Histone mRNA homeostasis in early embryos

1 PhD project offered in the IPP summer call Molecular Mechanisms in Genome Stability & Gene Regulation

Scientific Background

Gene regulation by small non-coding RNAs is a deeply conserved mode of gene control. It is used in developmental control of gene expression, but also in the protection of the genome against mobile genetic elements (i.e. transposons). The small RNA molecules function as sequence specific guides for proteins of the Argonaute family, which can repress translation, induce endonucleolytic cleavage or induce heterochromatin upon recognition of transcripts with sequence homology to the small RNA. Hence, the small RNA co-factors are essential players in these pathways as they fully determine the specificity. However, a lot still remains to be discovered about how such small RNAs are made, in particular in the context of genome defense against transposons. Understanding these steps better will increase our understanding of how our genomes discriminate ‘self’ from ‘non-self’, a non-trivial exercise! In addition, past work has shown that the dissection of such pathways has yielded great insights also in the understanding of more basic RNA biology. We are addressing these questions using two model organisms: the nematode C. elegans and the zebrafish. We are looking for people with a strong natural curiosity, perseverance and a high intrinsic motivation. Specific knowledge of the applied techniques is not essential, but a strong basis in molecular biology is required. We offer a highly interactive, stimulating and flexible research environment, with ample opportunities for personal development.

PhD Project: Biogenesis and regulation of small RNAs

Which small RNAs are made is of great importance, as the specificity of these pathways depends on it. Recently, we identified a novel nuclease that is a key factor in the generation of a specific type of small RNAs (named piRNAs), and we are further pursuing studies to understand how these piRNAs are made, starting from their transcription, all the way to their binding by a specific member of the Argonaute protein family (the Piwi protein). These are important research questions, as they relate to a much broader problem: how are certain RNA molecules destined to become used as protein-coding messengers, others to be degraded fast, and yet others to be used as (precursors for) non-coding RNAs, such as piRNAs. Resolving these questions will require a much better understanding of different modes of transcription initiation, elongation and termination, and RNA stabilization and de-stabilization, and RNA transport through the nucleus and the rest of the cell. Our recent, unpublished work has made intriguing entries into various of these aspects: we have identified a complex that stabilizes piRNA precursors, and are now studying how this connects to their transcription; we have generated mutants in a nuclear export factor that likely plays a role in piRNA precursor export and we have identified a novel locus that can serve as a source of piRNA precursor transcription.

Depending on expertise and interest, you can join us in studying these aspects, using C. elegans or the zebrafish as model system. The aims of the project can relate to understanding how ‘non-standard’ transcripts can be stabilized for further use, how the nuclear export of such transcripts is taking place, piRNA precursors actually look like, how the loading of small RNAs into an Argonaute protein takes place or how these processes can be regulated by post-translational modifications. Techniques that will be used in this project include microscopy, genetics, CRISPR-Cas genome editing, RNA interference, RNAseq, analysis of sequencing data and protein purification.

If you are interested in this project, please select René Ketting as your group preference in the IPP application platform.

Publications relevant to this project

Bronkhorst AW, Lee CY, Möckel MM, Ruegenberg S, de Jesus Domingues AM, Sadouki S, Piccinno R, Sumiyoshi T, Siomi MC, Stelzl L, Luck K, Ketting RF (2023) An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in Bombyx mori. EMBO J. 42(24):e114072. Link

Podvalnaya N, Bronkhorst AW, Lichtenberger R, Hellmann S, Nischwitz E, Falk T, Karaulanov E, Butter F, Falk S, Ketting RF (2023)
piRNA processing by a trimeric Schlafen-domain nuclease. Nature 622(7982):402-409. Link

Schreier J, Dietz S, Boermel M, Oorschot V, Seistrup AS, de Jesus Domingues AM, Bronkhorst AW, Nguyen DAH, Phillis S, Gleason EJ, L’Hernault SW, Phillips CM, Butter F, Ketting RF. (2022) Membrane-associated cytoplasmic granules carrying the Argonaute protein WAGO-3 enable paternal epigenetic inheritance in Caenorhabditis elegans. Nat. Cell Biol. 24(2):217-229 Link

Perez-Borrajero C, Podvalnaya N, Holleis K, Lichtenberger R, Karaulanov E, Simon B, Basquin J, Hennig* J, Ketting* RF, Falk* S. (2021) Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans. Genes Dev. 35(17-18):1304-1323. Link

Redl S, de Jesus Domingues AM, Caspani E, Möckel S, Salvenmoser W, Mendez-Lago M, Ketting RF. (2021) Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish. Development 148(2):dev193060. Link

Roovers EF, Kaaij LJT, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang H, Han C, Riemer S, Dosch R, Salvenmoser W, Grün D, Butter F, van Oudenaarden A, Ketting RF (2018) Tdrd6a regulates the aggregation of Buc into functional subcellular compartments that drive germ cell specification Dev. Cell 46(3): 285-301 Link

 

Contact Details

Prof. Dr René Ketting
Email
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