title: Degradation dynamics of microRNAs revealed by a novel pulse-chase approach.
abstract: The regulation of miRNAs is critical to the definition of cell identity and behavior in normal physiology and disease. To date, the dynamics of miRNA degradation and the mechanisms involved in remain largely obscure, in particular, in higher organisms. Here, we developed a pulse-chase approach based on metabolic RNA labeling to calculate miRNA decay rates at genome-wide scale in mammalian cells. Our analysis revealed heterogeneous miRNA half-lives, with many species behaving as stable molecules (T1/2> 24 h), while others, including passenger miRNAs and a number (25/129) of guide miRNAs, are quickly turned over (T1/2= 4-14 h). Decay rates were coupled with other features, including genomic organization, transcription rates, structural heterogeneity (isomiRs), and target abundance, measured through quantitative experimental approaches. This comprehensive analysis highlighted functional mechanisms that mediate miRNA degradation, as well as the importance of decay dynamics in the regulation of the miRNA pool under both steady-state conditions and during cell transitions.
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy;
authors.forename: Matteo J
authors.initials: MJ
authors.lastname: Marzi
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy;
authors.forename: Francesco
authors.initials: F
authors.lastname: Ghini
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy;
authors.forename: Benedetta
authors.initials: B
authors.lastname: Cerruti
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy;
authors.forename: Stefano
authors.initials: S
authors.lastname: de Pretis
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy;
authors.forename: Paola
authors.initials: P
authors.lastname: Bonetti
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy;
authors.forename: Chiara
authors.initials: C
authors.lastname: Giacomelli
authors.affiliation: Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy.
authors.forename: Marcin M
authors.initials: MM
authors.lastname: Gorski
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy.
authors.forename: Theresia
authors.initials: T
authors.lastname: Kress
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy;
authors.forename: Mattia
authors.initials: M
authors.lastname: Pelizzola
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy;
authors.forename: Heiko
authors.initials: H
authors.lastname: Muller
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy.
authors.forename: Bruno
authors.initials: B
authors.lastname: Amati
authors.affiliation: Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy;
authors.forename: Francesco
authors.initials: F
authors.lastname: Nicassio
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000378:metabolism; D005347:Fibroblasts; D005786:Gene Expression Regulation; D055106:Genome-Wide Association Study; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D034622:RNA Interference; D020871:RNA Stability; D043244:Ribonuclease III / Q000378:metabolism; D013997:Time Factors; D014158:Transcription, Genetic
chemical_list: D060565:Argonaute Proteins; D035683:MicroRNAs; D043244:Ribonuclease III
references.citation: Cell. 2008 Jan 11;132(1):9-14
references.pmid: 18191211
references.citation: Nat Rev Genet. 2010 Sep;11(9):597-610
references.pmid: 20661255
references.citation: Cell. 2014 Feb 27;156(5):893-906
references.pmid: 24581491
references.citation: Nucleic Acids Res. 2014 Apr;42(7):4629-39
references.pmid: 24464996
references.citation: RNA Biol. 2013 Oct;10(10):1623-30
references.pmid: 24025460
references.citation: Nat Rev Mol Cell Biol. 2009 Feb;10(2):116-25
references.pmid: 19165214
references.citation: Trends Genet. 2012 Nov;28(11):544-9
references.pmid: 22883467
