Abstract

Most studies of cohesin function consider the Stromalin Antigen (STAG/SA) proteins as core complex members given their ubiquitous interaction with the cohesin ring. Here, we provide functional data to support the notion that the SA subunit is not a mere passenger in this structure, but instead plays a key role in the localization of cohesin to diverse biological processes and promotes loading of the complex at these sites. We show that in cells acutely depleted for RAD21, SA proteins remain bound to chromatin, cluster in 3D and interact with CTCF, as well as with a wide range of RNA binding proteins involved in multiple RNA processing mechanisms. Accordingly, SA proteins interact with RNA, RNA binding proteins and R-loops, even in the absence of cohesin. Our results place SA1 on chromatin upstream of the cohesin ring and reveal a role for SA1 in cohesin loading which is independent of NIPBL, the canonical cohesin loader. We propose that SA1 takes advantage of structural R-loop platforms to link cohesin loading and chromatin structure with diverse functions. Since SA proteins are pan-cancer targets, and R-loops play an increasingly prevalent role in cancer biology, our results have important implications for the mechanistic understanding of SA proteins in cancer and disease.

Data availability

All data has been made freely available. Please see Page 21 of the manuscript for Accession numbers.

The following data sets were generated

Article and author information

Author details

  1. Hayley Porter

    Research Department of Cancer Biology, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Yang Li

    Research Department of Cancer Biology, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Maria Victoria  Neguembor

    Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1583-1304
  4. Manuel Beltran

    Regulatory Genomics Group, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Wazeer Varsally

    Research Department of Cancer Biology, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Laura Martin

    Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8801-6637
  7. Manuel Tavares Cornejo

    Regulatory Genomics Group, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  8. Dubravka Pezic

    Research Department of Cancer Biology, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  9. Amandeep Bhamra

    Proteomics Research, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  10. Silvia Surinova

    Proteomics Research, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  11. Richard G Jenner

    Regulatory Genomics Group, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  12. Maria Pia Cosma

    Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4207-5097
  13. Suzana Hadjur

    Research Department of Cancer Biology, University College London, London, United Kingdom
    For correspondence
    s.hadjur@ucl.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3146-3118

Funding

Wellcome Trust (106985/Z/15/Z)

  • Suzana Hadjur

Cancer Research UK (PhD studentship)

  • Hayley Porter

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2023, Porter et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,796
    views
  • 502
    downloads
  • 19
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Hayley Porter
  2. Yang Li
  3. Maria Victoria  Neguembor
  4. Manuel Beltran
  5. Wazeer Varsally
  6. Laura Martin
  7. Manuel Tavares Cornejo
  8. Dubravka Pezic
  9. Amandeep Bhamra
  10. Silvia Surinova
  11. Richard G Jenner
  12. Maria Pia Cosma
  13. Suzana Hadjur
(2023)
Cohesin-independent STAG proteins interact with RNA and R-loops and promote complex loading
eLife 12:e79386.
https://doi.org/10.7554/eLife.79386

Share this article

https://doi.org/10.7554/eLife.79386

Further reading

    1. Cell Biology
    Kaili Du, Hongyu Chen ... Dan Li
    Research Article

    Niemann–Pick disease type C (NPC) is a devastating lysosomal storage disease characterized by abnormal cholesterol accumulation in lysosomes. Currently, there is no treatment for NPC. Transcription factor EB (TFEB), a member of the microphthalmia transcription factors (MiTF), has emerged as a master regulator of lysosomal function and promoted the clearance of substrates stored in cells. However, it is not known whether TFEB plays a role in cholesterol clearance in NPC disease. Here, we show that transgenic overexpression of TFEB, but not TFE3 (another member of MiTF family) facilitates cholesterol clearance in various NPC1 cell models. Pharmacological activation of TFEB by sulforaphane (SFN), a previously identified natural small-molecule TFEB agonist by us, can dramatically ameliorate cholesterol accumulation in human and mouse NPC1 cell models. In NPC1 cells, SFN induces TFEB nuclear translocation via a ROS-Ca2+-calcineurin-dependent but MTOR-independent pathway and upregulates the expression of TFEB-downstream genes, promoting lysosomal exocytosis and biogenesis. While genetic inhibition of TFEB abolishes the cholesterol clearance and exocytosis effect by SFN. In the NPC1 mouse model, SFN dephosphorylates/activates TFEB in the brain and exhibits potent efficacy of rescuing the loss of Purkinje cells and body weight. Hence, pharmacological upregulating lysosome machinery via targeting TFEB represents a promising approach to treat NPC and related lysosomal storage diseases, and provides the possibility of TFEB agonists, that is, SFN as potential NPC therapeutic candidates.

    1. Cell Biology
    2. Developmental Biology
    Sarah Y Coomson, Salil A Lachke
    Insight

    A study in mice reveals key interactions between proteins involved in fibroblast growth factor signaling and how they contribute to distinct stages of eye lens development.