IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-49391-x.html
   My bibliography  Save this article

ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers

Author

Listed:
  • Yi Zhang

    (University of Colorado School of Medicine
    Case Western Reserve University)

  • Guojia Xie

    (National Institute of Diabetes and Digestive and Kidney Diseases, NIH)

  • Ji-Eun Lee

    (National Institute of Diabetes and Digestive and Kidney Diseases, NIH)

  • Mohamad Zandian

    (University of Colorado School of Medicine)

  • Deepthi Sudarshan

    (Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center)

  • Benjamin Estavoyer

    (Maisonneuve-Rosemont Hospital Research Center)

  • Caroline Benz

    (Uppsala University)

  • Tiina Viita

    (Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center)

  • Golareh Asgaritarghi

    (Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center)

  • Catherine Lachance

    (Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center)

  • Clémence Messmer

    (Maisonneuve-Rosemont Hospital Research Center)

  • Leandro Simonetti

    (Uppsala University)

  • Vikrant Kumar Sinha

    (University of Colorado School of Medicine)

  • Jean-Philippe Lambert

    (Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center)

  • Yu-Wen Chen

    (Academia Sinica)

  • Shu-Ping Wang

    (Academia Sinica)

  • Ylva Ivarsson

    (Uppsala University)

  • El Bachir Affar

    (Maisonneuve-Rosemont Hospital Research Center
    University of Montréal)

  • Jacques Côté

    (Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center)

  • Kai Ge

    (National Institute of Diabetes and Digestive and Kidney Diseases, NIH)

  • Tatiana G. Kutateladze

    (University of Colorado School of Medicine)

Abstract

The human methyltransferase and transcriptional coactivator MLL4 and its paralog MLL3 are frequently mutated in cancer. MLL4 and MLL3 monomethylate histone H3K4 and contain a set of uncharacterized PHD fingers. Here, we report a novel function of the PHD2 and PHD3 (PHD2/3) fingers of MLL4 and MLL3 that bind to ASXL2, a component of the Polycomb repressive H2AK119 deubiquitinase (PR-DUB) complex. The structure of MLL4 PHD2/3 in complex with the MLL-binding helix (MBH) of ASXL2 and mutational analyses reveal the molecular mechanism which is conserved in homologous ASXL1 and ASXL3. The native interaction of the Trithorax MLL3/4 complexes with the PR-DUB complex in vivo depends solely on MBH of ASXL1/2, coupling the two histone modifying activities. ChIP-seq analysis in embryonic stem cells demonstrates that MBH of ASXL1/2 is required for the deubiquitinase BAP1 recruitment to MLL4-bound active enhancers. Our findings suggest an ASXL1/2-dependent functional link between the MLL3/4 and PR-DUB complexes.

