IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-46850-3.html
   My bibliography  Save this article

Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona

Author

Listed:
  • Lenny J. Negrón-Piñeiro

    (New York University College of Dentistry)

  • Yushi Wu

    (New York University College of Dentistry)

  • Sydney Popsuj

    (Georgia Institute of Technology)

  • Diana S. José-Edwards

    (Washington University)

  • Alberto Stolfi

    (Georgia Institute of Technology)

  • Anna Di Gregorio

    (New York University College of Dentistry)

Abstract

Tissue-specific gene expression is fundamental in development and evolution, and is mediated by transcription factors and by the cis-regulatory regions (enhancers) that they control. Transcription factors and their respective tissue-specific enhancers are essential components of gene regulatory networks responsible for the development of tissues and organs. Although numerous transcription factors have been characterized from different organisms, the knowledge of the enhancers responsible for their tissue-specific expression remains fragmentary. Here we use Ciona to study the enhancers associated with ten transcription factors expressed in the notochord, an evolutionary hallmark of the chordate phylum. Our results illustrate how two evolutionarily conserved transcription factors, Brachyury and Foxa2, coordinate the deployment of other notochord transcription factors. The results of these detailed cis-regulatory analyses delineate a high-resolution view of the essential notochord gene regulatory network of Ciona, and provide a reference for studies of transcription factors, enhancers, and their roles in development, disease, and evolution.

Suggested Citation

  • Lenny J. Negrón-Piñeiro & Yushi Wu & Sydney Popsuj & Diana S. José-Edwards & Alberto Stolfi & Anna Di Gregorio, 2024. "Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46850-3
    DOI: 10.1038/s41467-024-46850-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-46850-3
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-46850-3?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. Frédéric Delsuc & Henner Brinkmann & Daniel Chourrout & Hervé Philippe, 2006. "Tunicates and not cephalochordates are the closest living relatives of vertebrates," Nature, Nature, vol. 439(7079), pages 965-968, February.
    2. Alexander M. Tsankov & Hongcang Gu & Veronika Akopian & Michael J. Ziller & Julie Donaghey & Ido Amit & Andreas Gnirke & Alexander Meissner, 2015. "Transcription factor binding dynamics during human ES cell differentiation," Nature, Nature, vol. 518(7539), pages 344-349, 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. Jerry S Chen & Abygail M Gumbayan & Robert W Zeller & Joseph M Mahaffy, 2014. "An Expanded Notch-Delta Model Exhibiting Long-Range Patterning and Incorporating MicroRNA Regulation," PLOS Computational Biology, Public Library of Science, vol. 10(6), pages 1-21, June.
    2. Ishtiaque Hossain & Pierre Priam & Sofia C. Reynoso & Sahil Sahni & Xiao X. Zhang & Laurence Côté & Joelle Doumat & Candus Chik & Tianxin Fu & Julie A. Lessard & William A. Pastor, 2024. "ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Francesco Panariello & Onelia Gagliano & Camilla Luni & Antonio Grimaldi & Silvia Angiolillo & Wei Qin & Anna Manfredi & Patrizia Annunziata & Shaked Slovin & Lorenzo Vaccaro & Sara Riccardo & Valenti, 2023. "Cellular population dynamics shape the route to human pluripotency," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    4. Karma Nanglu & Rudy Lerosey-Aubril & James C. Weaver & Javier Ortega-Hernández, 2023. "A mid-Cambrian tunicate and the deep origin of the ascidiacean body plan," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    5. Pedro Madrigal & Siwei Deng & Yuliang Feng & Stefania Militi & Kim Jee Goh & Reshma Nibhani & Rodrigo Grandy & Anna Osnato & Daniel Ortmann & Stephanie Brown & Siim Pauklin, 2023. "Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    6. Guang Li & ZongHuang Shu & Yiquan Wang, 2013. "Year-Round Reproduction and Induced Spawning of Chinese Amphioxus, Branchiostoma belcheri, in Laboratory," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-1, September.
    7. Anat Kreimer & Tal Ashuach & Fumitaka Inoue & Alex Khodaverdian & Chengyu Deng & Nir Yosef & Nadav Ahituv, 2022. "Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    8. Seth Teague & Gillian Primavera & Bohan Chen & Zong-Yuan Liu & LiAng Yao & Emily Freeburne & Hina Khan & Kyoung Jo & Craig Johnson & Idse Heemskerk, 2024. "Time-integrated BMP signaling determines fate in a stem cell model for early human development," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    9. Yanting Luo & Jianlin He & Xiguang Xu & Ming-an Sun & Xiaowei Wu & Xuemei Lu & Hehuang Xie, 2018. "Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells," PLOS Computational Biology, Public Library of Science, vol. 14(3), pages 1-21, March.
    10. Qiliang Ding & Matthew M. Edwards & Ning Wang & Xiang Zhu & Alexa N. Bracci & Michelle L. Hulke & Ya Hu & Yao Tong & Joyce Hsiao & Christine J. Charvet & Sulagna Ghosh & Robert E. Handsaker & Kevin Eg, 2021. "The genetic architecture of DNA replication timing in human pluripotent stem cells," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    11. M S Vijayabaskar & Debbie K Goode & Nadine Obier & Monika Lichtinger & Amber M L Emmett & Fatin N Zainul Abidin & Nisar Shar & Rebecca Hannah & Salam A Assi & Michael Lie-A-Ling & Berthold Gottgens & , 2019. "Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets," PLOS Computational Biology, Public Library of Science, vol. 15(11), pages 1-29, November.
    12. Xavier Grau-Bové & Lucie Subirana & Lydvina Meister & Anaël Soubigou & Ana Neto & Anamaria Elek & Silvia Naranjo & Oscar Fornas & Jose Luis Gomez-Skarmeta & Juan J. Tena & Manuel Irimia & Stéphanie Be, 2024. "An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    13. R Prasobh & Narayanan Manoj, 2009. "The Repertoire of Heterotrimeric G Proteins and RGS Proteins in Ciona intestinalis," PLOS ONE, Public Library of Science, vol. 4(10), pages 1-11, October.
    14. Ke Shui & Chenwei Wang & Xuedi Zhang & Shanshan Ma & Qinyu Li & Wanshan Ning & Weizhi Zhang & Miaomiao Chen & Di Peng & Hui Hu & Zheng Fang & Anyuan Guo & Guanjun Gao & Mingliang Ye & Luoying Zhang & , 2023. "Small-sample learning reveals propionylation in determining global protein homeostasis," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    15. Elizabeth D. Larson & Hideyuki Komori & Tyler J. Gibson & Cyrina M. Ostgaard & Danielle C. Hamm & Jack M. Schnell & Cheng-Yu Lee & Melissa M. Harrison, 2021. "Cell-type-specific chromatin occupancy by the pioneer factor Zelda drives key developmental transitions in Drosophila," Nature Communications, Nature, vol. 12(1), pages 1-17, 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_s41467-024-46850-3. 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.