Tien-Chi Huang
@tienchihuang.bsky.social
Interested in chromatin dynamics during mammalian development
www.nature.com/articles/s41... I hope we will get the answer in my lifetime. 😂
PRC2–RNA interactions through the lens of bioinformatics pipeline choices - Nature Reviews Molecular Cell Biology
Four recent studies that have differently assessed PRC2–RNA interactions reveal key technical pitfalls underlying research in the field.
nature.com
A massive update: At least ~15 companies~ are selling scientists antibodies using faked validation data. We've documented 18,000+ manipulated images on 17,000+ products sold by leading laboratory suppliers including Thermo Fisher, Abcam, Santa Cruz Biotechnology, Millipore Sigma and Bio-Techne. 1/🧵
As a component of aseptic technique, Bunsen burners do not universally decrease deposition of microbe-containing particles journals.asm.org/doi/full/10.... #jcampubs
Why is the X chromosome rich in L1 mobile elements? @science.org X-chromosome inactivation draws L1 mutagenesis to the human X chromosome | Science www.science.org/doi/10.1126/...
X-chromosome inactivation draws L1 mutagenesis to the human X chromosome
X-chromosome inactivation (XCI) enables gene dosage compensation in XX eutherians. Long interspersed element-1 (LINE-1 or L1) retrotransposons are unusually abundant on the human X chromosome and are ...
science.org
My first PhD paper is out in Nucleic Acids Research! We describe "Ab-trapping" - an antibody artifact that distorts assays relying on antibody diffusion (microscopy, CUT&Tag, CUT&RUN). The revisions made the story much stronger. Check it out! doi.org/10.1093/nar/...
Antibody-trapping presents a widespread pitfall for microscopy and genomics in the nucleus
Abstract. Chromatin has a complex 3D structure and diverse binding proteins that coordinate the genome’s most essential functions. Many microscopy and geno
doi.org
It's been a while... dusted off some old code to see what the current publication lag times are at cell bio journals. At the end of the post there's the poor paper with the longest delay in the dataset... Hold On Hope: publication lag times at cell biology journals quantixed.org/2026/04/09/h...
Hold On Hope: publication lag times at cell biology journals
Publication lag times are still a frustration for researchers. Although preprints circumvent the delay in sharing science with others, publication is still king when it comes to evaluation. Contracts are short and publication delays can be long…
quantixed.org
academic.oup.com/genetics/adv... Also thanks to Lyndall & @psarkies.bsky.social, @ahocher.bsky.social, and members of the lab for their comments and Francis Barr @oxfordbiochemistry.bsky.social for encouraging me to write down my thoughts. 2/2
Actually, what is a gain-of-function mutation?
Abstract. For more than a century, scientists have worked to characterize, understand, and predict the consequences of mutations. For almost as long, scien
academic.oup.com
Happy to share our latest paper. Our findings uncover a unique chromatin architecture and spatial chromosome arrangement in gonadal germ cells and document that alongside global DNA demethylation, the germline epigenetic reprogramming involves reorganisation of the 3D genome.
Global reorganization of genome architecture at the transition to gametogenesis - Nature Structural & Molecular Biology
Huang, Rigau and colleagues observe major changes in how DNA is organized in early germ cells before they start developing into sperm or eggs. These results show that germline removes structural ‘memo...
nature.com
5/ Marthe Gautier played a crucial role in identifying trisomy 21 as the cause of Down syndrome. Working with minimal institutional support, she built a cytogenetics laboratory from scratch and produced the preparations that revealed an extra chromosome in affected children.
Nature has retracted a paper after an investigation at a U.K. institution found the first author — then a doctoral student — manipulated data.
Nature retracts paper for data manipulation by Ph.D. student
Nature has retracted a paper after an investigation at a U.K. institution found the first author — then a doctoral student — manipulated data. The paper, which looked at the sensitivity of lu…
retractionwatch.com
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀 Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function now revised and journal accepted at www.science.org/doi/10.1126/... 🧵👇
Happy to share our latest preprint. We uncover a previously uncharacterised and evolutionarily conserved chromatin architecture in premeiotic gonadal germ cells, revealed through integrated cytological and high-resolution Hi-C approaches. www.biorxiv.org/content/10.1... Thread🧵🔽
[3] Navigating the pitfalls of mapping DNA and RNA modifications www.nature.com/articles/s41... [*] Please note the detection of exogeneous DNA mods is different from mapping natural endogenous DNA mods , because abundant exogeneous DNA mods are introduced (e.g. Fiber-seq, DiMeLo-seq, etc) n/n [END]
Navigating the pitfalls of mapping DNA and RNA modifications - Nature Reviews Genetics
The ability to map DNA and RNA modifications has improved our understanding of these marks, but in some cases inconsistent results have been problematic. Here, Kong et al. discuss how to recognize and...
nature.com
I believe that over the past ~ two decades, since the breakthrough papers on UHRF1, this is the first reported DNA methylation phenotype of its close paralog, UHRF2 (and not for lack of trying). Congrats to Ambre Bender and Michael Weber on this fantastic study! www.nature.com/articles/s41...
UHRF2 mediates resistance to DNA methylation reprogramming in primordial germ cells - Nature Communications
DNA methylation in mouse primordial germ cells (PGCs) is restricted to transposable elements, but how this unique DNA methylome is established is poorly understood. Here, the authors identify UHRF2 as...
nature.com
Reading published results is like looking at the distant star-everything you see happened in the deep past. Light years between a truly novel discovery and its communication within the scientific community.
Alexis Verger 🧬🧫🧪@alexis-verger.cpesr.fr · last yr.How it started / How it's going 😱 (www.biorxiv.org/content/10.1... / www.nature.com/articles/s41...) #preprint
Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5
Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics
Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...
nature.com
It was nice to hear this story in the GRC conference. Glad it’s out.
Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free condition
Using mouse pluripotent stem cells, Nosaka et al. created an ovarian somatic cell (OSC)-free system to induce an abundant number of oocyte-like cells at diplotene arrest, followed by their growth into...
cell.com
🚨 Preprint alert 🚨 Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇 doi.org/10.1101/2025...
Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics
Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-tra...
doi.org
Paper out !!🥳big thanks to all authors @marliesoomen.bsky.social @diego-rt.bsky.social @kaessmannlab.bsky.social @jonathangoeke.bsky.social @lorenzamottes.bsky.social & 'bluesky-less' Lots of interesting new TE (& genes) biology Data fully browsable💻 👉 embryo.helmholtz-munich.de/shiny_embryo/
There has been a couple of manuscripts released regarding transcription factor footprinting - or digital genomic footprinting (DGF) as we call it. I would like to put some of the claims, results and conclusions in context, since I have worked and published on this for ~15 years. 1/n
Microscopy Nodes is now up on bioRxiv! 🚀 This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev). High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬 www.biorxiv.org/content/10.1...
