Functions of short translated open reading frames (ORFs) in the context of development
Large-scale forward-genetic screens towards the end of the last century have identified the majority of known embryonic signalling pathways and embryonically essential genes. This relatively small set of genes with known essential embryonic functions is in stark contrast to the large number of transcripts that are expressed during embryogenesis (Pauli & Valen et al., 2012). Moreover, hundreds of these transcripts were recently predicted to encode small proteins (Chew et al., 2013; Pauli et al., 2014; Bazzini et al., 2014). Apart from novel protein-coding genes, these studies have also identified a large number of translated regions outside of protein-coding ORFs on 5’ leaders of coding genes (upstream ORFs (uORFs)) and on transcripts previously thought to be non-coding.
To determine if any of these uncharacterised, translated ORFs might have a function, we focused on the putative signalling protein, Toddler (Pauli et al., 2014). Toddler had previously been annotated as a non-coding RNA, but it encodes a short, conserved, and secreted peptide. Zebrafish embryos lacking Toddler peptide die during embryogenesis and lack a functional heart.
Local and ubiquitous expression of Toddler promotes mesendodermal cell movement during gastrulation, suggesting that Toddler is neither an attractant nor a repellent but acts globally as a motogen. Toddler drives internalization of G-protein-coupled APJ/Apelin receptors, and activation of APJ/Apelin receptor signalling rescues toddler mutants. These results indicate that Toddler is an activator of APJ/Apelin receptor signalling, promotes gastrulation movements, and might be the first in a series of uncharacterized developmental regulators. Moreover, the discovery of Toddler provides the proof of principle that functional, short translated ORFs remain to be identified.
We will build on these initial findings and investigate the functions and mechanisms of short translated ORFs during embryogenesis. We will mainly use zebrafish embryos since they are an ideal model system for functional genomics in a developing organism.
We will focus on three main areas:
- What are the molecular and cellular mechanisms by which Toddler/Apelin receptor signalling promotes gastrulation movements?
- What are the functions of other conserved yet uncharacterized short proteins during embryogenesis?
- How does regulatory translation, e.g. of upstream ORFs (uORFs), contribute to developmental transitions?
- Pauli, A., Valen, E., Schier, AF. (2015). Identifying (non-)coding RNAs and small peptides: challenges and opportunities. Bioessays. 37(1):103-12
- Pauli, A., Norris, ML., Valen, E., Chew, GL., Gagnon, JA., Zimmerman, S., Mitchell, A., Ma, J., Dubrulle, J., Reyon, D., Tsai, SQ., Joung, JK., Saghatelian, A., Schier, AF. (2014). Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science. 343(6172):1248636
- Chew, GL., Pauli, A., Rinn, JL., Regev, A., Schier, AF., Valen, E. (2013). Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development. 140(13):2828-34
- Pauli, A., Valen, E., Lin, MF., Garber, M., Vastenhouw, NL., Levin, JZ., Fan, L., Sandelin, A., Rinn, JL., Regev, A., Schier, AF. (2012). Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res. 22(3):577-91
- Pauli, A., Rinn, JL., Schier, AF. (2011). Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet. 12(2):136-49