Suggested Citation

  • Yi Zhang & Guojia Xie & Ji-Eun Lee & Mohamad Zandian & Deepthi Sudarshan & Benjamin Estavoyer & Caroline Benz & Tiina Viita & Golareh Asgaritarghi & Catherine Lachance & Clémence Messmer & Leandro Sim, 2024. "ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49391-x
    DOI: 10.1038/s41467-024-49391-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-49391-x
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-49391-x?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Joanna Wysocka & Tomek Swigut & Hua Xiao & Thomas A. Milne & So Yeon Kwon & Joe Landry & Monika Kauer & Alan J. Tackett & Brian T. Chait & Paul Badenhorst & Carl Wu & C. David Allis, 2006. "A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling," Nature, Nature, vol. 442(7098), pages 86-90, July.
    2. Dan R. Robinson & Yi-Mi Wu & Robert J. Lonigro & Pankaj Vats & Erin Cobain & Jessica Everett & Xuhong Cao & Erica Rabban & Chandan Kumar-Sinha & Victoria Raymond & Scott Schuetze & Ajjai Alva & Javed , 2017. "Integrative clinical genomics of metastatic cancer," Nature, Nature, vol. 548(7667), pages 297-303, August.
    3. Yanli Liu & Su Qin & Tsai-Yu Chen & Ming Lei & Shilpa S. Dhar & Jolene Caifeng Ho & Aiping Dong & Peter Loppnau & Yanjun Li & Min Gyu Lee & Jinrong Min, 2019. "Structural insights into trans-histone regulation of H3K4 methylation by unique histone H4 binding of MLL3/4," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    4. Salima Daou & Haithem Barbour & Oumaima Ahmed & Louis Masclef & Caroline Baril & Nadine Nkwe & Daméhan Tchelougou & Maxime Uriarte & Eric Bonneil & Derek Ceccarelli & Nazar Mashtalir & Mika Tanji & Je, 2018. "Monoubiquitination of ASXLs controls the deubiquitinase activity of the tumor suppressor BAP1," Nature Communications, Nature, vol. 9(1), pages 1-21, December.
    5. Fei Lan & Robert E. Collins & Rossella De Cegli & Roman Alpatov & John R. Horton & Xiaobing Shi & Or Gozani & Xiaodong Cheng & Yang Shi, 2007. "Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression," Nature, Nature, vol. 448(7154), pages 718-722, August.
    6. Antoine Campagne & Ming-Kang Lee & Dina Zielinski & Audrey Michaud & Stéphanie Corre & Florent Dingli & Hong Chen & Lara Z. Shahidian & Ivaylo Vassilev & Nicolas Servant & Damarys Loew & Eric Pasmant , 2019. "BAP1 complex promotes transcription by opposing PRC1-mediated H2A ubiquitylation," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    7. Johanna C. Scheuermann & Andrés Gaytán de Ayala Alonso & Katarzyna Oktaba & Nga Ly-Hartig & Robert K. McGinty & Sven Fraterman & Matthias Wilm & Tom W. Muir & Jürg Müller, 2010. "Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB," Nature, Nature, vol. 465(7295), pages 243-247, May.
    8. Xiaobing Shi & Tao Hong & Kay L. Walter & Mark Ewalt & Eriko Michishita & Tiffany Hung & Dylan Carney & Pedro Peña & Fei Lan & Mohan R. Kaadige & Nicolas Lacoste & Christelle Cayrou & Foteini Davrazou, 2006. "ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression," Nature, Nature, vol. 442(7098), pages 96-99, July.
    9. Danny D. Sahtoe & Willem J. van Dijk & Reggy Ekkebus & Huib Ovaa & Titia K. Sixma, 2016. "BAP1/ASXL1 recruitment and activation for H2A deubiquitination," Nature Communications, Nature, vol. 7(1), pages 1-13, April.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Nidhi Rohatgi & Wei Zou & Yongjia Li & Kevin Cho & Patrick L. Collins & Eric Tycksen & Gaurav Pandey & Carl J. DeSelm & Gary J. Patti & Anwesha Dey & Steven L. Teitelbaum, 2023. "BAP1 promotes osteoclast function by metabolic reprogramming," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Dimitrios Spiliotopoulos & Andrea Spitaleri & Giovanna Musco, 2012. "Exploring PHD Fingers and H3K4me0 Interactions with Molecular Dynamics Simulations and Binding Free Energy Calculations: AIRE-PHD1, a Comparative Study," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-13, October.
