Spliceosome factors target timeless (tim) mRNA to control clock protein accumulation and circadian behavior in Drosophila

Elife. 2018 Dec 5:7:e39821. doi: 10.7554/eLife.39821.


Transcription-translation feedback loops that comprise eukaryotic circadian clocks rely upon temporal delays that separate the phase of active transcription of clock genes, such as Drosophila period (per) and timeless (tim), from negative feedback by the two proteins. However, our understanding of the mechanisms involved is incomplete. Through an RNA interference screen, we found that pre-mRNA processing 4 (PRP4) kinase, a component of the U4/U5.U6 triple small nuclear ribonucleoprotein (tri-snRNP) spliceosome, and other tri-snRNP components regulate cycling of the molecular clock as well as rest:activity rhythms. Unbiased RNA-Sequencing uncovered an alternatively spliced intron in tim whose increased retention upon prp4 downregulation leads to decreased TIM levels. We demonstrate that the splicing of tim is rhythmic with a phase that parallels delayed accumulation of the protein in a 24 hr cycle. We propose that alternative splicing constitutes an important clock mechanism for delaying the daily accumulation of clock proteins, and thereby negative feedback by them.

Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).

Keywords: D. melanogaster; Drosophila; circadian rhythms; feedback loop; genetics; genomics; molecular clock; splicing; timeless.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • CLOCK Proteins / genetics*
  • CLOCK Proteins / metabolism
  • Circadian Clocks / genetics
  • Circadian Rhythm / genetics
  • Drosophila Proteins / genetics*
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / genetics*
  • Drosophila melanogaster / metabolism
  • Exons
  • Feedback, Physiological*
  • Introns
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Period Circadian Proteins / genetics
  • Period Circadian Proteins / metabolism
  • Protein Serine-Threonine Kinases / genetics
  • Protein Serine-Threonine Kinases / metabolism
  • RNA Splicing*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Ribonucleoproteins, Small Nuclear / genetics
  • Ribonucleoproteins, Small Nuclear / metabolism
  • Sequence Analysis, RNA
  • Signal Transduction
  • Spliceosomes / genetics*
  • Spliceosomes / metabolism


  • Clk protein, Drosophila
  • Drosophila Proteins
  • Nuclear Proteins
  • PER protein, Drosophila
  • Period Circadian Proteins
  • RNA, Messenger
  • Ribonucleoproteins, Small Nuclear
  • tim protein, Drosophila
  • CLOCK Proteins
  • CG7028 protein, Drosophila
  • Protein Serine-Threonine Kinases