IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-42507-9.html
   My bibliography  Save this article

Functional dissection of PRC1 subunits RYBP and YAF2 during neural differentiation of embryonic stem cells

Author

Listed:
  • Yanjiang Liu

    (Guangzhou Medical University
    Guangzhou National Laboratory
    University of Chinese Academy of Sciences)

  • Gongcheng Hu

    (Guangzhou National Laboratory)

  • Shengxiong Yang

    (Guangzhou Medical University
    Guangzhou National Laboratory)

  • Mingze Yao

    (Guangzhou Medical University)

  • Zicong Liu

    (Guangzhou Medical University)

  • Chenghong Yan

    (Guangzhou Medical University)

  • Yulin Wen

    (Guangzhou Medical University
    Guangzhou National Laboratory
    University of Chinese Academy of Sciences)

  • Wangfang Ping

    (Guangzhou Medical University)

  • Juehan Wang

    (Guangzhou Medical University
    Guangzhou National Laboratory
    University of Chinese Academy of Sciences)

  • Yawei Song

    (Guangzhou Medical University)

  • Xiaotao Dong

    (Guangzhou Medical University)

  • Guangjin Pan

    (Guangzhou Medical University
    University of Chinese Academy of Sciences)

  • Hongjie Yao

    (Guangzhou Medical University
    Guangzhou National Laboratory
    University of Chinese Academy of Sciences)

Abstract

Polycomb repressive complex 1 (PRC1) comprises two different complexes: CBX-containing canonical PRC1 (cPRC1) and RYBP/YAF2-containing variant PRC1 (vPRC1). RYBP-vPRC1 or YAF2-vPRC1 catalyzes H2AK119ub through a positive-feedback model; however, whether RYBP and YAF2 have different regulatory functions is still unclear. Here, we show that the expression of RYBP and YAF2 decreases and increases, respectively, during neural differentiation of embryonic stem cells (ESCs). Rybp knockout impairs neural differentiation by activating Wnt signaling and derepressing nonneuroectoderm-associated genes. However, Yaf2 knockout promotes neural differentiation and leads to redistribution of RYBP binding, increases enrichment of RYBP and H2AK119ub on the RYBP-YAF2 cotargeted genes, and prevents ectopic derepression of nonneuroectoderm-associated genes in neural-differentiated cells. Taken together, this study reveals that RYBP and YAF2 function differentially in regulating mESC neural differentiation.

Suggested Citation

  • Yanjiang Liu & Gongcheng Hu & Shengxiong Yang & Mingze Yao & Zicong Liu & Chenghong Yan & Yulin Wen & Wangfang Ping & Juehan Wang & Yawei Song & Xiaotao Dong & Guangjin Pan & Hongjie Yao, 2023. "Functional dissection of PRC1 subunits RYBP and YAF2 during neural differentiation of embryonic stem cells," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42507-9
    DOI: 10.1038/s41467-023-42507-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-42507-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-42507-9?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. Hengbin Wang & Liangjun Wang & Hediye Erdjument-Bromage & Miguel Vidal & Paul Tempst & Richard S. Jones & Yi Zhang, 2004. "Role of histone H2A ubiquitination in Polycomb silencing," Nature, Nature, vol. 431(7010), pages 873-878, October.
    2. Mingze Yao & Xueke Zhou & Jiajian Zhou & Shixin Gong & Gongcheng Hu & Jiao Li & Kaimeng Huang & Ping Lai & Guang Shi & Andrew P. Hutchins & Hao Sun & Huating Wang & Hongjie Yao, 2018. "PCGF5 is required for neural differentiation of embryonic stem cells," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    3. Asad M. Taherbhoy & Oscar W. Huang & Andrea G. Cochran, 2015. "BMI1–RING1B is an autoinhibited RING E3 ubiquitin ligase," Nature Communications, Nature, vol. 6(1), pages 1-13, November.
    4. Caryn S. Ross-Innes & Rory Stark & Andrew E. Teschendorff & Kelly A. Holmes & H. Raza Ali & Mark J. Dunning & Gordon D. Brown & Ondrej Gojis & Ian O. Ellis & Andrew R. Green & Simak Ali & Suet-Feung C, 2012. "Differential oestrogen receptor binding is associated with clinical outcome in breast cancer," Nature, Nature, vol. 481(7381), pages 389-393, January.
    5. Jiao Li & Kaimeng Huang & Gongcheng Hu & Isaac A. Babarinde & Yaoyi Li & Xiaotao Dong & Yu-Sheng Chen & Liping Shang & Wenjing Guo & Junwei Wang & Zhaoming Chen & Andrew P. Hutchins & Yun-Gui Yang & H, 2019. "An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Jie Zhang & Gongcheng Hu & Yuli Lu & Huawei Ren & Yin Huang & Yulin Wen & Binrui Ji & Diyang Wang & Haidong Wang & Huisheng Liu & Ning Ma & Lingling Zhang & Guangjin Pan & Yibo Qu & Hua Wang & Wei Zha, 2024. "CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment," Nature Communications, Nature, vol. 15(1), pages 1-21, December.

