Artem Ilin

Cool story! Do you think Nxf2 has a role in 3'UTRs conversion to piRNA source loci?

piRNAs are essential for transposon silencing in the animal germline.
But how do hosts trap transposon sequences in genomic loci that help establish a piRNA response?

Looking at a natural transposon invasion, Baptiste Rafanel and Kirsten Senti made some remarkable observations.

Dynamics and distribution of eccDNA in Arabidopsis. Left: Schematic representation of eccDNA amplification and sequencing via CIDER-Seq pipeline. Top right: EccDNA size distribution in Arabidopsis Col-0 leaf tissues (n = 4,158). The x-axis shows eccDNA size in kb and the y-axis shows the percentage of eccDNAs belonging to each window. Middle right: Size ranges of eccDNAs with marked median and quantiles (n = 4,190). Bottom right: Percentages of eccDNA reads mapping to TAIR CDS, TE, or intergenic databases (values represent the average of three replicates).

Previous studies of extrachromosomal circular DNA #eccDNA in #plants are based on short-read seq. @vanderschuren-lab.bsky.social uses long-read seq to obtain a map of full-length eccDNAs from #Arabidopsis, identifying their genomic origins & epigenetic regulation @plosbiology.org 🧪 plos.io/44Mq3RI

Colossal BS is getting even shadier

Not going to throw any shade at Margaret Kidwell but it would be nice to know if anyone tried to do the follow-up. There are just three articles in pubmed about that mite species, one of which is the correction to the news article on the Houck paper, that gives important detail to theory imo

I wouldn't call it a follow-up: different species of mites and transfer of bacteria instead of TEs, although the results are pretty cool. In the field, we talk constantly about TE HT, but the vectors are rarely properly brought up, unfortunately.

4/4 So what's crazy to me is that it's been more than 30 years since that paper and, despite P-element popularity, there were no follow-ups from other researchers or mites genome sequencing to check whether they don't have P-elements in their DNA. I guess people really hate mites🤷‍♂️ #TESky

3/4 could've happened when mites fed on one species and then injected TE DNA into another species! This seems to be possible bc of the common areal habitat of two flies species, but the authors also point out that the events of a successful HT would have a very low probability.

2/4 that actually feed on medium, do not incorporate P. 3) But the most important, they've showed that P in first mites was coming from their feeding, by finding non-TE assoc seqs in those mites meaning that horizontal transfer (HT) between D. willistoni and melanogaster

1/4 Okay, this is actually crazy. Let's deconstruct the paper. 1. Authors showed that mites feeding on fly eggs and larvae "acquired" P-element DNA. The same mites assoc. w/ flies lacking P, did not have P. 2) They ruled out the contamination with medium and showed that common mites,

Cephalotes - Alex Wild is a diverse genus of heavily-armored, tree-dwelling myrmicine ants found in forested regions of the new world tropics and subtropics. A number of canopy species show the unusual habit of controlled ...

My full gallery of turtle ants is here:

Possible Horizontal Transfer of Drosophila Genes by the Mite Proctolaelaps regalis There is strong inferential evidence for recent horizontal gene transfer of the P (mobile) element to Drosophila melanogaster from a species of the Drosophila willistoni group. One potential vector of...

I need you, and I can't stress this enough, to read this paper by Margaret Kidwell et al. on horizontal transfer of P elements from mites to flies and back...from *1991*: www.science.org/doi/10.1126/...

Grateful to @mannerviklab.bsky.social and @biologsp.bsky.social for hosting a nano-scCUT&Tag workshop for all @scentinel.bsky.social partners. Amazing tour at @scilifelab.se and wonderful hospitality by the Sweds...they did spoil us! missing the cool summer weather and the calmness of Stockholm...

Retrotransposon 3S18 forms self-protective aggregates and prolongs mid-oogenesis Transposons are parasitic elements prevalent across nearly all species. Here, Shen et al. tracked the dynamics of a unique retrotransposon in live ovaries, showing that upon activation, this retrotran...

It's interesting that other Bel/Pao family TE, Copia, forms full fledge viral particles (also, a LOT of them) but here I saw nothing about gag function of 3S18. Is it dispensable? Do any particles form at all?🤔

A postdoc position in the Torben Heick Jensen lab, Aarhus University, Denmark: Mammalian Nuclear RNA Production and Turnover Systems - Ledig stilling på Aarhus Universitet Ledig stilling ved Institut for Molekylærbiologi og Genetik - RNA-biologi og -innovation, Aarhus Universitet

Second call for postdoc positions in the lab. Please follow the link below to apply or get in touch for further information.
mbg.au.dk/aktuelt/ledi...

