piRNAs (Piwi-interacting RNAs, 23-30 nt long) are a new class of small non-coding RNAs and have been discovered in the germline of many species. Their primary function is to repress transposable elements in the germline. A large part of piRNAs are produced from transposable elements and from repeated sequences composed of transposable element remnants (the piRNA clusters). Like miRNAs, piRNAs are loaded into specific Argonaute proteins, called PIWI proteins for the piRNA pathway, and they interact with their target mRNAs by complementarity. PIWI proteins have an endonuclease activity and repression of target mRNAs from transposable elements occurs mostly through endonucleolytic cleavage by the PIWI proteins. The piRNA pathway has a crucial function in the germline: piRNAs are thought to maintain germline DNA integrity because they prevent transposition of transposable elements and therefore the formation of double strand breaks.
In the last years, we have pioneered the discovery of a new function of piRNAs and PIWI proteins. An unexpected role of the piRNA pathway in gene regulation in the embryo was uncovered: piRNAs produced from transposable elements target nanos mRNA. nanos encodes the posterior morphogen in the embryo, which is essential for abdomen and germ cell development. A complete base-pairing of these piRNAs with nanos mRNA guides the interaction with the PIWI proteins Aubergine (Aub) and Ago3, which in turn participate in the recruitment of the CCR4-NOT deadenylation complex. This leads to the deadenylation (poly(A) tail shortening) and translational repression of nanos mRNA in the somatic part of the embryo, which is required for embryonic patterning. These data allowed us to propose the new concept of gene regulation by piRNAs and of a developmental function of transposable elements through the regulation of gene expression.
Following this discovery, a number of studies have now validated the regulation of cellular (non-transposable element) mRNAs by piRNAs in different species including C. elegans, Bombyx mori and the mouse. These data strongly suggest that the role of the piRNA pathway in gene regulation is widespread, although is it just emerging. Therefore this regulation should have a major impact in many biological processes, including diseases, as is the case for regulation by miRNAs.
More recently, the team addressed the global regulation of maternal mRNAs by the piRNA pathway in the Drosophila embryo. We performed iCLIP (individual-nucleotide resolution UV cross-linking and immunoprecipitation) of Aub in early embryos and identified several hundreds maternal mRNAs interacting with Aub. Gene expression profiling revealed that a proportion of those, about 200 mRNAs, undergo Aub-dependent destabilization during the maternal-to-zygotic transition. Interestingly, Aub-dependent unstable mRNAs encode germ cell determinants, thus indicating a key developmental role of mRNA regulation by piRNAs for the decay and localization of mRNAs encoding germ cell determinants in the embryo. Another set of mRNAs interacting with Aub, about 250 mRNAs, remain stable in the embryo. These stable mRNAs are enriched in Gene Ontology terms linked to later steps of embryogenesis (e.g. neurogenesis, organ development), suggesting that they could be translationally repressed, although not destabilized by piRNAs and Aub. This represents at least two potential mechanisms of regulation by piRNAs with two different outcomes: mRNA decay by recruitment of the deadenylation complex or endonucleolytic cleavage, and translational repression without mRNA decay.
Although this link between the piRNA pathway and translational regulation has been known for some time, the molecular mechanisms of this regulation have not been addressed. This PhD project aims to address the molecular mechanisms of translational regulation by the piRNA pathway.
In the last years, we have pioneered the discovery of a new function of piRNAs and PIWI proteins. An unexpected role of the piRNA pathway in gene regulation in the embryo was uncovered: piRNAs produced from transposable elements target nanos mRNA. nanos encodes the posterior morphogen in the embryo, which is essential for abdomen and germ cell development. A complete base-pairing of these piRNAs with nanos mRNA guides the interaction with the PIWI proteins Aubergine (Aub) and Ago3, which in turn participate in the recruitment of the CCR4-NOT deadenylation complex. This leads to the deadenylation (poly(A) tail shortening) and translational repression of nanos mRNA in the somatic part of the embryo, which is required for embryonic patterning. These data allowed us to propose the new concept of gene regulation by piRNAs and of a developmental function of transposable elements through the regulation of gene expression.
Following this discovery, a number of studies have now validated the regulation of cellular (non-transposable element) mRNAs by piRNAs in different species including C. elegans, Bombyx mori and the mouse. These data strongly suggest that the role of the piRNA pathway in gene regulation is widespread, although is it just emerging. Therefore this regulation should have a major impact in many biological processes, including diseases, as is the case for regulation by miRNAs.
More recently, the team addressed the global regulation of maternal mRNAs by the piRNA pathway in the Drosophila embryo. We performed iCLIP (individual-nucleotide resolution UV cross-linking and immunoprecipitation) of Aub in early embryos and identified several hundreds maternal mRNAs interacting with Aub. Gene expression profiling revealed that a proportion of those, about 200 mRNAs, undergo Aub-dependent destabilization during the maternal-to-zygotic transition. Interestingly, Aub-dependent unstable mRNAs encode germ cell determinants, thus indicating a key developmental role of mRNA regulation by piRNAs for the decay and localization of mRNAs encoding germ cell determinants in the embryo. Another set of mRNAs interacting with Aub, about 250 mRNAs, remain stable in the embryo. These stable mRNAs are enriched in Gene Ontology terms linked to later steps of embryogenesis (e.g. neurogenesis, organ development), suggesting that they could be translationally repressed, although not destabilized by piRNAs and Aub. This represents at least two potential mechanisms of regulation by piRNAs with two different outcomes: mRNA decay by recruitment of the deadenylation complex or endonucleolytic cleavage, and translational repression without mRNA decay.
Although this link between the piRNA pathway and translational regulation has been known for some time, the molecular mechanisms of this regulation have not been addressed. This PhD project aims to address the molecular mechanisms of translational regulation by the piRNA pathway.
