Multiplexed mRNA assembly into ribonucleoprotein particles plays an operon-like role in the control of yeast cell physiology

  1. Rohini R Nair
  2. Dimitry Zabezhinsky
  3. Rita Gelin-Licht
  4. Brian J Haas
  5. Michael CA Dyhr
  6. Hannah S Sperber
  7. Chad Nusbaum
  8. Jeffrey E Gerst  Is a corresponding author
  1. Weizmann Institute of Science, Israel
  2. Broad Institute of MIT and Harvard, United States

Abstract

Prokaryotes utilize polycistronic messages (operons) to co-translate proteins involved in the same biological processes. Whether eukaryotes achieve similar regulation by selectively assembling and translating monocistronic messages derived from different chromosomes is unknown. We employed transcript-specific RNA pulldowns and RNA-seq/RT-PCR to identify yeast mRNAs that co-precipitate as ribonucleoprotein (RNP) complexes. Consistent with the hypothesis of eukaryotic RNA operons, mRNAs encoding components of the mating pathway, heat shock proteins, and mitochondrial outer membrane proteins multiplex in trans, forming discrete mRNP complexes (called transperons). Chromatin-capture and allele tagging experiments reveal that genes encoding multiplexed mRNAs physically interact, thus, RNA assembly may result from co-regulated gene expression. Transperon assembly and function depends upon histone H4 and depletion leads to defects in RNA multiplexing, decreased pheromone responsiveness and mating, and increased heat shock sensitivity. We propose that intergenic associations and non-canonical histone H4 functions contribute to transperon formation in eukaryotic cells and regulate cell physiology.

Data availability

All data is available within the text, figures, and tables of the manuscript

Article and author information

Author details

  1. Rohini R Nair

    Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.
  2. Dimitry Zabezhinsky

    Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.
  3. Rita Gelin-Licht

    Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.
  4. Brian J Haas

    Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, United States
    Competing interests
    No competing interests declared.
  5. Michael CA Dyhr

    Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.
  6. Hannah S Sperber

    Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.
  7. Chad Nusbaum

    Technology Labs, Broad Institute of MIT and Harvard, Cambridge, MA, United States
    Competing interests
    Chad Nusbaum, Chad Nusbaum is affiliated with Cellarity Inc. The author has no financial interests to declare..
  8. Jeffrey E Gerst

    Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    For correspondence
    jeffrey.gerst@weizmann.ac.il
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8411-6881

Funding

German-Israeli Foundation for Scientific Research and Development (I-1190-96.13/2012)

  • Jeffrey E Gerst

Minerva Foundation (711130)

  • Jeffrey E Gerst

Astrachan Olga Klein Fund, Weizmann Institute

  • Jeffrey E Gerst

National Institutes of Health (NHGRI U54HG00306)

  • Chad Nusbaum

Israel Council of Higher Education

  • Rita Gelin-Licht

Israel Science Foundation (578/18)

  • Jeffrey E Gerst

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

Reviewing Editor

  1. Karsten Weis, ETH Zurich, Switzerland

Publication history

  1. Received: December 23, 2020
  2. Accepted: May 2, 2021
  3. Accepted Manuscript published: May 4, 2021 (version 1)
  4. Accepted Manuscript updated: May 7, 2021 (version 2)
  5. Version of Record published: May 20, 2021 (version 3)

Copyright

© 2021, Nair 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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  1. Rohini R Nair
  2. Dimitry Zabezhinsky
  3. Rita Gelin-Licht
  4. Brian J Haas
  5. Michael CA Dyhr
  6. Hannah S Sperber
  7. Chad Nusbaum
  8. Jeffrey E Gerst
(2021)
Multiplexed mRNA assembly into ribonucleoprotein particles plays an operon-like role in the control of yeast cell physiology
eLife 10:e66050.
https://doi.org/10.7554/eLife.66050

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    Patients with cardiomyopathy of Duchenne Muscular Dystrophy (DMD) are at risk of developing life-threatening arrhythmias, but the mechanisms are unknown. We aimed to determine the role of ion channels controlling cardiac excitability in the mechanisms of arrhythmias in DMD patients.

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    To test whether dystrophin mutations lead to defective cardiac NaV1.5–Kir2.1 channelosomes and arrhythmias, we generated iPSC-CMs from two hemizygous DMD males, a heterozygous female, and two unrelated control males. We conducted studies including confocal microscopy, protein expression analysis, patch-clamping, non-viral piggy-bac gene expression, optical mapping and contractility assays.

    Results:

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    Funding:

    Supported by National Institutes of Health R01 HL122352 grant; ‘la Caixa’ Banking Foundation (HR18-00304); Fundación La Marató TV3: Ayudas a la investigación en enfermedades raras 2020 (LA MARATO-2020); Instituto de Salud Carlos III/FEDER/FSE; Horizon 2020 - Research and Innovation Framework Programme GA-965286 to JJ; the CNIC is supported by the Instituto de Salud Carlos III (ISCIII), the Ministerio de Ciencia e Innovación (MCIN) and the Pro CNIC Foundation), and is a Severo Ochoa Center of Excellence (grant CEX2020-001041-S funded by MICIN/AEI/10.13039/501100011033). American Heart Association postdoctoral fellowship 19POST34380706s to JVEN. Israel Science Foundation to OB and MA [824/19]. Rappaport grant [01012020RI]; and Niedersachsen Foundation [ZN3452] to OB; US-Israel Binational Science Foundation (BSF) to OB and TH [2019039]; Dr. Bernard Lublin Donation to OB; and The Duchenne Parent Project Netherlands (DPPNL 2029771) to OB. National Institutes of Health R01 AR068428 to DM and US-Israel Binational Science Foundation Grant [2013032] to DM and OB.