Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation during Drosophila development

  1. Li Zhou
  2. Mandy YT Lim
  3. Prameet Kaur
  4. Abil Saj
  5. Diane Bortolamiol-Becet
  6. Vikneswaran Gopal
  7. Nicholas Tolwinski
  8. Greg Tucker-Kellogg
  9. Katsutomo Okamura  Is a corresponding author
  1. National University of Singapore, Singapore
  2. Yale-NUS College, Singapore
  3. Genome Institute of Singapore, Singapore
  4. Sloan-Kettering Institute, United States

Abstract

Mature microRNAs (miRNAs) are processed from primary transcripts (pri-miRNAs), and their expression is controlled at transcriptional and post-transcriptional levels. However, how regulation at multiple levels achieves precise control remains elusive. Using published and new datasets, we profile a time course of mature and pri-miRNAs in Drosophila embryos and reveal the dynamics of miRNA production and degradation as well as dynamic changes in pri-miRNA isoform selection. We found that 5' nucleotides influence stability of mature miRNAs. Furthermore, distinct half-lives of miRNAs from the mir-309 cluster shape their temporal expression patterns, and the importance of rapid degradation of the miRNAs in gene regulation is detected as distinct evolutionary signatures at the target sites in the transcriptome. Finally, we show that rapid degradation of miR-3/-309 may be important for regulation of the planar cell polarity pathway component Vang. Altogether, the results suggest that complex mechanisms regulate miRNA expression to support normal development.

Data availability

The small RNA library data produced for this study are deposited at NCBI SRA under SRP109269.

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

Article and author information

Author details

  1. Li Zhou

    Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  2. Mandy YT Lim

    Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  3. Prameet Kaur

    Division of Science, Yale-NUS College, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  4. Abil Saj

    Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  5. Diane Bortolamiol-Becet

    Department of Developmental Biology, Sloan-Kettering Institute, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Vikneswaran Gopal

    Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  7. Nicholas Tolwinski

    Department of Biological Sciences, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  8. Greg Tucker-Kellogg

    Department of Biological Sciences, National University of Singapore, Singapore, Singapore
    Competing interests
    The authors declare that no competing interests exist.
  9. Katsutomo Okamura

    Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
    For correspondence
    okamurak@tll.org.sg
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8316-0960

Funding

National Research Foundation Singapore (NRF2011NRF-NRFF001-042)

  • Li Zhou
  • Mandy YT Lim
  • Katsutomo Okamura

National Institutes of Health (R01-GM083300)

  • Diane Bortolamiol-Becet

Ministry of Education - Singapore (MOE2014-T2-2-039)

  • Nicholas Tolwinski

National University of Singapore (R-154-000-536-133)

  • Greg Tucker-Kellogg

National Institutes of Health (R01-NS083833)

  • Diane Bortolamiol-Becet

National University of Singapore (R-154-000-562-112)

  • Greg Tucker-Kellogg

National University of Singapore (R-154-000-582-651)

  • Greg Tucker-Kellogg

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

Copyright

© 2018, Zhou 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

  • 5,865
    views
  • 565
    downloads
  • 36
    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. Li Zhou
  2. Mandy YT Lim
  3. Prameet Kaur
  4. Abil Saj
  5. Diane Bortolamiol-Becet
  6. Vikneswaran Gopal
  7. Nicholas Tolwinski
  8. Greg Tucker-Kellogg
  9. Katsutomo Okamura
(2018)
Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation during Drosophila development
eLife 7:e38389.
https://doi.org/10.7554/eLife.38389

Share this article

https://doi.org/10.7554/eLife.38389

Further reading

    1. Chromosomes and Gene Expression
    2. Neuroscience
    Robyn D Moir, Emilio Merheb ... Ian M Willis
    Research Article

    Pathogenic variants in subunits of RNA polymerase (Pol) III cause a spectrum of Polr3-related neurodegenerative diseases including 4H leukodystrophy. Disease onset occurs from infancy to early adulthood and is associated with a variable range and severity of neurological and non-neurological features. The molecular basis of Polr3-related disease pathogenesis is unknown. We developed a postnatal whole-body mouse model expressing pathogenic Polr3a mutations to examine the molecular mechanisms by which reduced Pol III transcription results primarily in central nervous system phenotypes. Polr3a mutant mice exhibit behavioral deficits, cerebral pathology and exocrine pancreatic atrophy. Transcriptome and immunohistochemistry analyses of cerebra during disease progression show a reduction in most Pol III transcripts, induction of innate immune and integrated stress responses and cell-type-specific gene expression changes reflecting neuron and oligodendrocyte loss and microglial activation. Earlier in the disease when integrated stress and innate immune responses are minimally induced, mature tRNA sequencing revealed a global reduction in tRNA levels and an altered tRNA profile but no changes in other Pol III transcripts. Thus, changes in the size and/or composition of the tRNA pool have a causal role in disease initiation. Our findings reveal different tissue- and brain region-specific sensitivities to a defect in Pol III transcription.

    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression
    Ting-Wen Chen, Hsiao-Wei Liao ... Chung-Te Chang
    Research Article

    The mRNA 5'-cap structure removal by the decapping enzyme DCP2 is a critical step in gene regulation. While DCP2 is the catalytic subunit in the decapping complex, its activity is strongly enhanced by multiple factors, particularly DCP1, which is the major activator in yeast. However, the precise role of DCP1 in metazoans has yet to be fully elucidated. Moreover, in humans, the specific biological functions of the two DCP1 paralogs, DCP1a and DCP1b, remain largely unknown. To investigate the role of human DCP1, we generated cell lines that were deficient in DCP1a, DCP1b, or both to evaluate the importance of DCP1 in the decapping machinery. Our results highlight the importance of human DCP1 in decapping process and show that the EVH1 domain of DCP1 enhances the mRNA-binding affinity of DCP2. Transcriptome and metabolome analyses outline the distinct functions of DCP1a and DCP1b in human cells, regulating specific endogenous mRNA targets and biological processes. Overall, our findings provide insights into the molecular mechanism of human DCP1 in mRNA decapping and shed light on the distinct functions of its paralogs.