. conceived,

designed, and supervised all of the work. H.E., T.K., H.K., and S.S.

wrote the paper. All of the authors discussed the results and

commented on the manuscript.Competing interests:Authors declare

no competing interests.Data and materials availability:The cryo-EM

reconstructions and atomic models of the nucleosome-transcribing

RNAPII ECs have been deposited in the Electron Microscopy Data Bank

(EMDB) and the Protein Data Bank (PDB), under the accession

codes (EMD-9713 and PDB ID 6IR9 for EC-nucleosome at

SHL(–1); EMD-0672 and PDB ID 6J4X for EC-nucleosome at

SHL(–1)+1A; EMD-0673 and PDB ID 6J4Y for EC-nucleosome

at SHL(–1)+1B; EMD-0671 and PDB ID 6J4W for EC-nucleosome

at SHL(–5); EMD-0674 and PDB ID 6J4Z for the SHL(–1) complex

with Spt4/5 and foreign DNA; EMD-0675 and PDB ID 6J50 for the tilted

SHL(–1) complex with Spt4/5 and foreign DNA; EMD-0676 and PDB ID

6J51 for the SHL(–1)+1complex with Spt4/5, foreign DNA, and weak Elf1).

SUPPLEMENTARY MATERIALS

http://www.sciencemag.org/content/363/6428/744/suppl/DC1

Materials and Methods

Figs. S1 to S16

Tables S1 and S2

References ( 31 – 40 )

Movie S1

31 October 2018; accepted 24 January 2019

Published online 7 February 2019

10.1126/science.aav8912

Eharaet al.,Science 363 , 744–747 (2019) 15 February 2019 4of4

Fig. 4. Roles of Elf1 and Spt4/5 in the nucleosome transcription.Elf1 and Spt4/5 modify the
RNAPII surface to intervene with the RNAPII-nucleosome interaction. At SHL(–6), SHL(–5), and SHL
(–2), the elongation factors facilitate the EC passage by preventing the direct RNAPII-nucleosome
interaction that causes pausing. They facilitate the EC passage through SHL(–1), not only by
changing the RNAPII-nucleosome interactions to adjust the RNAPII wedge to the histone-DNA
contact site but also by weakening the histone-DNA contacts via the Elf1 basic tail.

RESEARCH | REPORT

on February 18, 2019^

http://science.sciencemag.org/

Downloaded from