    3. Moritz Binder & Ryan M. Carr & Terra L. Lasho & Christy M. Finke & Abhishek A. Mangaonkar & Christopher L. Pin & Kurt R. Berger & Amelia Mazzone & Sandeep Potluri & Tamas Ordog & Keith D. Robertson & , 2022. "Oncogenic gene expression and epigenetic remodeling of cis-regulatory elements in ASXL1-mutant chronic myelomonocytic leukemia," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    4. James Godwin & Mohan Govindasamy & Kiruba Nedounsejian & Eduardo March & Ronan Halton & Clara Bourbousse & Léa Wolff & Antoine Fort & Michal Krzyszton & Jesús López Corrales & Szymon Swiezewski & Fred, 2024. "The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    5. Josh N. Vo & Yi-Mi Wu & Jeanmarie Mishler & Sarah Hall & Rahul Mannan & Lisha Wang & Yu Ning & Jin Zhou & Alexander C. Hopkins & James C. Estill & Wallace K. B. Chan & Jennifer Yesil & Xuhong Cao & Ar, 2022. "The genetic heterogeneity and drug resistance mechanisms of relapsed refractory multiple myeloma," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    6. Yi Liu & Brian Debo & Mingfeng Li & Zhennan Shi & Wanqiang Sheng & Yang Shi, 2021. "LSD1 inhibition sustains T cell invigoration with a durable response to PD-1 blockade," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    7. Steffen Mueller & Gail Dennison & Shujun Liu, 2021. "An Assessment on Ethanol-Blended Gasoline/Diesel Fuels on Cancer Risk and Mortality," IJERPH, MDPI, vol. 18(13), pages 1-23, June.
    8. Guidantonio Malagoli Tagliazucchi & Anna J. Wiecek & Eloise Withnell & Maria Secrier, 2023. "Genomic and microenvironmental heterogeneity shaping epithelial-to-mesenchymal trajectories in cancer," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    9. Biaobin Jiang & Quanhua Mu & Fufang Qiu & Xuefeng Li & Weiqi Xu & Jun Yu & Weilun Fu & Yong Cao & Jiguang Wang, 2021. "Machine learning of genomic features in organotropic metastases stratifies progression risk of primary tumors," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    10. Satoyo Oya & Mayumi Takahashi & Kazuya Takashima & Tetsuji Kakutani & Soichi Inagaki, 2022. "Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    11. Zhe Jiang & YoungJun Ju & Amjad Ali & Philip E. D. Chung & Patryk Skowron & Dong-Yu Wang & Mariusz Shrestha & Huiqin Li & Jeff C. Liu & Ioulia Vorobieva & Ronak Ghanbari-Azarnier & Ethel Mwewa & Maria, 2023. "Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    12. Mandy S. M. Wan & Reyhan Muhammad & Marios G. Koliopoulos & Theodoros I. Roumeliotis & Jyoti S. Choudhary & Claudio Alfieri, 2023. "Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    13. Yanli Liu & Aman Iqbal & Weiguo Li & Zuyao Ni & Yalong Wang & Jurupula Ramprasad & Karan Joshua Abraham & Mengmeng Zhang & Dorothy Yanling Zhao & Su Qin & Peter Loppnau & Honglv Jiang & Xinghua Guo & , 2022. "A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    14. Shengyong Yu & Chunhua Zhou & Jiangping He & Zhaokai Yao & Xingnan Huang & Bowen Rong & Hong Zhu & Shijie Wang & Shuyan Chen & Xialian Wang & Baomei Cai & Guoqing Zhao & Yuhan Chen & Lizhan Xiao & He , 2022. "BMP4 drives primed to naïve transition through PGC-like state," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    15. Marco Bolis & Daniela Bossi & Arianna Vallerga & Valentina Ceserani & Manuela Cavalli & Daniela Impellizzieri & Laura Di Rito & Eugenio Zoni & Simone Mosole & Angela Rita Elia & Andrea Rinaldi & Ricar, 2021. "Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    16. Amy L. Hughes & Aleksander T. Szczurek & Jessica R. Kelley & Anna Lastuvkova & Anne H. Turberfield & Emilia Dimitrova & Neil P. Blackledge & Robert J. Klose, 2023. "A CpG island-encoded mechanism protects genes from premature transcription termination," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    17. Jae Eun Choi & Yuanyuan Qiao & Ilona Kryczek & Jiali Yu & Jonathan Gurkan & Yi Bao & Mahnoor Gondal & Jean Ching-Yi Tien & Tomasz Maj & Sahr Yazdani & Abhijit Parolia & Houjun Xia & JiaJia Zhou & Shua, 2024. "PIKfyve, expressed by CD11c-positive cells, controls tumor immunity," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    18. Huiqiang Cai & Bin Zhang & Johanne Ahrenfeldt & Justin V. Joseph & Maria Riedel & Zongliang Gao & Sofie K. Thomsen & Ditte S. Christensen & Rasmus O. Bak & Henrik Hager & Mikkel H. Vendelbo & Xin Gao , 2024. "CRISPR/Cas9 model of prostate cancer identifies Kmt2c deficiency as a metastatic driver by Odam/Cabs1 gene cluster expression," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    19. Brian D. Lehmann & Antonio Colaprico & Tiago C. Silva & Jianjiao Chen & Hanbing An & Yuguang Ban & Hanchen Huang & Lily Wang & Jamaal L. James & Justin M. Balko & Paula I. Gonzalez-Ericsson & Melinda , 2021. "Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    20. Amanda Fitzpatrick & Marjan Iravani & Adam Mills & David Vicente & Thanussuyah Alaguthurai & Ioannis Roxanis & Nicholas C. Turner & Syed Haider & Andrew N. J. Tutt & Clare M. Isacke, 2023. "Genomic profiling and pre-clinical modelling of breast cancer leptomeningeal metastasis reveals acquisition of a lobular-like phenotype," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49391-x. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.