Joe Bowness

Congrats Guifeng! Great to see this out in its final form

09.09.2025 13:04 — 👍 0    🔁 0    💬 1    📌 0

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...

16.07.2025 16:55 — 👍 105    🔁 38    💬 8    📌 1

Decoding cnidarian cell type gene regulation Animal cell types are defined by differential access to genomic information, a process orchestrated by the combinatorial activity of transcription factors that bind to cis -regulatory elements (CREs) to control gene expression. However, the regulatory logic and specific gene networks that define cell identities remain poorly resolved across the animal tree of life. As early-branching metazoans, cnidarians can offer insights into the early evolution of cell type-specific genome regulation. Here, we profiled chromatin accessibility in 60,000 cells from whole adults and gastrula-stage embryos of the sea anemone Nematostella vectensis. We identified 112,728 CREs and quantified their activity across cell types, revealing pervasive combinatorial enhancer usage and distinct promoter architectures. To decode the underlying regulatory grammar, we trained sequence-based models predicting CRE accessibility and used these models to infer ontogenetic relationships among cell types. By integrating sequence motifs, transcription factor expression, and CRE accessibility, we systematically reconstructed the gene regulatory networks that define cnidarian cell types. Our results reveal the regulatory complexity underlying cell differentiation in a morphologically simple animal and highlight conserved principles in animal gene regulation. This work provides a foundation for comparative regulatory genomics to understand the evolutionary emergence of animal cell type diversity. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, ERC-StG 851647 Ministerio de Ciencia e Innovación, https://ror.org/05r0vyz12, PID2021-124757NB-I00, FPI Severo Ochoa PhD fellowship European Union, https://ror.org/019w4f821, Marie Skłodowska-Curie INTREPiD co-fund agreement 75442, Marie Skłodowska-Curie grant agreement 101031767

I am very happy to have posted my first bioRxiv preprint. A long time in the making - and still adding a few final touches to it - but we're excited to finally have it out there in the wild:
www.biorxiv.org/content/10.1...
Read below for a few highlights...

06.07.2025 18:14 — 👍 59    🔁 24    💬 1    📌 2

Selective interaction of the protein SMCHD1 with specific chromatin regions is governed by the loading factor LRIF1 and SMCHD1 ATPase activity The chromosomal protein SMCHD1 is a GHKL ATPase that plays important roles in epigenetic silencing, including on the inactive X chromosome (Xi) and at the D4Z4 macrosatellite linked to regulation of D...

Fresh preprint by @flavia-con.bsky.social from our lab uncovers how SMCHD1 finds & binds chromatin using live-cell single-molecule imaging🔬

She reveals how SMCHD1 dynamically engages chromatin, including the inactive X chromosome, to maintain gene silencing.

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

26.06.2025 19:35 — 👍 12    🔁 7    💬 1    📌 0

Peer researchers in NHS research: approved in principle, undermined in practice? - Research Involvement and Engagement Background Despite the increasing support and expectation for involving people with lived experience in healthcare research in England, challenges persist when navigating organisational structures. Th...

Extremely proud of my sis for persevering through a huge number of roadblocks to get this article published! It's really important these stories are documented & get heard widely as stimuli to redress inequalities in systems of research doi.org/10.1186/s409... (she's now on a publishing 🔥 streak!)

20.06.2025 13:29 — 👍 2    🔁 0    💬 0    📌 0

Monumental work! Huge congrats to all involved

21.05.2025 16:28 — 👍 5    🔁 1    💬 0    📌 0

It was such a pleasure to visit the beautiful cities of Bonn and Cologne, and have the opportunity to present my postdoc work at the @dzne.science. Thank you so much for hosting me @jsschrepping.bsky.social!

17.05.2025 13:25 — 👍 9    🔁 0    💬 1    📌 0

Great to see the final form of this huge effort from the lab now published! Congrats Robert @juruehle.bsky.social @larsplus.bsky.social and all 🎉🎉
Read all about it this really cool work below ⬇️

09.05.2025 08:16 — 👍 9    🔁 1    💬 0    📌 0

Awesome! Congrats Iana (+co)!

08.05.2025 11:47 — 👍 3    🔁 0    💬 1    📌 0

Diversity and evolution of chromatin regulatory states across eukaryotes Histone post-translational modifications (hPTMs) are key regulators of chromatin states, influencing gene expression, epigenetic memory, and transposable element repression across eukaryotic genomes. ...

Excited to share this story from the “Chromatin Dream Team” in the @arnausebe.bsky.social lab on chromatin evo across eukaryotes! 12 histone mark profiles from 12 species, including rhizarians, discobans, and cryptomonads. Read on to see what we found! www.biorxiv.org/content/10.1... 1/n

19.03.2025 12:02 — 👍 53    🔁 26    💬 1    📌 4

Perfectly summarised! It was great to be part of such a fantastic event, and seamlessly cooperative organisation team. 😄

03.03.2025 08:56 — 👍 2    🔁 0    💬 0    📌 0

Preprint alert. Excited to share our latest work. We demonstrate that the primary function of m6A on Xist is to promote RNA degradation. www.biorxiv.org/content/10.1...

10.01.2025 17:58 — 👍 4    🔁 1    💬 0    📌 1