Cell-specific exon methylation and CTCF binding in neurons regulates calcium ion channel splicing and function

  1. Eduardo Javier López Soto
  2. Diane Lipscombe  Is a corresponding author
  1. Brown University, United States


Cell-specific alternative splicing modulates myriad cell functions and is disrupted in disease. The mechanisms governing alternative splicing are known for relatively few genes and typically focus on RNA splicing factors. In sensory neurons, cell-specific alternative splicing of the presynaptic CaV channel Cacna1b gene modulates opioid sensitivity. How this splicing is regulated is unknown. We find that cell and exon -specific DNA hypomethylation permits CTCF binding, the master regulator of mammalian chromatin structure, which, in turn, controls splicing in a DRG-derived cell line. In vivo, hypomethylation of an alternative exon specifically in nociceptors, likely permits CTCF binding and expression of CaV2.2 channel isoforms with increased opioid sensitivity in mice. Following nerve injury, exon methylation is increased, and splicing is disrupted. Our studies define the molecular mechanisms of cell-specific alternative splicing of a functionally validated exon in normal and disease states – and reveal a potential target for the treatment of chronic pain.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files.

Article and author information

Author details

  1. Eduardo Javier López Soto

    Neuroscience, Brown University, Providence, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Diane Lipscombe

    Neuroscience, Brown University, Providence, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7146-9119


National Institute of Neurological Disorders and Stroke (NS055251)

  • Diane Lipscombe

Warren Alpert Foundation

  • Eduardo Javier López Soto

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

Reviewing Editor

  1. David D Ginty, Harvard Medical School, United States


Animal experimentation: Mice were housed and bred at Brown University. All protocols and procedures were approved by the Brown University Institutional Animal Care and Use Committee (IACUC # 1706000275).Mice were anesthetized with 3% isoflurane, and all effort was made to minimize suffering.

Version history

  1. Received: January 6, 2020
  2. Accepted: March 26, 2020
  3. Accepted Manuscript published: March 26, 2020 (version 1)
  4. Version of Record published: April 3, 2020 (version 2)


© 2020, López Soto & Lipscombe

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.


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  1. Eduardo Javier López Soto
  2. Diane Lipscombe
Cell-specific exon methylation and CTCF binding in neurons regulates calcium ion channel splicing and function
eLife 9:e54879.

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