PRD-2 directly regulates casein kinase I and counteracts nonsense mediated decay in the Neurospora circadian clock

  1. Christina M Kelliher
  2. Randy Lambreghts
  3. Qijun Xiang
  4. Christopher L Baker
  5. Jennifer J Loros
  6. Jay C Dunlap  Is a corresponding author
  1. Geisel School of Medicine at Dartmouth, United States
  2. The Jackson Laboratory, United States

Abstract

Circadian clocks in fungi and animals are driven by a functionally conserved transcription-translation feedback loop. In Neurospora crassa, negative feedback is executed by a complex of Frequency (FRQ), FRQ-interacting RNA helicase (FRH), and Casein Kinase I (CKI), which inhibits the activity of the clock's positive arm, the White Collar Complex (WCC). Here, we show that the prd-2 (period-2) gene, whose mutation is characterized by recessive inheritance of a long 26-hour period phenotype, encodes an RNA-binding protein that stabilizes the ck-1a transcript, resulting in CKI protein levels sufficient for normal rhythmicity. Moreover, by examining the molecular basis for the short circadian period of upf-1prd-6 mutants, we uncovered a strong influence of the Nonsense Mediated Decay pathway on CKI levels. The finding that circadian period defects in two classically-derived Neurospora clock mutants each arise from disruption of ck-1a regulation is consistent with circadian period being exquisitely sensitive to levels of casein kinase I.

Data availability

RNA-Sequencing data have been deposited in GEO under accession GSE155999

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Christina M Kelliher

    Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4554-1818
  2. Randy Lambreghts

    Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Qijun Xiang

    Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Christopher L Baker

    Genetics and Genomics, The Jackson Laboratory, Bar Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Jennifer J Loros

    Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Jay C Dunlap

    Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, United States
    For correspondence
    jay.dunlap@Dartmouth.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1577-0457

Funding

National Institutes of Health (F32 GM128252)

  • Christina M Kelliher

National Institutes of Health (R35 GM118021)

  • Jay C Dunlap

National Institutes of Health (R35 GM118022)

  • Jennifer J Loros

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

Reviewing Editor

  1. Detlef Weigel, Max Planck Institute for Developmental Biology, Germany

Publication history

  1. Received: October 14, 2020
  2. Accepted: December 8, 2020
  3. Accepted Manuscript published: December 9, 2020 (version 1)
  4. Version of Record published: December 17, 2020 (version 2)
  5. Version of Record updated: December 23, 2020 (version 3)

Copyright

© 2020, Kelliher 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

  • 856
    Page views
  • 128
    Downloads
  • 2
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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. Christina M Kelliher
  2. Randy Lambreghts
  3. Qijun Xiang
  4. Christopher L Baker
  5. Jennifer J Loros
  6. Jay C Dunlap
(2020)
PRD-2 directly regulates casein kinase I and counteracts nonsense mediated decay in the Neurospora circadian clock
eLife 9:e64007.
https://doi.org/10.7554/eLife.64007

Further reading

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics
    Bethany Sump et al.
    Research Article

    For some inducible genes, the rate and molecular mechanism of transcriptional activation depends on the prior experiences of the cell. This phenomenon, called epigenetic transcriptional memory, accelerates reactivation and requires both changes in chromatin structure and recruitment of poised RNA Polymerase II (RNAPII) to the promoter. Memory of inositol starvation in budding yeast involves a positive feedback loop between transcription factor-dependent interaction with the nuclear pore complex and histone H3 lysine 4 dimethylation (H3K4me2). While H3K4me2 is essential for recruitment of RNAPII and faster reactivation, RNAPII is not required for H3K4me2. Unlike RNAPII-dependent H3K4me2 associated with transcription, RNAPII-independent H3K4me2 requires Nup100, SET3C, the Leo1 subunit of the Paf1 complex and, upon degradation of an essential transcription factor, is inherited through multiple cell cycles. The writer of this mark (COMPASS) physically interacts with the potential reader (SET3C), suggesting a molecular mechanism for the spreading and re-incorporation of H3K4me2 following DNA replication.

    1. Genetics and Genomics
    2. Neuroscience
    Alyssa J Lawler et al.
    Tools and Resources

    Recent discoveries of extreme cellular diversity in the brain warrant rapid development of technologies to access specific cell populations within heterogeneous tissue. Available approaches for engineering-targeted technologies for new neuron subtypes are low yield, involving intensive transgenic strain or virus screening. Here, we present Specific Nuclear-Anchored Independent Labeling (SNAIL), an improved virus-based strategy for cell labeling and nuclear isolation from heterogeneous tissue. SNAIL works by leveraging machine learning and other computational approaches to identify DNA sequence features that confer cell type-specific gene activation and then make a probe that drives an affinity purification-compatible reporter gene. As a proof of concept, we designed and validated two novel SNAIL probes that target parvalbumin-expressing (PV+) neurons. Nuclear isolation using SNAIL in wild-type mice is sufficient to capture characteristic open chromatin features of PV+ neurons in the cortex, striatum, and external globus pallidus. The SNAIL framework also has high utility for multispecies cell probe engineering; expression from a mouse PV+ SNAIL enhancer sequence was enriched in PV+ neurons of the macaque cortex. Expansion of this technology has broad applications in cell type-specific observation, manipulation, and therapeutics across species and disease models.