🖥️🧬 The University of Innsbruck is offering PostDoc fellowships for women: www.uibk.ac.at/en/research/...

Do you have a strong plan for a bioinformatics project (e.g. spatial/single-cell/multiomic data analysis, AI for oncology, immunogenomics)? I would be happy to support you with your application!

Long-read RNA sequencing of transposable elements from single cells using CELLO-seq - Nature Protocols Single-cell long-read RNA sequencing enables the high-fidelity mapping of single-cell expression data from highly sequence-similar transposable elements to unique genomic loci by correcting errors fro...

Very happy to share our protocols paper for CELLO-seq. This will make single cell long read RNA-seq more accessible and provides analysis guidelines. We hope this helps the #transposon #TEsky community and folks working on #singleCell isoform and allelic #gene expression. doi.org/10.1038/s415...

😴😢

Hi, if you are looking to come to Canada for a post-doc or a PhD, consider my lab to study the genetic basis of social interactions, using the fruit fly! My university (Western University) has a new program to welcome you! See below! #drosophila #postdoc #canada #PhD #social #behaviouralneurogenetic

Arthropod Model Organisms | LEGO® Ideas Scientists have learned a great deal about biology from a handful of "model organisms" – animals with unique characteristics that make them excellent for labora…

I can't believe this only ended up getting 3,590 supporters when it needed 10,000; it was a sad day. This has unlocked a new fixation, and I will campaign to get this reopened... #Drosophila #Tribolium #CoolScience #FruitFlies

beta.ideas.lego.com/product-idea...

The sticker from the anti nuclear energy movement formed in 70s in Denmark with modified text: Nuclear war? Yes please

The irony was not lost on me

Grundtvigs kirke left me speechless

Spatiotemporal Tracking of Three Novel Transposable Element Invasions in Drosophila melanogaster over the Last 30 Years Abstract. Transposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting a significant influence on evolution througho

You think P-element was the latest TE invasion in #Drosophila melanogaster? Think again! #TEsky

Latest in #G3journal: Cytological studies revealed that ELYS, a conserved nuclear pore complex subunit in #Drosophila, is involved in the apposition of female and male pronuclei, affecting the parental genome configuration of the first mitotic spindle during fertilization.

buff.ly/68yqGrg

Drosophila hamlet mediates epithelial tissue assembly of the reproductive system Hamlet regulates heterotypic epithelial fusion by controlling spatial and temporal expression of known and novel epithelial regulators like Wnt and Tl pathway components, a mechanism potentially conse...

To be or not to be 🤴💀: read how hamlet orchestrates the assembly of adult male reproductive system in #Drosophila in a new paper from our colleagues! Led by Huazhen Wang, a PhD student in Qi Dai group, the study explores how this protein mediates the fusion of testis and supportive gonadal tissue

Abundant piRNA production mediated by the Drosophila GTSF1 homolog Tpp ensures Aubergine localization and germ plasm assembly | PNAS Germ cells transmit genetic information to offspring and maintain the genome of the species. In many animals including Drosophila, germ cell format...

Sometimes, I have wicked thoughts about piRNA field being exhausted at this point, but then I see papers like this and am proven that it's alive and kicking. Kudos to authors for not naming a new factor Obelix or Pumpkin.
www.pnas.org/doi/10.1073/...

Transcriptional and post-transcriptional regulation of transposable elements and their roles in development and disease - Nature Reviews Molecular Cell Biology Transposable elements (TEs) comprise nearly half of the human genome. This Review discusses transcriptional and post-transcriptional mechanisms that repress TE activity, how TEs escape this suppressio...

We wrote a review on Transposable Elements (TEs) and almost all aspects of TE silencing and their roles in biological processes & disease.
www.nature.com/articles/s41...

Verboten is a nice touch

One could say that kebab pizza is an acquired taste. I haven't acquired it yet, tho

About half of C. elegans genes have unknown functions. There isn’t even an agreement on how many genes humans have and I believe most human genes remain uncharacterised with only anecdotal evidence for a specific function. So yeah, go play with your virtual cell and all.