IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-62991-5.html
   My bibliography  Save this article

Chromatin retained MUSHER lncRNA integrates ABA and DOG1 signalling pathways to enhance Arabidopsis seeds dormancy

Author

Listed:
  • Sebastian Przemyslaw Sacharowski

    (Institute of Biochemistry and Biophysics PAS)

  • Michal Krzyszton

    (Institute of Biochemistry and Biophysics PAS)

  • Lien Brzezniak

    (Institute of Biochemistry and Biophysics PAS)

  • Karol Jerzy Rogowski

    (ElementZero Biolabs)

  • Miguel Montez

    (Norwich Research Park)

  • Katarzyna Rosol

    (Institute of Biochemistry and Biophysics PAS)

  • Magdalena Wrona

    (Institute of Biochemistry and Biophysics PAS)

  • Ruslan Yatusevich

    (Institute of Biochemistry and Biophysics PAS)

  • Veena Halale Manjunath

    (Institute of Biochemistry and Biophysics PAS
    Institute of Biochemistry and Biophysics PAS)

  • Lukasz Szewc

    (Adam Mickiewicz University)

  • Artur Jarmolowski

    (Adam Mickiewicz University)

  • Szymon Swiezewski

    (Institute of Biochemistry and Biophysics PAS)

Abstract

Many plant lncRNAs regulate gene expression by binding to chromatin, but how they are retained at the target loci is unclear. We identify a chromatin-localized lncRNA - MUSHER, which activates two parallel regulatory pathways to increase Arabidopsis seed dormancy. MUSHER is upregulated in response to high temperatures, contributing to the induction of secondary dormancy. It promotes DOG1 expression by recruitment of the CPSF complex to enhance the proximal cleavage and polyadenylation at the DOG1 transcript. It also increases ABA sensitivity in seeds by activating PIR1 gene transcription. These genes, located on different chromosomes, are both bound by MUSHER, despite lacking sequence homology. The chromatin association of MUSHER enables the integration of the DOG1- and ABA pathways to adjust seed germination timing. Additionally, MUSHER and other lncRNAs interact with U1 snRNP, which is required for their chromatin localisation, revealing a role for U1 snRNP in plants.

