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!

Congratulations to Annika and Max on their cichlid temporal niche partitioning paper!

Does being active at different times of the day support speciation in adaptive radiations? Max and Annika screened 60 different Lake Tanganyika cichlid species (with help from the Salzburger lab). They found a huge range of diversity, with many species active at different times of day, including diurnal and nocturnal species (day and night active respectively). Read the paper here.

Congratulations to Phil whose killifish paper is now out in Science!

An exciting story about how killifish have adapted their development from Phil and co-authors is now out! Killifish manage to survive extreme drought by their eggs entering a dormant diapause state. Phil and co-authors found that embryonic cells of killifish lack maternally pre-patterned of the dorsal ventral axis. Instead, the cells self-organise to form the body axis.

Read the paper here

Read a news article here

Find out more about Phil’s lab at University of Washington here

Congratulations Vassilis on his paper on missing arousal molecule orexin/hypocretin in Botiidae fish species

We’re excited to see Vassilis’s paper on chromobotia fish sleep is out! When he was young he had an aquarium of chromobotia fishes. They come from the inland waters in Indonesia on the islands of Sumatra and Borneo. Vassilis could show that these fish have a very consolidated sleep compared to zebrafish, they even lie down on their sides! Surprisingly, this fish species lacked a functional version of the orexin/hypocretin arousal neuropeptide. Lack of this gene causes narcolepsy in dogs and humans. However, it doesn’t cause narcolepsy in these fish.

Learn more in the article

Yiqun's paper is now on BioRXiv! Congratulations!

Cellular differentiation - where stem cells become specialised cell types, for example, the differentiation of embryonic stem cells to functional cell types like neurons or liver cells, is not completely understood. Yiqun’s study presents a novel approach for identifying functional gene modules and demonstrates how transcription factors can control both general and specialised cell functions.

Congratulations to Yiqun and the other collaborators, which includes the lab of Jeff Farrell - a former lab member now at NIH!

Read the paper here

Madalena preprint on 5'UTR regulatory logic is online!

Congratulations Mada and co-authors on their work The regulatory landscape of 5′ UTRs in translational control during zebrafish embryogenesis. Mada 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 again to Mada and the team!

Congratulations to Max and co-authors on their new BioRxiv paper on the evolution of day-night activty!

The daily change between night and day is an important signal in our environment. Animal species have adapted their activity patterns to optimise for activity for certain times of day. For example, eagles are diurnal (day active) while owls are nocturnal (night active). Published work suggests that mammals were mostly nocturnal during when they first evolved, and only diversified into diurnal species after the mass extinction of dinosaurs. However, we don’t know how these evolutionary patterns could look like for bony fishes - which make up about half of all vertebrate species. In this paper, we used a meta-analysis of activity patterns combined with phylogenetic reconstruction to investigate the evolutionary transitions of diurnality and nocturnailty of extant lineages. We find that the last common ancestor of bony fishes and all vertebrates was likely nocturnal. And that bony fishes are especially good at switching between diurnality and nocturnality (twice as much as the other vertebrates - birds, reptiles, mammals and amphibians). This work suggests that nocturnal lineages are more likely to survive through mass extinction events.

Read more in the manuscript Frequent transitions from night-to-day activity after mass extinctions here

And check out this piece in Science News here

Congratulations and farewell to Max Shafer who leaves us to start his own lab in Toronto!

Max and his wife Ahilya have moved to the University of Toronto to start their own labs. Max will be at the Department of Cell and Systems Biology and will continue working on the genetic regulation and evolution of sleep in cichlids and other fishes, learn more about his lab and their future research here.

We wish them all the best for this exciting new step in their scientific and personal lives!

Vassilis starts new job at Novartis!

Vassilis has moved from the Schier Lab to start an exciting position supporting data analysis at Norvatis! Vassilis has been a core part of the Schier lab, bringing genuine curiosity as well as a calm depth and breadth of knowledge. He will be sorely missed by all of us. Vassilis had ambitious aims during his postdoc, working on different aspects of sleep in clown loaches and, with Will, Amelia and Clare, on sleep homeostasis in mice. Keep tuned in the next year to hear more about these projects!