IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-47092-z.html
   My bibliography  Save this article

Intron detention tightly regulates the stemness/differentiation switch in the adult neurogenic niche

Author

Listed:
  • Ainara González-Iglesias

    (Instituto de Neurociencias (CSIC-UMH))

  • Aida Arcas

    (Instituto de Neurociencias (CSIC-UMH)
    University of Navarra)

  • Ana Domingo-Muelas

    (Universidad de Valencia
    Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)
    Carlos Simon Foundation
    University of Pennsylvania)

  • Estefania Mancini

    (The Barcelona Institute of Science and Technology)

  • Joan Galcerán

    (Instituto de Neurociencias (CSIC-UMH)
    Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER))

  • Juan Valcárcel

    (The Barcelona Institute of Science and Technology
    Universitat Pompeu Fabra (UPF)
    Institució Catalana de Recerca i Estudis Avançats (ICREA))

  • Isabel Fariñas

    (Universidad de Valencia
    Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED))

  • M. Angela Nieto

    (Instituto de Neurociencias (CSIC-UMH)
    Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER))

Abstract

The adult mammalian brain retains some capacity to replenish neurons and glia, holding promise for brain regeneration. Thus, understanding the mechanisms controlling adult neural stem cell (NSC) differentiation is crucial. Paradoxically, adult NSCs in the subependymal zone transcribe genes associated with both multipotency maintenance and neural differentiation, but the mechanism that prevents conflicts in fate decisions due to these opposing transcriptional programmes is unknown. Here we describe intron detention as such control mechanism. In NSCs, while multiple mRNAs from stemness genes are spliced and exported to the cytoplasm, transcripts from differentiation genes remain unspliced and detained in the nucleus, and the opposite is true under neural differentiation conditions. We also show that m6A methylation is the mechanism that releases intron detention and triggers nuclear export, enabling rapid and synchronized responses. m6A RNA methylation operates as an on/off switch for transcripts with antagonistic functions, tightly controlling the timing of NSCs commitment to differentiation.

