Degradation dynamics of microRNAs revealed by a novel pulse-chase approach
- Matteo J Marzi1,
- Francesco Ghini1,
- Benedetta Cerruti1,
- Stefano de Pretis1,
- Paola Bonetti1,
- Chiara Giacomelli1,
- Marcin G Gorski2,
- Theresia Kress1,
- Mattia Pelizzola1,
- Heiko Muller3,
- Bruno Amati1 and
- Francesco Nicassio1,4
- 1 Istituto Italiano di Tecnologia Milano Italy;
- 2 European Institute of Oncology (IEO);
- 3 istituto Italiano di Tecnologia Milano Italy
- ↵* Corresponding author; email: francesco.nicassio{at}iit.it
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>24h), while others, including passenger miRNAs and a number (25/129) of guide miRNAs, are quickly turned over (T1/2=4-14h). 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.
- Received August 31, 2015.
- Accepted January 19, 2016.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International license), as described at http://creativecommons.org/licenses/by-nc/4.0/.
