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Reposted by Tomàs Montserrat Ayuso

Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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🚨 New preprint alert!

Excited to share my first PhD paper, supervised by @annaesteveco.bsky.social at @cnag-eu.bsky.social:

📄 A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses
📄 Preprint: www.biorxiv.org/content/10.1...

🧬 Read on for the dataset & code!

A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses

Human endogenous retroviruses (HERVs) occupy nearly 8% of the human genome, yet their protein-coding potential remains largely unexplored. Like their exogenous counterparts, HERVs derive from ancestra...

www.biorxiv.org

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Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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We hope this helps others working on retroviral domains, paleovirology, or TE functional genomics.

🙏 Thanks to @cnag-eu.bsky.social and @annaesteveco.bsky.social for support.

We welcome feedback, questions, or collaborations as we submit to a peer-reviewed journal.

Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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🧰 All annotations are open-access:

- BED + FASTA files
- InterProScan + Phobius output
- Domain sequences & conservation scores
- Scripts on GitHub

🧬 Data: doi.org/10.5281/zeno...

💻 Code: github.com/funcgen/herv...

Domain-Level Annotations and Conservation Scores for Human Endogenous Retroviruses

💡Introduction: This dataset provides a comprehensive, genome-wide annotation of conserved retroviral protein domains within human endogenous retroviruses (HERVs). Using a reproducible pipeline based ...

doi.org

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Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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🧠 Intriguingly, HERV activity has been linked to neurodegenerative diseases (ALS, MS, AD) and immune defense.

- HERV-encoded proteins may modulate immunity
- Some may even restrict exogenous viruses

Our dataset enables deeper exploration of these hypotheses.

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Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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🧬 One famous case of HERV co-option is Syncytin, a retroviral Env protein now essential for placenta formation.

Could other HERV proteins—preserved across millions of years—also serve beneficial roles in the human host?

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Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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Why does this matter?

✔️ Residual protein function?
✔️ Host co-option?
✔️ Antiviral defense?
✔️ Role in development, immunity, neurodegeneration?

Our resource supports new lines of research into the functional potential of HERV proteins.

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Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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🔍 We also found 13 HERVK loci encoding Gag, Pol, and Env with strong domain conservation and intact 5′/3′ LTRs.

- Some domains even share the same ORF—suggesting fused or intact polyproteins.

- A few insert into human gene introns—potential regulatory effects?

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Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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💡 Subfamily patterns:

- HERVK: Full polyproteins across several loci

- HERVH: Conserves enzymatic domains, but not structural

- HERVE: Unexpectedly retains protease & RT domains

Young and ancient families both preserve functional fragments!

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Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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🧠 3 examples:

- HERVK Env (99.5% coverage, fusion domains) chr5:156658763–156665917

- HERVH RNase H (DEDD motif) chr14:53129175–53135122

- HERV-E protease (full-length) chr1:20154322–20160102

More details in the preprint!

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Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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💡 To our surprise, thousands of domains are highly conserved, with >1,000 showing nearly full alignment (>95% coverage).

We even recovered key catalytic motifs (e.g. DEDD in RNase H) and transmembrane regions in Env.

These are not just fossils—they may retain function.

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Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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💻 Using a reproducible pipeline (HMMER + InterProScan), we identified 17,540 retroviral domains—incl. Gag, RT, RNase H, protease, integrase, and Env.

We then quantified alignment coverage to assess structural conservation.

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Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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🧬 HERVs make up ~8% of the human genome.

Yet no systematic annotation of protein domains within their internal sequences—quantifying structural conservation—has been released.

We analyzed >120,000 ORFs to address this gap.

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Tomàs Montserrat Ayuso @tmontsay.bsky.social · Jul 31

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🚨 New preprint alert!

Excited to share my first PhD paper, supervised by @annaesteveco.bsky.social at @cnag-eu.bsky.social:

📄 A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses
📄 Preprint: www.biorxiv.org/content/10.1...

🧬 Read on for the dataset & code!

A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses

Human endogenous retroviruses (HERVs) occupy nearly 8% of the human genome, yet their protein-coding potential remains largely unexplored. Like their exogenous counterparts, HERVs derive from ancestra...

www.biorxiv.org

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Reposted by Tomàs Montserrat Ayuso

CNAG @cnag-eu.bsky.social · May 26

🧬Great presentation by our Functional Genomics Team Leader, @annaesteveco.bsky.social, at #eshg2025!

