IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-32165-8.html
   My bibliography  Save this article

Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation

Author

Listed:
  • Satoyo Oya

    (The University of Tokyo)

  • Mayumi Takahashi

    (National Institute of Genetics)

  • Kazuya Takashima

    (National Institute of Genetics)

  • Tetsuji Kakutani

    (The University of Tokyo
    National Institute of Genetics)

  • Soichi Inagaki

    (The University of Tokyo
    PRESTO, Japan Science and Technology Agency)

Abstract

Mono-, di-, and trimethylation of histone H3 lysine 4 (H3K4me1/2/3) are associated with transcription, yet it remains controversial whether H3K4me1/2/3 promote or result from transcription. Our previous characterizations of Arabidopsis H3K4 demethylases suggest roles for H3K4me1 in transcription. However, the control of H3K4me1 remains unexplored in Arabidopsis, in which no methyltransferase for H3K4me1 has been identified. Here, we identify three Arabidopsis methyltransferases that direct H3K4me1. Analyses of their genome-wide localization using ChIP-seq and machine learning reveal that one of the enzymes cooperates with the transcription machinery, while the other two are associated with specific histone modifications and DNA sequences. Importantly, these two types of localization patterns are also found for the other H3K4 methyltransferases in Arabidopsis and mice. These results suggest that H3K4me1/2/3 are established and maintained via interplay with transcription as well as inputs from other chromatin features, presumably enabling elaborate gene control.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32165-8
    DOI: 10.1038/s41467-022-32165-8
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-32165-8
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-32165-8?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. Epskamp, Sacha & Cramer, Angélique O.J. & Waldorp, Lourens J. & Schmittmann, Verena D. & Borsboom, Denny, 2012. "qgraph: Network Visualizations of Relationships in Psychometric Data," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 48(i04).
    2. 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.
    3. Fan Zhang & Bin Qi & Likai Wang & Bo Zhao & Siddharth Rode & Nathaniel D. Riggan & Joseph R. Ecker & Hong Qiao, 2016. "EIN2-dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signalling," Nature Communications, Nature, vol. 7(1), pages 1-14, December.
    4. Hiroya Ishihara & Kaoru Sugimoto & Paul T. Tarr & Haruka Temman & Satoshi Kadokura & Yayoi Inui & Takuya Sakamoto & Taku Sasaki & Mitsuhiro Aida & Takamasa Suzuki & Soichi Inagaki & Kengo Morohashi & , 2019. "Primed histone demethylation regulates shoot regenerative competency," Nature Communications, Nature, vol. 10(1), pages 1-15, 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. Xiaozhen Zhao & Yiming Wang & Bingqin Yuan & Hanxi Zhao & Yujie Wang & Zheng Tan & Zhiyuan Wang & Huijun Wu & Gang Li & Wei Song & Ravi Gupta & Kenichi Tsuda & Zhonghua Ma & Xuewen Gao & Qin Gu, 2024. "Temporally-coordinated bivalent histone modifications of BCG1 enable fungal invasion and immune evasion," Nature Communications, Nature, vol. 15(1), pages 1-16, 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. Georgia Mangion & Melanie Simmonds-Buckley & Stephen Kellett & Peter Taylor & Amy Degnan & Charlotte Humphrey & Kate Freshwater & Marisa Poggioli & Cristina Fiorani, 2022. "Modelling Identity Disturbance: A Network Analysis of the Personality Structure Questionnaire (PSQ)," IJERPH, MDPI, vol. 19(21), pages 1-17, October.
    2. Xiao Yang & Nilam Ram & Scott D. Gest & David M. Lydon-Staley & David E. Conroy & Aaron L. Pincus & Peter C. M. Molenaar, 2018. "Socioemotional Dynamics of Emotion Regulation and Depressive Symptoms: A Person-Specific Network Approach," Complexity, Hindawi, vol. 2018, pages 1-14, November.
    3. Michael J. Brusco & Douglas Steinley & Ashley L. Watts, 2022. "Disentangling relationships in symptom networks using matrix permutation methods," Psychometrika, Springer;The Psychometric Society, vol. 87(1), pages 133-155, March.
