IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v11y2020i1d10.1038_s41467-020-15634-w.html
   My bibliography  Save this article

Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome

Author

Listed:
  • Marina Reixachs-Solé

    (Australian National University
    EMBL Australia Partner Laboratory Network at the Australian National University)

  • Jorge Ruiz-Orera

    (Max Delbrück Center for Molecular Medicine in the Helmholtz Association)

  • M. Mar Albà

    (IMIM - Hospital del Mar Medical Research Institute
    Catalan Institution for Research and Advanced Studies
    Pompeu Fabra University)

  • Eduardo Eyras

    (Australian National University
    EMBL Australia Partner Laboratory Network at the Australian National University
    IMIM - Hospital del Mar Medical Research Institute
    Catalan Institution for Research and Advanced Studies)

Abstract

The differential production of transcript isoforms from gene loci is a key cellular mechanism. Yet, its impact in protein production remains an open question. Here, we describe ORQAS (ORF quantification pipeline for alternative splicing), a pipeline for the translation quantification of individual transcript isoforms using ribosome-protected mRNA fragments (ribosome profiling). We find evidence of translation for 40–50% of the expressed isoforms in human and mouse, with 53% of the expressed genes having more than one translated isoform in human, and 33% in mouse. Differential splicing analysis revealed that about 40% of the splicing changes at RNA level are concordant with changes in translation. Furthermore, orthologous cassette exons between human and mouse preserve the directionality of the change, and are enriched in microexons in a comparison between glia and glioma. ORQAS leverages ribosome profiling to uncover a widespread and evolutionarily conserved impact of differential splicing on translation, particularly of microexon-containing isoforms.

Suggested Citation

  • Marina Reixachs-Solé & Jorge Ruiz-Orera & M. Mar Albà & Eduardo Eyras, 2020. "Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15634-w
    DOI: 10.1038/s41467-020-15634-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-020-15634-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-020-15634-w?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
    ---><---

    Citations

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


    Cited by:

    1. Kyung Ah Han & Taek-Han Yoon & Jinhu Kim & Jusung Lee & Ju Yeon Lee & Gyubin Jang & Ji Won Um & Jong Kyoung Kim & Jaewon Ko, 2024. "Specification of neural circuit architecture shaped by context-dependent patterned LAR-RPTP microexons," Nature Communications, Nature, vol. 15(1), pages 1-21, 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:11:y:2020:i:1:d:10.1038_s41467-020-15634-w. 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.

    We have no bibliographic references for this item. You can help adding them by using 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.