    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. Natalie DeForest & Yuqi Wang & Zhiyi Zhu & Jacqueline S. Dron & Ryan Koesterer & Pradeep Natarajan & Jason Flannick & Tiffany Amariuta & Gina M. Peloso & Amit R. Majithia, 2024. "Genome-wide discovery and integrative genomic characterization of insulin resistance loci using serum triglycerides to HDL-cholesterol ratio as a proxy," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Wenjing Yan & Yongwang Zhong & Xin Hu & Tuan Xu & Yinghua Zhang & Stephen Kales & Yanyan Qu & Daniel C. Talley & Bolormaa Baljinnyam & Christopher A. LeClair & Anton Simeonov & Brian M. Polster & Ruil, 2023. "Auranofin targets UBA1 and enhances UBA1 activity by facilitating ubiquitin trans-thioesterification to E2 ubiquitin-conjugating enzymes," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    3. Nickole Moon & Christopher P. Morgan & Ruth Marx-Rattner & Alyssa Jeng & Rachel L. Johnson & Ijeoma Chikezie & Carmen Mannella & Mary D. Sammel & C. Neill Epperson & Tracy L. Bale, 2024. "Stress increases sperm respiration and motility in mice and men," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    4. Yawen Lei & Yaoguang Yu & Wei Fu & Tao Zhu & Caihong Wu & Zhihao Zhang & Zewang Yu & Xin Song & Jianqu Xu & Zhenwei Liang & Peitao Lü & Chenlong Li, 2024. "BCL7A and BCL7B potentiate SWI/SNF-complex-mediated chromatin accessibility to regulate gene expression and vegetative phase transition in plants," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    5. Jorine M. Eeftens & Manya Kapoor & Davide Michieletto & Clifford P. Brangwynne, 2021. "Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    6. Xinyi Chen & Yiran Guo & Ting Zhao & Jiuwei Lu & Jian Fang & Yinsheng Wang & Gang Greg Wang & Jikui Song, 2024. "Structural basis for the H2AK119ub1-specific DNMT3A-nucleosome interaction," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    7. Yong Yean Kim & Berkley E. Gryder & Ranuka Sinniah & Megan L. Peach & Jack F. Shern & Abdalla Abdelmaksoud & Silvia Pomella & Girma M. Woldemichael & Benjamin Z. Stanton & David Milewski & Joseph J. B, 2024. "KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    8. Haoxi Chai & Harianto Tjong & Peng Li & Wei Liao & Ping Wang & Chee Hong Wong & Chew Yee Ngan & Warren J. Leonard & Chia-Lin Wei & Yijun Ruan, 2023. "ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    9. Tulsi Patel & Jennifer Hammelman & Siaresh Aziz & Sumin Jang & Michael Closser & Theodore L. Michaels & Jacob A. Blum & David K. Gifford & Hynek Wichterle, 2022. "Transcriptional dynamics of murine motor neuron maturation in vivo and in vitro," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    10. Sayantani Ghosh Dastidar & Bony Kumar & Bo Lauckner & Damien Parrello & Danielle Perley & Maria Vlasenok & Antariksh Tyagi & Nii Koney-Kwaku Koney & Ata Abbas & Sergei Nechaev, 2023. "Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    11. Jie Zhang & Gongcheng Hu & Yuli Lu & Huawei Ren & Yin Huang & Yulin Wen & Binrui Ji & Diyang Wang & Haidong Wang & Huisheng Liu & Ning Ma & Lingling Zhang & Guangjin Pan & Yibo Qu & Hua Wang & Wei Zha, 2024. "CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    12. Qiutao Xu & Yaping Yue & Biao Liu & Zhengting Chen & Xuan Ma & Jing Wang & Yu Zhao & Dao-Xiu Zhou, 2023. "ACL and HAT1 form a nuclear module to acetylate histone H4K5 and promote cell proliferation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    13. Jamal B. Williams & Qing Cao & Wei Wang & Young-Ho Lee & Luye Qin & Ping Zhong & Yong Ren & Kaijie Ma & Zhen Yan, 2023. "Inhibition of histone methyltransferase Smyd3 rescues NMDAR and cognitive deficits in a tauopathy mouse model," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    14. Konstantin Okonechnikov & Aylin Camgöz & Owen Chapman & Sameena Wani & Donglim Esther Park & Jens-Martin Hübner & Abhijit Chakraborty & Meghana Pagadala & Rosalind Bump & Sahaana Chandran & Katerina K, 2023. "3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    15. Stanislav Tsitkov & Kelsey Valentine & Velina Kozareva & Aneesh Donde & Aaron Frank & Susan Lei & Jennifer Eyk & Steve Finkbeiner & Jeffrey D. Rothstein & Leslie M. Thompson & Dhruv Sareen & Clive N. , 2024. "Disease related changes in ATAC-seq of iPSC-derived motor neuron lines from ALS patients and controls," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    16. Xianchun Lan & Song Ding & Tianzhe Zhang & Ying Yi & Conghui Li & Wenwen Jin & Jian Chen & Kaiwei Liang & Hengbin Wang & Wei Jiang, 2022. "PCGF6 controls neuroectoderm specification of human pluripotent stem cells by activating SOX2 expression," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    17. Jing Chen & Zhen Hu & Mukta Phatak & John Reichard & Johannes M Freudenberg & Siva Sivaganesan & Mario Medvedovic, 2013. "Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules," PLOS Computational Biology, Public Library of Science, vol. 9(9), pages 1-12, September.
    18. Joyce J. Thompson & Daniel J. Lee & Apratim Mitra & Sarah Frail & Ryan K. Dale & Pedro P. Rocha, 2022. "Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    19. Junhao Li & Manoj K. Jaiswal & Jo-Fan Chien & Alexey Kozlenkov & Jinyoung Jung & Ping Zhou & Mahammad Gardashli & Luc J. Pregent & Erica Engelberg-Cook & Dennis W. Dickson & Veronique V. Belzil & Eran, 2023. "Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    20. Paola Cattaneo & Michael G. B. Hayes & Nina Baumgarten & Dennis Hecker & Sofia Peruzzo & Galip S. Aslan & Paolo Kunderfranco & Veronica Larcher & Lunfeng Zhang & Riccardo Contu & Gregory Fonseca & Sim, 2022. "DOT1L regulates chamber-specific transcriptional networks during cardiogenesis and mediates postnatal cell cycle withdrawal," Nature Communications, Nature, vol. 13(1), pages 1-19, 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:14:y:2023:i:1:d:10.1038_s41467-023-42507-9. 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.