Suggested Citation

  • Ainara González-Iglesias & Aida Arcas & Ana Domingo-Muelas & Estefania Mancini & Joan Galcerán & Juan Valcárcel & Isabel Fariñas & M. Angela Nieto, 2024. "Intron detention tightly regulates the stemness/differentiation switch in the adult neurogenic niche," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47092-z
    DOI: 10.1038/s41467-024-47092-z
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-47092-z
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-47092-z?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. Nian Liu & Qing Dai & Guanqun Zheng & Chuan He & Marc Parisien & Tao Pan, 2015. "N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions," Nature, Nature, vol. 518(7540), pages 560-564, February.
    2. Robert C. Spitale & Ryan A. Flynn & Qiangfeng Cliff Zhang & Pete Crisalli & Byron Lee & Jong-Wha Jung & Hannes Y. Kuchelmeister & Pedro J. Batista & Eduardo A. Torre & Eric T. Kool & Howard Y. Chang, 2015. "Structural imprints in vivo decode RNA regulatory mechanisms," Nature, Nature, vol. 519(7544), pages 486-490, March.
    3. Emily M. Harcourt & Anna M. Kietrys & Eric T. Kool, 2017. "Chemical and structural effects of base modifications in messenger RNA," Nature, Nature, vol. 541(7637), pages 339-346, January.
    4. Robert C. Spitale & Ryan A. Flynn & Qiangfeng Cliff Zhang & Pete Crisalli & Byron Lee & Jong-Wha Jung & Hannes Y. Kuchelmeister & Pedro J. Batista & Eduardo A. Torre & Eric T. Kool & Howard Y. Chang, 2015. "Erratum: Structural imprints in vivo decode RNA regulatory mechanisms," Nature, Nature, vol. 527(7577), pages 264-264, November.
    5. Avni Baser & Maxim Skabkin & Susanne Kleber & Yonglong Dang & Gülce S. Gülcüler Balta & Georgios Kalamakis & Manuel Göpferich & Damian Carvajal Ibañez & Roman Schefzik & Alejandro Santos Lopez & Enric, 2019. "Onset of differentiation is post-transcriptionally controlled in adult neural stem cells," Nature, Nature, vol. 566(7742), pages 100-104, February.
    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. Ryan Damme & Kongpan Li & Minjie Zhang & Jianhui Bai & Wilson H. Lee & Joseph D. Yesselman & Zhipeng Lu & Willem A. Velema, 2022. "Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Haoran Zhu & Yuning Yang & Yunhe Wang & Fuzhou Wang & Yujian Huang & Yi Chang & Ka-chun Wong & Xiangtao Li, 2023. "Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    3. Bo Yu & Pan Li & Qiangfeng Cliff Zhang & Lin Hou, 2022. "Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    4. Sepideh Tavakoli & Mohammad Nabizadeh & Amr Makhamreh & Howard Gamper & Caroline A. McCormick & Neda K. Rezapour & Ya-Ming Hou & Meni Wanunu & Sara H. Rouhanifard, 2023. "Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    5. Gongwang Yu & Yao Liu & Zizhang Li & Shuyun Deng & Zhuoxing Wu & Xiaoyu Zhang & Wenbo Chen & Junnan Yang & Xiaoshu Chen & Jian-Rong Yang, 2023. "Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    6. Shurong Liu & Junhong Huang & Jie Zhou & Siyan Chen & Wujian Zheng & Chang Liu & Qiao Lin & Ping Zhang & Di Wu & Simeng He & Jiayi Ye & Shun Liu & Keren Zhou & Bin Li & Lianghu Qu & Jianhua Yang, 2024. "NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    7. Tammy C. T. Lan & Matty F. Allan & Lauren E. Malsick & Jia Z. Woo & Chi Zhu & Fengrui Zhang & Stuti Khandwala & Sherry S. Y. Nyeo & Yu Sun & Junjie U. Guo & Mark Bathe & Anders Näär & Anthony Griffith, 2022. "Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    8. Harshita Sharma & Matthew N. Z. Valentine & Naoko Toki & Hiromi Nishiyori Sueki & Stefano Gustincich & Hazuki Takahashi & Piero Carninci, 2024. "Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    9. Jasmin Bartl & Marco Zanini & Flavia Bernardi & Antoine Forget & Lena Blümel & Julie Talbot & Daniel Picard & Nan Qin & Gabriele Cancila & Qingsong Gao & Soumav Nath & Idriss Mahoungou Koumba & Mariet, 2022. "The HHIP-AS1 lncRNA promotes tumorigenicity through stabilization of dynein complex 1 in human SHH-driven tumors," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    10. Zhangli Su & Ida Monshaugen & Briana Wilson & Fengbin Wang & Arne Klungland & Rune Ougland & Anindya Dutta, 2022. "TRMT6/61A-dependent base methylation of tRNA-derived fragments regulates gene-silencing activity and the unfolded protein response in bladder cancer," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    11. Zhiyuan Luo & Qilian Ma & Shan Sun & Ningning Li & Hongfeng Wang & Zheng Ying & Shengdong Ke, 2023. "Exon-intron boundary inhibits m6A deposition, enabling m6A distribution hallmark, longer mRNA half-life and flexible protein coding," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    12. Pierre Sabatier & Christian M. Beusch & Amir A. Saei & Mike Aoun & Noah Moruzzi & Ana Coelho & Niels Leijten & Magnus Nordenskjöld & Patrick Micke & Diana Maltseva & Alexander G. Tonevitsky & Vincent , 2021. "An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    13. Maciej Bak & Erik Nimwegen & Ian U. Kouzel & Tamer Gur & Ralf Schmidt & Mihaela Zavolan & Andreas J. Gruber, 2024. "MAPP unravels frequent co-regulation of splicing and polyadenylation by RNA-binding proteins and their dysregulation in cancer," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    14. Xiaochuan Liu & Hao Chen & Zekun Li & Xiaoxiao Yang & Wen Jin & Yuting Wang & Jian Zheng & Long Li & Chenghao Xuan & Jiapei Yuan & Yang Yang, 2024. "InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    15. Ana Domingo-Muelas & Pere Duart-Abadia & Jose Manuel Morante-Redolat & Antonio Jordán-Pla & Germán Belenguer & Jaime Fabra-Beser & Lucía Paniagua-Herranz & Ana Pérez-Villalba & Adrián Álvarez-Varela &, 2023. "Post-transcriptional control of a stemness signature by RNA-binding protein MEX3A regulates murine adult neurogenesis," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    16. Katja Hartstock & Nadine A. Kueck & Petr Spacek & Anna Ovcharenko & Sabine Hüwel & Nicolas V. Cornelissen & Amarnath Bollu & Christoph Dieterich & Andrea Rentmeister, 2023. "MePMe-seq: antibody-free simultaneous m6A and m5C mapping in mRNA by metabolic propargyl labeling and sequencing," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    17. Cristina Leoni & Marian Bataclan & Taku Ito-Kureha & Vigo Heissmeyer & Silvia Monticelli, 2023. "The mRNA methyltransferase Mettl3 modulates cytokine mRNA stability and limits functional responses in mast cells," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    18. Elzbieta Kierzek & Xiaoju Zhang & Richard M. Watson & Scott D. Kennedy & Marta Szabat & Ryszard Kierzek & David H. Mathews, 2022. "Secondary structure prediction for RNA sequences including N6-methyladenosine," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    19. Jibin Abraham Punnoose & Kevin J. Thomas & Arun Richard Chandrasekaran & Javier Vilcapoma & Andrew Hayden & Kacey Kilpatrick & Sweta Vangaveti & Alan Chen & Thomas Banco & Ken Halvorsen, 2023. "High-throughput single-molecule quantification of individual base stacking energies in nucleic acids," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    20. Weiwei Dai & Ruotong Tian & Liubing Yu & Shasha Bian & Yuling Chen & Bowen Yin & Yuxuan Luan & Siqi Chen & Zhuoyang Fan & Rucheng Yan & Xin Pan & Yingyong Hou & Rong Li & Juxiang Chen & Minfeng Shu, 2024. "Overcoming therapeutic resistance in oncolytic herpes virotherapy by targeting IGF2BP3-induced NETosis in malignant glioma," Nature Communications, Nature, vol. 15(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:15:y:2024:i:1:d:10.1038_s41467-024-47092-z. 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.