Michalis Averof

NB. Data should be released in the coming week

Credit to all co-authors for a great collaboration. Gillian Forbes, Emilia Skafida, Irene Karapidaki developed the approach and generated resources. Mathilde Paris led the omics and data crunching. Thanks to @frm-officiel.bsky.social @erc.europa.eu @ec.europa.eu for supporting our research. /5

Producing these resources might seem costly, but we found we could detect islands of sequence conservation with low coverage genome sequencing (~10X), by mapping sequence reads across species (no need assemble the genomes). Saves a lot of money and effort, particularly on large genomes. /4

These approaches allow us to narrow down the search for cis-reg elements and to search genome-wide for elements with particular properties. This has allowed us to identify ubiquitous, muscle- and neuron-specific cis elements, driving robust expression of transgenic reporter constructs. /3

We combined 2 approaches to identify cis-reg elements. First, we produced bulk & single nucleus ATACseq data, to focus on sequences that are accessible for gene regulation. Second, we sequenced the genomes of 3 additional Parhyale spp, to identify islands of seq conservation across the genome. /2

In animals with large genomes, finding cis-regulatory elements can be very challenging. Enhancers can be located tens/hundreds of kb away from their target promoters. We face this challenge in Parhyale, with >3 Gbp genome.
We just published a preprint describing how we are tackling this problem. /1

I like this concept of the genome as a compressed representation of an organism. Not like a ZIP file that recreates the same file in smaller form, but more like an AI model where a compact sequence (DNA) generates an organism through probabilistic interactions using molecules that it encodes itself.

Mapping of NGS reads to a reference genome
@mbsj-official.bsky.social

"This cover depicts The Bridge in the NGS Rain where people are being exposed to torrents of genomic information [...]. The man standing in the middle of the bridge is pictured deep in thought, considering how to utilize this sequence data set of the ALDH2 gene." @mbsj-official.bsky.social

Just discovered the wonderful covers of 'Genes to Cells', the journal of the Molecular Biology Society of Japan @mbsj-official.bsky.social – absolutely beautiful!

here some examples inspired by mitosis, CRISPR, the DNA helix, and plant pigments

À quoi ressemble le quotidien dans un laboratoire de recherche ?
En 2025, Arthur Monternier, étudiant en art, a passé six mois dans notre laboratoire. Il raconte son expérience dans cette bande dessinée.

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How is everyday life in a research lab?
Last year Arthur Monternier, an art student, joined our lab for 6 months. He conveys his experience in this comic strip.

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nice work! are you assuming that mayflies represent the ancestral state? why are there no changes is the long branch leading to mayflies?

Happy new year to all!

(photo by Karl Blossfeldt, Art Forms in Nature, 1928)

you can find them all here: libraryofbabel.info/About.html

I see, thank you. As a naive outsider, I'm interested in the scientific question, not much in the personal differences.

In biology we can probably live with "immensely complex", no? Would it be fair to conclude that you differ in your assessment of how likely and how complex these models could be?

how large is it?

Yes. But independently of this move, ERC is undeniably contributing to the latter.

I suspect this is EU trying to respond to the mess in USA, without really adressing the problem at home. ERC probably operating under a lot of constraints.

Assholes no, that's unfair to the ERC. But I do agree that more (smaller) grants are needed, rather than larger ones. There's a big gap to fill between national- and ERC-level grants. Independent of age.

That's what 'the napolitans' we up to when they briefly invaded our lab! Wonderful memories from December 2021 and November 2022. Congratulations!!

Our ultimate goal: exploring biology beyond well established research organisms, by building tools that will make new things visible

Ending 🧵 with a marker for visualising chanoflagellates, closest unicellular relatives of animals, by @jujumathieu.bsky.social and @thibautbrunet.bsky.social

By studying these markers in a multiple organisms, we could identify ones that label the cell membrane most clearly and consistently across species (circle sizes represent how well markers perform in each species). Gathering the info involved more than 10 research labs.
see doi.org/10.1101/2024... 🧵

Some of the markers do not label the cell surface clearly, but shuttle across different parts of the cell. You can see in this early crustacean embryo, how the fluorescence pattern changes as the cells multiply. The video was made by Manon Koenig, Irene Karapidaki and @berylbiologist.bsky.social

🧵

Our lab studies how animals regenerate their body, e.g. how crustaceans regenerate broken legs. One of our aims is to understand if regeneration re-uses the gene networks that built the legs in the first place. Arthur Monternier, an artist in our team, captured the question in this cartoon.

And this is the surface of the larvae of mediterranean stinging jellyfish. It's composed of cells measuring about a hundredth of a millimetre in size. The cells' outlines are visible thanks to fluorescent markers identified by Clara Deleau and @cnidevo.bsky.social

see doi.org/10.1101/2024...

🧵

These are embryos of a jellyfish, made up of cells that are about a fiftieth of a millimetre in size. Their outlines are visible thanks to fluorescent markers identified by Sarah Asaf and @clytia-vlfr.bsky.social

see doi.org/10.1101/2024...

🧵

What are these?

You are looking at embryos of a sea squirt. Each of the 'soap bubbles' is a living cell, about a fourtieth of a millimetre in size. The outlines of the cells are visible thanks to fluorescent markers identified by Hitoyoshi Yasuo @hitoyas.bsky.social

see doi.org/10.1101/2024... 🧵

the basis of optimism is sheer terror (Oscar Wilde); perhaps this applies here