MicroRNAs are ~22nt small RNAs that regulate gene expression post transcriptionally. They have the potential to regulate a large fraction of the human genes, and have been implicated in multiple aspects of biology from embryonic development, to cellular physiology and disease. Despite their paramount importance in gene regulation, the mechanisms by which miRNAs regulate gene expression remains remain controversial. Three models for miRNA mediated repression have been proposed: repression of translation initiation, repression of translation elongation and mRNA deadenylation. This proposal aims to undertake a systematic analysis of the relative timing of the different events (aim 1, 2) and the molecular effect of disrupting mRNA deadenylation (aim 2) on miRNA mediated gene regulation using an in vivo system. In this proposal we use the zebrafish embryo as an in vivo system to understand the molecular effect of endogenous miRNAs in their targets by comparing wild type embryos with embryos mutants in the miRNA processing pathway. Using high throughput sequencing in this system we propose to i) undertake a temporal genome wide analysis of translation by measuring ribosome density in the mRNA using Ribosome foot- printing (Aim 1), ii) analyze the dynamics of deadenylation in the presence and the absence of endogenous miRNAs (Aim 2), and iii) analyze the effect of blocking the deadenylation machinery on miRNA mediated translational repression and mRNA decay (Aim 2). These experiments will allow us to determine the sequence of events, and the relative contribution of mRNA deadenylation and translational repression during miRNA-mediated gene regulation. MicroRNAs have been implicated in a wide range of developmental defects, neurological disorders, and human disease including tumor formation and metastasis. The results derived from this proposal will provide fundamental insights into the molecular machinery required for miRNAs mediated gene regulation and has the potential to reveal important components in the miRNA pathway that may be used as therapeutic targets to treat human diseases and cancer.

Public Health Relevance

MicroRNAs constitute the tiniest genes in the genome, and have been implicated in human development, cancer and other human diseases. This proposal aims to understand the mechanism by which these microRNAs regulate other genes in the cell, what might help us develop specific ways to modulate their activity during human disease.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Molecular Genetics A Study Section (MGA)
Program Officer
Bender, Michael T
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Yale University
Schools of Medicine
New Haven
United States
Zip Code
Yartseva, Valeria; Takacs, Carter M; Vejnar, Charles E et al. (2017) RESA identifies mRNA-regulatory sequences at high resolution. Nat Methods 14:201-207
Moreno-Mateos, Miguel A; Fernandez, Juan P; Rouet, Romain et al. (2017) CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing. Nat Commun 8:2024
Bazzini, Ariel A; Del Viso, Florencia; Moreno-Mateos, Miguel A et al. (2016) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. EMBO J 35:2087-2103
Yartseva, Valeria; Giraldez, Antonio J (2015) The Maternal-to-Zygotic Transition During Vertebrate Development: A Model for Reprogramming. Curr Top Dev Biol 113:191-232
Moreno-Mateos, Miguel A; Vejnar, Charles E; Beaudoin, Jean-Denis et al. (2015) CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods 12:982-8
Lee, Mihye; Choi, Yeon; Kim, Kijun et al. (2014) Adenylation of maternally inherited microRNAs by Wispy. Mol Cell 56:696-707
Lee, Miler T; Bonneau, Ashley R; Giraldez, Antonio J (2014) Zygotic genome activation during the maternal-to-zygotic transition. Annu Rev Cell Dev Biol 30:581-613
Yoda, Mayuko; Cifuentes, Daniel; Izumi, Natsuko et al. (2013) Poly(A)-specific ribonuclease mediates 3'-end trimming of Argonaute2-cleaved precursor microRNAs. Cell Rep 5:715-26
Bazzini, Ariel A; Lee, Miler T; Giraldez, Antonio J (2012) Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336:233-7