Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA

Schraga Schwartz, Douglas A. Bernstein, Maxwell R. Mumbach, Marko Jovanovic, Rebecca H. Herbst, Brian X. León-Ricardo, Jesse M. Engreitz, Mitchell Guttman, Rahul Satija, Eric S. Lander, Gerald Fink, Aviv Regev

Research output: Contribution to journalArticle

Abstract

Pseudouridine is the most abundant RNA modification, yet except for a few well-studied cases, little is known about the modified positions and their function(s). Here, we develop Ψ-seq for transcriptome-wide quantitative mapping of pseudouridine. We validate Ψ-seq with spike-ins and de novo identification of previously reported positions and discover hundreds of unique sites in human and yeast mRNAs and snoRNAs. Perturbing pseudouridine synthases (PUS) uncovers which pseudouridine synthase modifies each site and their target sequence features. mRNA pseudouridinylation depends on both site-specific and snoRNA-guided pseudouridine synthases. Upon heat shock in yeast, Pus7p-mediated pseudouridylation is induced at >200 sites, and PUS7 deletion decreases the levels of otherwise pseudouridylated mRNA, suggesting a role in enhancing transcript stability. rRNA pseudouridine stoichiometries are conserved but reduced in cells from dyskeratosis congenita patients, where the PUS DKC1 is mutated. Our work identifies an enhanced, transcriptome-wide scope for pseudouridine and methods to dissect its underlying mechanisms and function.

Original languageEnglish (US)
Pages (from-to)148-162
Number of pages15
JournalCell
Volume159
Issue number1
DOIs
StatePublished - Sep 25 2014

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Pseudouridine
Transcriptome
Small Nucleolar RNA
Messenger RNA
Yeast
Dyskeratosis Congenita
Yeasts
Stoichiometry
Shock
Hot Temperature
RNA
pseudouridine synthases

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Schwartz, S., Bernstein, D. A., Mumbach, M. R., Jovanovic, M., Herbst, R. H., León-Ricardo, B. X., ... Regev, A. (2014). Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell, 159(1), 148-162. https://doi.org/10.1016/j.cell.2014.08.028

Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. / Schwartz, Schraga; Bernstein, Douglas A.; Mumbach, Maxwell R.; Jovanovic, Marko; Herbst, Rebecca H.; León-Ricardo, Brian X.; Engreitz, Jesse M.; Guttman, Mitchell; Satija, Rahul; Lander, Eric S.; Fink, Gerald; Regev, Aviv.

In: Cell, Vol. 159, No. 1, 25.09.2014, p. 148-162.

Research output: Contribution to journalArticle

Schwartz, S, Bernstein, DA, Mumbach, MR, Jovanovic, M, Herbst, RH, León-Ricardo, BX, Engreitz, JM, Guttman, M, Satija, R, Lander, ES, Fink, G & Regev, A 2014, 'Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA', Cell, vol. 159, no. 1, pp. 148-162. https://doi.org/10.1016/j.cell.2014.08.028
Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell. 2014 Sep 25;159(1):148-162. https://doi.org/10.1016/j.cell.2014.08.028
Schwartz, Schraga ; Bernstein, Douglas A. ; Mumbach, Maxwell R. ; Jovanovic, Marko ; Herbst, Rebecca H. ; León-Ricardo, Brian X. ; Engreitz, Jesse M. ; Guttman, Mitchell ; Satija, Rahul ; Lander, Eric S. ; Fink, Gerald ; Regev, Aviv. / Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. In: Cell. 2014 ; Vol. 159, No. 1. pp. 148-162.
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