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Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

Author

Listed:
  • Svetlana O. Dodonova

    (Max Planck Institute for Biophysical Chemistry)

  • Fangjie Zhu

    (University of Cambridge)

  • Christian Dienemann

    (Max Planck Institute for Biophysical Chemistry)

  • Jussi Taipale

    (University of Cambridge)

  • Patrick Cramer

    (Max Planck Institute for Biophysical Chemistry)

Abstract

‘Pioneer’ transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming1,2. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells3. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.

Suggested Citation

  • Svetlana O. Dodonova & Fangjie Zhu & Christian Dienemann & Jussi Taipale & Patrick Cramer, 2020. "Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function," Nature, Nature, vol. 580(7805), pages 669-672, April.
  • Handle: RePEc:nat:nature:v:580:y:2020:i:7805:d:10.1038_s41586-020-2195-y
    DOI: 10.1038/s41586-020-2195-y
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    Cited by:

    1. Bieke Decaesteker & Amber Louwagie & Siebe Loontiens & Fanny De Vloed & Sarah-Lee Bekaert & Juliette Roels & Suzanne Vanhauwaert & Sara De Brouwer & Ellen Sanders & Alla Berezovskaya & Geertrui Deneck, 2023. "SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Marios G. Koliopoulos & Reyhan Muhammad & Theodoros I. Roumeliotis & Fabienne Beuron & Jyoti S. Choudhary & Claudio Alfieri, 2022. "Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. Tyler M. Weaver & Nicole M. Hoitsma & Jonah J. Spencer & Lokesh Gakhar & Nicholas J. Schnicker & Bret D. Freudenthal, 2022. "Structural basis for APE1 processing DNA damage in the nucleosome," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    4. Sveinn Bjarnason & Jordan A. P. McIvor & Andreas Prestel & Kinga S. Demény & Jakob T. Bullerjahn & Birthe B. Kragelund & Davide Mercadante & Pétur O. Heidarsson, 2024. "DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    5. Yichen Zhong & Hakimeh Moghaddas Sani & Bishnu P. Paudel & Jason K. K. Low & Ana P. G. Silva & Stefan Mueller & Chandrika Deshpande & Santosh Panjikar & Xavier J. Reid & Max J. Bedward & Antoine M. Oi, 2022. "The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    6. Luca Pagliaroli & Patrizia Porazzi & Alyxandra T. Curtis & Chiara Scopa & Harald M. M. Mikkers & Christian Freund & Lucia Daxinger & Sandra Deliard & Sarah A. Welsh & Sarah Offley & Connor A. Ott & Br, 2021. "Inability to switch from ARID1A-BAF to ARID1B-BAF impairs exit from pluripotency and commitment towards neural crest formation in ARID1B-related neurodevelopmental disorders," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    7. Deblina Banerjee & Sukriti Bagchi & Zhihui Liu & Hsien-Chao Chou & Man Xu & Ming Sun & Sara Aloisi & Zalman Vaksman & Sharon J. Diskin & Mark Zimmerman & Javed Khan & Berkley Gryder & Carol J. Thiele, 2024. "Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    8. Ya Gao & Daisylyn Senna Tan & Mathias Girbig & Haoqing Hu & Xiaomin Zhou & Qianwen Xie & Shi Wing Yeung & Kin Shing Lee & Sik Yin Ho & Vlad Cojocaru & Jian Yan & Georg K. A. Hochberg & Alex Mendoza & , 2024. "The emergence of Sox and POU transcription factors predates the origins of animal stem cells," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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