references.citation: Sci Signal. 2010;3(124):ra43
references.pmid: 20516477
references.citation: Nature. 2009 Sep 24;461(7263):546-9
references.pmid: 19734881
references.citation: Cell. 2010 Nov 24;143(5):703-9
references.pmid: 21111232
references.citation: Annu Rev Cell Dev Biol. 2007;23:175-205
references.pmid: 17506695
references.citation: Mol Cell. 2014 Dec 4;56(5):696-707
references.pmid: 25454948
references.citation: Nat Methods. 2012 Apr;9(4):403-9
references.pmid: 22388288
references.citation: Mol Cell. 2015 Sep 3;59(5):858-66
references.pmid: 26340425
references.citation: Nat Rev Genet. 2015 Jul;16(7):421-33
references.pmid: 26077373
references.citation: Nat Rev Cancer. 2015 Jun;15(6):321-33
references.pmid: 25998712
references.citation: Nature. 2012 Feb 16;482(7385):347-55
references.pmid: 22337054
references.citation: Nat Cell Biol. 2013 Jun;15(6):546-54
references.pmid: 23728460
references.citation: Nat Rev Mol Cell Biol. 2014 Aug;15(8):509-24
references.pmid: 25027649
references.citation: Nucleic Acids Res. 2011 Jul;39(13):5692-703
references.pmid: 21447562
references.citation: Mol Cell. 2013 May 9;50(3):344-55
references.pmid: 23664376
references.citation: Science. 2010 Jun 18;328(5985):1534-9
references.pmid: 20558712
references.citation: Nature. 2011 May 19;473(7347):337-42
references.pmid: 21593866
references.citation: Nat Biotechnol. 2011 May;29(5):436-42
references.pmid: 21516085
references.citation: Nat Biotechnol. 2005 Feb;23(2):232-7
references.pmid: 15685165
references.citation: Genome Res. 2011 Sep;21(9):1450-61
references.pmid: 21813625
references.citation: Science. 2008 Sep 12;321(5895):1490-2
references.pmid: 18787168
references.citation: Nucleic Acids Res. 2015 Feb 27;43(4):2326-41
references.pmid: 25653157
references.citation: Nature. 2011 May 5;473(7345):105-8
references.pmid: 21478871
references.citation: RNA. 2008 Sep;14(9):1959-72
references.pmid: 18658122
references.citation: Nucleic Acids Res. 2014 Oct;42(18):11777-91
references.pmid: 25223788
references.citation: Bioinformatics. 2015 Sep 1;31(17):2829-35
references.pmid: 25957348
references.citation: Trends Biochem Sci. 2012 Oct;37(10):436-46
references.pmid: 22921610
references.citation: Nat Genet. 2011 Sep;43(9):854-9
references.pmid: 21857679
references.citation: Cell. 2010 May 14;141(4):618-31
references.pmid: 20478254
references.citation: Mol Cell. 2014 Nov 6;56(3):347-59
references.pmid: 25449132
references.citation: Science. 2007 Apr 27;316(5824):575-9
references.pmid: 17379774
references.citation: Genome Res. 2003 Aug;13(8):1863-72
references.pmid: 12902380
references.citation: RNA. 2012 May;18(5):1014-28
references.pmid: 22450760
references.citation: Curr Biol. 2011 Mar 8;21(5):369-76
references.pmid: 21353554
references.citation: Proc Natl Acad Sci U S A. 2009 Apr 28;106(17):7016-21
references.pmid: 19359480
references.citation: Nucleic Acids Res. 2012 May;40(10):4615-25
references.pmid: 22210897
references.citation: Cell. 2009 Jan 23;136(2):215-33
references.pmid: 19167326
references.citation: Mol Cell Biol. 2010 Jun;30(12):2983-95
references.pmid: 20404092
references.citation: Nat Methods. 2012 Aug;9(8):840-6
references.pmid: 22751203
references.citation: Cell. 2009 Feb 20;136(4):642-55
references.pmid: 19239886
references.citation: Front Bioeng Biotechnol. 2014 Sep 29;2:38
references.pmid: 25325056
references.citation: Cell. 2007 Dec 14;131(6):1097-108
references.pmid: 18083100
references.citation: RNA. 2010 May;16(5):1032-9
references.pmid: 20348442
references.citation: Science. 2007 Jan 5;315(5808):97-100
references.pmid: 17204650
references.citation: Nucleic Acids Res. 2009 Sep;37(17):e115
references.pmid: 19561200
references.citation: Mol Cell. 2011 Sep 16;43(6):993-1004
references.pmid: 21925387
references.citation: EMBO Rep. 2015 Apr;16(4):500-11
references.pmid: 25724380