Suggested Citation

  • Sebastian Przemyslaw Sacharowski & Michal Krzyszton & Lien Brzezniak & Karol Jerzy Rogowski & Miguel Montez & Katarzyna Rosol & Magdalena Wrona & Ruslan Yatusevich & Veena Halale Manjunath & Lukasz Sz, 2025. "Chromatin retained MUSHER lncRNA integrates ABA and DOG1 signalling pathways to enhance Arabidopsis seeds dormancy," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62991-5
    DOI: 10.1038/s41467-025-62991-5
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-62991-5
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-62991-5?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. Quentin Angelo Thomas & Ryan Ard & Jinghan Liu & Bingnan Li & Jingwen Wang & Vicent Pelechano & Sebastian Marquardt, 2020. "Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    2. Xinyue Zhao & Jingrui Li & Bi Lian & Hanqing Gu & Yan Li & Yijun Qi, 2018. "Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    3. Szymon Swiezewski & Fuquan Liu & Andreas Magusin & Caroline Dean, 2009. "Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target," Nature, Nature, vol. 462(7274), pages 799-802, December.
    4. Noriyuki Nishimura & Wataru Tsuchiya & James J. Moresco & Yuki Hayashi & Kouji Satoh & Nahomi Kaiwa & Tomoko Irisa & Toshinori Kinoshita & Julian I. Schroeder & John R. Yates & Takashi Hirayama & Tosh, 2018. "Control of seed dormancy and germination by DOG1-AHG1 PP2C phosphatase complex via binding to heme," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    5. Albert E. Almada & Xuebing Wu & Andrea J. Kriz & Christopher B. Burge & Phillip A. Sharp, 2013. "Promoter directionality is controlled by U1 snRNP and polyadenylation signals," Nature, Nature, vol. 499(7458), pages 360-363, July.
    6. Peter Kindgren & Ryan Ard & Maxim Ivanov & Sebastian Marquardt, 2018. "Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    7. Stefanie Rosa & Susan Duncan & Caroline Dean, 2016. "Mutually exclusive sense–antisense transcription at FLC facilitates environmentally induced gene repression," Nature Communications, Nature, vol. 7(1), pages 1-7, December.
    8. Minglei Yang & Pan Zhu & Jitender Cheema & Rebecca Bloomer & Pawel Mikulski & Qi Liu & Yueying Zhang & Caroline Dean & Yiliang Ding, 2022. "In vivo single-molecule analysis reveals COOLAIR RNA structural diversity," Nature, Nature, vol. 609(7926), pages 394-399, September.
    9. Yoav Lubelsky & Igor Ulitsky, 2018. "Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells," Nature, Nature, vol. 555(7694), pages 107-111, March.
    10. Yafei Yin & J. Yuyang Lu & Xuechun Zhang & Wen Shao & Yanhui Xu & Pan Li & Yantao Hong & Li Cui & Ge Shan & Bin Tian & Qiangfeng Cliff Zhang & Xiaohua Shen, 2020. "U1 snRNP regulates chromatin retention of noncoding RNAs," Nature, Nature, vol. 580(7801), pages 147-150, 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. Isaac A. Babarinde & Xiuling Fu & Gang Ma & Yuhao Li & Zhangting Liang & Jianfei Xu & Zhen Xiao & Yu Qiao & Zheng Lin & Katerina Oleynikova & Mobolaji T. Akinwole & Xuemeng Zhou & Alexey Ruzov & Andre, 2025. "Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages," Nature Communications, Nature, vol. 16(1), pages 1-24, December.
    2. Benjamin J. M. Tremblay & Cristina P. Santini & Yajiao Cheng & Xue Zhang & Stefanie Rosa & Julia I. Qüesta, 2024. "Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    3. Liang Chen & Yucong Wang & Jiamei Lin & Zhenxing Song & Qinwei Wang & Wenfang Zhao & Yan Wang & Xiaoyu Xiu & Yuqi Deng & Xiuzhi Li & Qiqi Li & Xiaolin Wang & Jingxin Li & Xu Liu & Kunpeng Liu & Jincon, 2022. "Exportin 4 depletion leads to nuclear accumulation of a subset of circular RNAs," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    4. Zhen-Hui Wang & Xin-Feng Wang & Tianyuan Lu & Ming-Rui Li & Peng Jiang & Jing Zhao & Si-Tong Liu & Xue-Qi Fu & Jonathan F. Wendel & Yves Peer & Bao Liu & Lin-Feng Li, 2022. "Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    5. 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.
    6. Sagar Mahale & Meenakshi Setia & Bharat Prajapati & Santhilal Subhash & Mukesh Pratap Yadav & Subazini Thankaswamy Kosalai & Ananya Deshpande & Jagannath Kuchlyan & Mirco Di Marco & Fredrik Westerlund, 2022. "HnRNPK maintains single strand RNA through controlling double-strand RNA in mammalian cells," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    7. Obroucheva NV & Lityagina SV & Sinkevich IA, 2019. "Distinct Pathways of Regulation Seed Dormancy and Germination by Abscisic Acid," International Journal of Cell Science & Molecular Biology, Juniper Publishers Inc., vol. 5(4), pages 74-78, January.
    8. Kenzui Taniue & Anzu Sugawara & Chao Zeng & Han Han & Xinyue Gao & Yuki Shimoura & Atsuko Nakanishi Ozeki & Rena Onoguchi-Mizutani & Masahide Seki & Yutaka Suzuki & Michiaki Hamada & Nobuyoshi Akimits, 2024. "The MTR4/hnRNPK complex surveils aberrant polyadenylated RNAs with multiple exons," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    9. Jie Liu & Xuehua Zhong, 2024. "Epiallelic variation of non-coding RNA genes and their phenotypic consequences," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    10. Zhenhui Zhong & Yafei Wang & Ming Wang & Fan Yang & Quentin Angelo Thomas & Yan Xue & Yaxin Zhang & Wanlu Liu & Yasaman Jami-Alahmadi & Linhao Xu & Suhua Feng & Sebastian Marquardt & James A. Wohlschl, 2022. "Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    11. Xavier Contreras & David Depierre & Charbel Akkawi & Marina Srbic & Marion Helsmoortel & Maguelone Nogaret & Matthieu LeHars & Kader Salifou & Alexandre Heurteau & Olivier Cuvier & Rosemary Kiernan, 2023. "PAPγ associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    12. Riccardo Calandrelli & Xingzhao Wen & John Lalith Charles Richard & Zhifei Luo & Tri C. Nguyen & Chien-Ju Chen & Zhijie Qi & Shuanghong Xue & Weizhong Chen & Zhangming Yan & Weixin Wu & Kathia Zaleta-, 2023. "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    13. Pawel Mikulski & Philip Wolff & Tiancong Lu & Mathias Nielsen & Elsa Franco Echevarria & Danling Zhu & Julia I. Questa & Gerhard Saalbach & Carlo Martins & Caroline Dean, 2022. "VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    14. Charles Limouse & Owen K. Smith & David Jukam & Kelsey A. Fryer & William J. Greenleaf & Aaron F. Straight, 2023. "Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    15. Min-Han Lin & Madeline K. Jensen & Nathan D. Elrod & Kai-Lieh Huang & Kevin A. Welle & Eric J. Wagner & Liang Tong, 2022. "Inositol hexakisphosphate is required for Integrator function," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    16. Ting Fu & Kofi Amoah & Tracey W. Chan & Jae Hoon Bahn & Jae-Hyung Lee & Sari Terrazas & Rockie Chong & Sriram Kosuri & Xinshu Xiao, 2024. "Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genes," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    17. Maya Ron & Igor Ulitsky, 2022. "Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs," Nature Communications, Nature, vol. 13(1), pages 1-13, 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:16:y:2025:i:1:d:10.1038_s41467-025-62991-5. 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.