    4. Denny Borsboom, 2022. "Possible Futures for Network Psychometrics," Psychometrika, Springer;The Psychometric Society, vol. 87(1), pages 253-265, March.
    5. Jayawickreme, Nuwan & Mootoo, Candace & Fountain, Christine & Rasmussen, Andrew & Jayawickreme, Eranda & Bertuccio, Rebecca F., 2017. "Post-conflict struggles as networks of problems: A network analysis of trauma, daily stressors and psychological distress among Sri Lankan war survivors," Social Science & Medicine, Elsevier, vol. 190(C), pages 119-132.
    6. Zhou, Jianhua & Zhang, Lulu & Gong, Xue, 2023. "Longitudinal network relations between symptoms of problematic internet game use and internalizing and externalizing problems among Chinese early adolescents," Social Science & Medicine, Elsevier, vol. 333(C).
    7. Yi-Lung Chen & Hsing-Ying Ho & Ray C. Hsiao & Wei-Hsin Lu & Cheng-Fang Yen, 2020. "Correlations between Quality of Life, School Bullying, and Suicide in Adolescents with Attention-Deficit Hyperactivity Disorder," IJERPH, MDPI, vol. 17(9), pages 1-12, May.
    8. Kan, Kees-Jan & van der Maas, Han L.J. & Levine, Stephen Z., 2019. "Extending psychometric network analysis: Empirical evidence against g in favor of mutualism?," Intelligence, Elsevier, vol. 73(C), pages 52-62.
    9. Knyspel, Jacob & Plomin, Robert, 2024. "Comparing factor and network models of cognitive abilities using twin data," Intelligence, Elsevier, vol. 104(C).
    10. Sacha Epskamp, 2020. "Psychometric network models from time-series and panel data," Psychometrika, Springer;The Psychometric Society, vol. 85(1), pages 206-231, March.
    11. 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.
    12. de Boer, Nina Sofie, 2020. "Exploring the Long-Term Health Consequences of ADHD using a Multivariable Mendelian Randomization Network Approach," Thesis Commons c4wz5, Center for Open Science.
    13. Don Watson & Manfred Krug & Claus-Christian Carbon, 2022. "The relationship between citations and the linguistic traits of specific academic discourse communities identified by using social network analysis," Scientometrics, Springer;Akadémiai Kiadó, vol. 127(4), pages 1755-1781, April.
    14. Matt Crum & Nikhil Ram-Mohan & Michelle M Meyer, 2019. "Regulatory context drives conservation of glycine riboswitch aptamers," PLOS Computational Biology, Public Library of Science, vol. 15(12), pages 1-24, December.
    15. Shinsuke Ohnuki & Yoshikazu Ohya, 2018. "High-dimensional single-cell phenotyping reveals extensive haploinsufficiency," PLOS Biology, Public Library of Science, vol. 16(5), pages 1-23, May.
    16. Payton J. Jones & Patrick Mair & Thorsten Simon & Achim Zeileis, 2020. "Network Trees: A Method for Recursively Partitioning Covariance Structures," Psychometrika, Springer;The Psychometric Society, vol. 85(4), pages 926-945, December.
    17. Simon Foster & Meichun Mohler-Kuo, 2020. "The proportion of non-depressed subjects in a study sample strongly affects the results of psychometric analyses of depression symptoms," PLOS ONE, Public Library of Science, vol. 15(7), pages 1-13, July.
    18. Takehiko Ito, 2021. "The influence of psychological network on the willingness to communicate in a second language," PLOS ONE, Public Library of Science, vol. 16(9), pages 1-15, September.
    19. Nadja Bodner & Laura Bringmann & Francis Tuerlinckx & Peter Jonge & Eva Ceulemans, 2022. "ConNEcT: A Novel Network Approach for Investigating the Co-occurrence of Binary Psychopathological Symptoms Over Time," Psychometrika, Springer;The Psychometric Society, vol. 87(1), pages 107-132, March.
    20. Juliana Ribeiro Francelino Sampaio & Suely Arruda Vidal & Paulo Savio Angeiras de Goes & Paulo Felipe R. Bandeira & José Eulálio Cabral Filho, 2021. "Sociodemographic, Behavioral and Oral Health Factors in Maternal and Child Health: An Interventional and Associative Study from the Network Perspective," IJERPH, MDPI, vol. 18(8), pages 1-13, April.

    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:13:y:2022:i:1:d:10.1038_s41467-022-32165-8. 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.