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Hello! We did it! I mean they did it! A project that started way before I arrived at the BF2i lab, and was lucky (not sure I felt lucky at the time) to get onboard in my first months of arriving in the lab (back in 2017!). So here it is : we sequenced a coleoptera genome (the rice grain weevil) and found loads of repeats! We did a pretty good post on the project that you can find it here https://threadreaderapp.com/thread/1458370899439202307.html and here https://threadreaderapp.com/thread/1458478910472179715.html
Have fun reading it!
I am really happy that our collaboration with Eirini is finally out. Mariana put some real effort into the TE analysis, starting when we were first approached by Eirini nearly two years ago. It was a bumpy road but the final manuscript is really nice. Eirini & co have put together a very thorough story on the sensing of TE transcripts by MDA5, and the consequent activation of quiescent haematopoietic stem cells.
One of the hard things in this project was to make sense of the whole TE transcripts. Analysing TE expression is not an easy task (10.1038/s41576-020-0251-y). TE families, TE copies, copies within genes ... Hopefully for Mariana and I, it is easier to work with the mouse/human genome than it is with our crazy insect species with 70% TE content and massive bursts of transposition!
A follow up analysis could check where those TE copies upregulated upon chemotherapy treatment are located : are whole families upregulated or simply a couple of copies (our analysis points towards a few copies only), where are those copies found, are those transcripts a consequence of pervasive transcription? And the L1 donwregulation seems also pretty consistent and I would like to see more analysis done on MDA5 knockouts. We'll wait and see!
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