Congratulations to Emily as her paper on internal mechanosensation is published!

Congratulations to Emily on her newly published paper The DEG/ENaC channel DEGT-1 is a proprioceptor of C. elegans foregut movement. We not only receive sensation from the outside world such as sight and hearing, but also from our internal worlds such as hunger and balance. One form of internal perception is proprioception where we receive feedback of our body’s position and how it movement. Here she has uncovered the role of a channel for internal sensation of pharynx movement. You can read the paper here.

Congratulations Annika and Max on their cichlid paper coming out in Nature Eco. Evo.!

Congratulations to Max and Annika and all their coauthors on their new paper! Cichlid fishes are exceptionally fast at speciation. Lake Tanganyika is only about 10 million years old and has about 250 endemically evolved cichlid species. Our lab collaborated with Lake Tanganika cichlid species experts the Salzburger lab, and found that cichlids have diverse activity patterns. Some are night active (nocturnal), some day active (diurnal) and others are most active during the dawn and dusk, while others have no clear rhythm. This temporal niche partitioning could have supported the rapid diversification of these species.

Read also the news and views here.

Max now has his own lab at the University of Toronto.

The beautiful fish drawings come from talented artist Julie Johnson.

New review on Nodal signalling in embryonic development!

Nodal signalling molecules are crucial for key steps in embryonic development. The function of these TGFβ family ligands are largely conserved across vertebrates. Yet there remain many unanswered questions on how these molecules and the genes they regulate control embryonic tissue patterning. Read more about it in this extensive review by Alex and two talented PhD students from the lab: Jake and Mireia!

Madalena’s paper now published in Dev Cell

Madalena’s paper “The regulatory landscape of 5′ UTRs in translational control during zebrafish embryogenesis” is now out in Developmental Cell. Congratulations to all authors!

Madalena used a massively parallel reporter assay (MPRA) of 18,154 RNA sequences to uncover the translation initiation potential of endogenous 5’UTRs by polysome profiling. They look at the regulation across zebrafish embryogenesis (2, 4, 6 and 10 hours post fertilisation). From this data they identified different regulatory dynamics and 86 potential regulatory motifs. Some of motifs are known RNA protein binding motifs, but many are new. This is exciting as each motif is a new lead to find regulatory proteins and further our understanding of how RNA to protein translation is controlled.

Congratulations Madalena and coauthors on their new tRNA paper!

Congratulations to Madalena and co-authors on their paper The dynamics and functional impact of tRNA repertoires during early embryogenesis in zebrafish.

An embryo starts life with a set of RNAs and proteins from its mother.  During development the embryo starts transcribing its own genes into RNA, a process known as the maternal-to-zygotic transition. The protein-coding mRNAs are translated into protein by ribosomes and transfer RNAs (tRNAs). tRNAs decode the triplet nucleotide codons of the mRNA to determine which protein subunits are added to the new protein. Codon identity is an important factor determining RNA stability. However, how the pools of tRNAs change from the initial maternal pool to the zygotic pool was unknown. In this work Madalena and colleagues profiled the tRNA pools across embryonic development in zebrafish. They found that maternal and zygotic tRNA pools are distinct. Interestingly, the transition between pools did not result in a better match to the codon content of the zygotic transcriptome. Instead, they found that global translation increases at gastrulation and sensitises decoding rates to tRNA supply. This destabilises maternal mRNAs which are enriched in slowly translated codons.

This work was a collaboration with the lab of Danny Nediakova at the MPI for Biochemistry in Munich.

Congratulations to Yinan and co-authors!

A monumental effort by Yinan and coauthors for their exciting work “Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis” now out on BioRxiv! Here, they introduce a new system whole-embryo imaging platform using multiplexed error-robust fluorescent in-situ hybridization (weMERFISH). Using this method hey spatiality quantified 495 genes in early zebrafish embryos. Moreover, they could use the signature of these genes to infer the full transcriptome and chromatin accessibility of the cells using data from the accompanying paper from Jialin and co-authors (here). This data is browsable online! Check it out here.

Read the paper here. This work was possible due to great collaborations with the labs of Bogdan Bintu (UCSD), Guoqiang Yu (Tsinghua University), Susan Mango (Biozentrum) and Ahilya Sawh (University of Toronto).

Congratulations to Jialin and authors!

A huge congratulations to Jialin and co-authors on their work “Dissecting the regulatory logic of specification and differentiation during vertebrate embryogenesis“, now out on BioRxiv! This work generated a single-cell mulit-omics (both transcriptome and chromatin accessibility) atlas of early zebrafish embryogenesis. This allowed them to uncover new logic of expression regulation. A fantastic resource for the community! Read the work here

This work was a collaboration with the lab of Georg Seelig at the University of Washington who was on sabbatical here in the Schier lab. He was fun to have around!