1. Chromosomes and Gene Expression
  2. Neuroscience
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Striking circadian neuron diversity and cycling of Drosophila alternative splicing

  1. Qingqing Wang
  2. Katharine C Abruzzi  Is a corresponding author
  3. Michael Rosbash
  4. Donald C Rio  Is a corresponding author
  1. University of California, Berkeley, United States
  2. Howard Hughes Medical Institute, Brandeis University, United States
Research Article
  • Cited 15
  • Views 2,570
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Cite this article as: eLife 2018;7:e35618 doi: 10.7554/eLife.35618

Abstract

Although alternative pre-mRNA splicing (AS) significantly diversifies the neuronal proteome, the extent of AS is still unknown due in part to the large number of diverse cell types in the brain. To address this complexity issue, we used an annotation-free computational method to analyze and compare the AS profiles between small specific groups of Drosophila circadian neurons. The method, the Junction Usage Model (JUM), allows the comprehensive profiling of both known and novel AS events from specific RNA-seq libraries. The results show that many diverse and novel pre-mRNA isoforms are preferentially expressed in one class of clock neuron and also absent from the more standard Drosophila head RNA preparation. These AS events are enriched in potassium channels important for neuronal firing, and there are also cycling isoforms with no detectable underlying transcriptional oscillations. The results suggest massive AS regulation in the brain that is also likely important for circadian regulation.

Data availability

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

The following previously published data sets were used

Article and author information

Author details

  1. Qingqing Wang

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Katharine C Abruzzi

    Department of Biology, National Center of Behavioral Genomics, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    For correspondence
    katea@brandeis.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3949-3095
  3. Michael Rosbash

    Department of Biology, National Center of Behavioral Genomics, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3366-1780
  4. Donald C Rio

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    For correspondence
    don_rio@berkeley.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4775-3515

Funding

Arnold and Mabel Beckman Foundation (Postdoctoral Fellowship)

  • Qingqing Wang

Howard Hughes Medical Institute

  • Michael Rosbash

National Institutes of Health (R01GM097352)

  • Donald C Rio

National Institutes of Health (R35GM118121)

  • Donald C Rio

National Institutes of Health (NIH P50102706)

  • Donald C Rio

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

Reviewing Editor

  1. Joseph S Takahashi, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, United States

Publication history

  1. Received: February 1, 2018
  2. Accepted: May 31, 2018
  3. Accepted Manuscript published: June 4, 2018 (version 1)
  4. Version of Record published: June 29, 2018 (version 2)

Copyright

© 2018, Wang 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.

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