title: Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.
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.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Schraga
authors.initials: S
authors.lastname: Schwartz
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Bernstein
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Maxwell R
authors.initials: MR
authors.lastname: Mumbach
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Marko
authors.initials: M
authors.lastname: Jovanovic
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Rebecca H
authors.initials: RH
authors.lastname: Herbst
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan 00931, Puerto Rico.
authors.forename: Brian X
authors.initials: BX
authors.lastname: León-Ricardo
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA.
authors.forename: Jesse M
authors.initials: JM
authors.lastname: Engreitz
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Mitchell
authors.initials: M
authors.lastname: Guttman
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Rahul
authors.initials: R
authors.lastname: Satija
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA; Department of Biology, MIT, Cambridge, MA 02139, USA.
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA. Electronic address: gfink@wi.mit.edu.
authors.forename: Gerald
authors.initials: G
authors.lastname: Fink
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA. Electronic address: aregev@broad.mit.edu.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
mesh_terms: D000818:Animals; D002176:Candida albicans / Q000235:genetics / Q000378:metabolism; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D019871:Dyskeratosis Congenita / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D006801:Humans; D019751:Intramolecular Transferases / Q000737:chemistry / Q000378:metabolism; D051379:Mice; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D011560:Pseudouridine / Q000032:analysis* / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry*; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D022661:RNA, Untranslated / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000378:metabolism; D013379:Substrate Specificity; D019098:Telomerase / Q000737:chemistry / Q000235:genetics
chemical_list: D018797:Cell Cycle Proteins; C112148:DKC1 protein, human; D009687:Nuclear Proteins; C474390:Pus7 protein, S cerevisiae; D012333:RNA, Messenger; D012335:RNA, Ribosomal; D022661:RNA, Untranslated; D029701:Saccharomyces cerevisiae Proteins; C422952:telomerase RNA; D011560:Pseudouridine; D012313:RNA; D019098:Telomerase; D019751:Intramolecular Transferases; C096995:pseudouridine synthases