Pervasive and Cooperative Deadenylation of 3′UTRs by Embryonic MicroRNA Families

Abstract

To understand how miRNA-mediated silencing impacts on embryonic mRNAs, we conducted a functional survey of abundant maternal and zygotic miRNA families in the C. elegans embryo. We show that the miR-35-42, and the miR-51-56 miRNA families define maternal and zygotic miRNA-induced silencing complexes (miRISCs), respectively, that share a large number of components. Using a novel cell-free C. elegans embryonic extract, we demonstrate that the miRISC directs the rapid deadenylation of reporter mRNAs with natural 3’UTRs. The deadenylated targets are translationally suppressed and remarkably stable. Sampling of the predicted miR-35-42 targets reveals that roughly half are deadenylated in a miRNA-dependent manner, but with each target displaying a distinct efficiency and pattern of deadenylation. Finally, we demonstrate that functional cooperation between distinct miRISCs within 3’UTRs is required to potentiate deadenylation. With this report, we reveal the extensive and direct impact of miRNA-mediated deadenylation on embryonic mRNAs.

miRNAs cooperate in apoptosis regulation during C. elegans development

“…In this study, we investigate the roles in programmed cell death during C. elegans development of the miR-35 and miR-58 families of miRNAs (Lau et al 2001;Kato et al 2009;Alvarez-Saavedra and Horvitz 2010;Wu et al 2010). The miR-35 family consists of eight members, collectively referred to as miR-35-42, which are found at high levels in oocytes and throughout early and mid-stage embryos but whose levels decline post-gastrulation (>350 embryonic nuclei) (Stoeckius et al 2009;Alvarez-Saavedra and Horvitz 2010;Isik et al 2010;Wu et al 2010).…”

“…The miR-35 family consists of eight members, collectively referred to as miR-35-42, which are found at high levels in oocytes and throughout early and mid-stage embryos but whose levels decline post-gastrulation (>350 embryonic nuclei) (Stoeckius et al 2009;Alvarez-Saavedra and Horvitz 2010;Isik et al 2010;Wu et al 2010). The loss of all eight members in mir-35-41(nDf50) mir-42(nDf49) mutants (referred to as "mir-35 family mutants") results in 100% embryonic lethality (AlvarezSaavedra and Horvitz 2010).…”

“…Animals lacking only the seven miRNAs miR-35-41 are viable but display altered RNAi sensitivity, reduced fecundity, and impaired responsiveness to hypoxia (Massirer et al 2012;McJunkin and Ambros 2014;Kagias and Pocock 2015). The miR-58 family is homologous to bantam miRNA in Drosophila and consists of six members: four members that are found at increasing levels throughout embryos starting from mid-stage embryogenesis (miR-80, miR-58.1, miR-81, and miR-82) and two members that are found only at low levels at any stage of development (miR-58.2 and miR-2209.1) (Stoeckius et al 2009;Alvarez-Saavedra and Horvitz 2010;Isik et al 2010;Wu et al 2010). The loss of all four abundant members in mir-80(nDf53); mir-58.1(n4640); mir-81-82(nDf54) mutants (referred to as "mir-58 family mutants") results in reduced body and brood size as well as defects in locomotion and dauer formation (Alvarez-Saavedra and Horvitz 2010).…”

“…The loss of all four abundant members in mir-80(nDf53); mir-58.1(n4640); mir-81-82(nDf54) mutants (referred to as "mir-58 family mutants") results in reduced body and brood size as well as defects in locomotion and dauer formation (Alvarez-Saavedra and Horvitz 2010). A previous study demonstrated that egl-1 mRNA is an in vitro target of both miR-35 and miR-58 family miRNAs (Wu et al 2010). Furthermore, it was proposed that miR-35 and miR-58 family miRNAs cause translational repression of egl-1 mRNA by mediating its deadenylation (Wu et al 2010).…”

“…A previous study demonstrated that egl-1 mRNA is an in vitro target of both miR-35 and miR-58 family miRNAs (Wu et al 2010). Furthermore, it was proposed that miR-35 and miR-58 family miRNAs cause translational repression of egl-1 mRNA by mediating its deadenylation (Wu et al 2010). Another study reported that the loss of the mir-58 family causes impairment of germline apoptosis; however, a target was not identified (Subasic et al 2015).…”