Degradation dynamics of micrornas revealed by a novel pulse-chase approach

Matteo J. Marzi, Francesco Ghini, Benedetta Cerruti, Stefano De Pretis, Paola Bonetti, Chiara Giacomelli, Marcin M. Gorski, Theresia Kress, Mattia Pelizzola, Heiko Muller, Bruno Amati, Francesco Nicassio

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)554-565
Number of pages12
JournalGenome Research
Issue number4
Publication statusPublished - Apr 1 2016

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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