🗣️She showcased our work on “Integrative multi-omics for undiagnosed Rare Diseases (Omics-RD)”

👏 Congratulations, Anna, and well done to the team behind this project!
#RareDiseases #CNAG

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Reposted by Tomàs Montserrat Ayuso

CNAG @cnag-eu.bsky.social · May 22

🌍Today is #BiodiversityDay!
🧬At CNAG, we decode genomes to protect life on Earth and guide conservation efforts

🦉In the last two years, we have assembled nearly 50 reference genomes under the umbrella of @ebpgenome.bsky.social, @ergabiodiv.bsky.social, and @catbiogenoma.bsky.social
#Biodiversity

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Reposted by Tomàs Montserrat Ayuso

Gennady Gorin @goringennady.bsky.social · Apr 15

New preprint out!
This is probably my most important paper. To my deep chagrin, it has no math.
XIST is a non-coding RNA exclusive to XX females. It silences one of the X chromosomes.
So what is it doing in male heart Schwann cells?

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Apr 15

Male XIST expression in cardiac pseudo-glia does not induce X chromosome inactivation https://www.biorxiv.org/content/10.1101/2025.04.09.648005v1

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Reposted by Tomàs Montserrat Ayuso

CNAG @cnag-eu.bsky.social · Feb 19

🌟Great News: CNAG is now on BlueSky!
🚀From Barcelona to the world, we’re bringing you the latest in genomics!

Stay tuned for breaking news, cutting-edge technologies, groundbreaking research, and upcoming events

🔗https://www.cnag.eu
#Genomics #Innovation #Research #BlueSky #CNAG

a blue sky with a butterfly and the word bluesky on it

ALT: a blue sky with a butterfly and the word bluesky on it

media.tenor.com

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Reposted by Tomàs Montserrat Ayuso

Anshul Kundaje @anshulkundaje.bsky.social · Jan 7

Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/

www.encodeproject.org/single-cell/...

Single cell – ENCODEHomo sapiens clickable body map

www.encodeproject.org

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Reposted by Tomàs Montserrat Ayuso

Anshul Kundaje @anshulkundaje.bsky.social · Dec 25

Our ChromBPNet preprint out!

www.biorxiv.org/content/10.1...

Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

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Reposted by Tomàs Montserrat Ayuso

Will Macnair @willmacnair.bsky.social · Dec 20

So happy to see this work published!

This is still the biggest single nuclei dataset of MS, and poses some fascinating questions. We found that the proportions of cell types across lesion types varied as expected, e.g. in active lesions we saw fewer oligos and more microglia.

Anna Williams @annawilliamslab.bsky.social · Dec 20

Delighted to see this research now out. Thank you to @willmacnair.bsky.social, @gocastelobranco.bsky.social, @rebeccakssmith.bsky.social, @sjaekel.bsky.social, charles ffrench-Constant, Dheeraj Malhotra and many more not on bluesky for making it happen.

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Reposted by Tomàs Montserrat Ayuso

Institute for Regeneration and Repair @edinuni-irr.bsky.social · Dec 20

People living with multiple sclerosis #MS could be prescribed personalised treatment in future, helped by research published in Neuron today in which Prof Anna Williams and colleagues studied more than half a million brain cells. @mssocietyuk
regeneration-repair.ed.ac.uk/personalised...
#CRM

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Reposted by Tomàs Montserrat Ayuso

Anna Esteve Codina @annaesteveco.bsky.social · Dec 13

Huge effort from @anaconesa.bsky.social at @scb.iec.cat comparing long-read RNA technologies @pacbio.bsky.social @nanoporetech.com and softwares #sqanti3, #bambu, #talon, #isoquant, for isoform discovery, still challenging to disentangle real biology from artefacts

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Reposted by Tomàs Montserrat Ayuso

Lee Zamparo @lzamparo.bsky.social · Dec 13

Also filter on markers like MALAT1, cell intronic mapping reads cf. bmcgenomics.biomedcentral.com/articles/10....

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Reposted by Tomàs Montserrat Ayuso

Anna Esteve Codina @annaesteveco.bsky.social · Dec 12

Brilliant presentation by @jamesasharpe.bsky.social at XII Jornades de Bioinformàtica i Genòmica by @scb.iec.cat about mechanistic dynamical models and #Turing patterns to go from genes to phenotypes

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Reposted by Tomàs Montserrat Ayuso

Anna Esteve Codina @annaesteveco.bsky.social · Dec 12

Spreading our work at the XII Jornades de Bioinformàtica i Genòmica de la @scb.iec.cat @tmontsay.bsky.social about our recent discovery rdcu.be/d04Gz of pervasive presence of not completly lysed cells in reference cell atlases @humancellatlas.org compromising quality & model training

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