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Dorien Pastoors

@dpastoors.bsky.social

Postdoc at DFCI, Boston, USA | molecular biology & hematology 🧫 | data visualization in #ggplot | swimming, running, baking | HemeSky feed

405 Posts1623 Follower999 Folgt
Jesse Engreitz@jengreitz.bsky.social · 3d ago

Systematic mapping of enhancers, silencers, and topological elements using prime editing deletion screens www.biorxiv.org/content/10.6... Check out our preprint on next-generation tech for mapping distal regulatory effects! We’re excited to help set this up - please get in touch Thread 👇

Systematic mapping of enhancers, silencers, and topological elements with prime editing deletion screens

Noncoding regulatory elements in the human genome can control gene expression through distinct mechanisms, including acting as enhancers, silencers, or topological elements. However, we lack tools to ...

biorxiv.org

Shawn Cai@xshawncai.bsky.social · 3d ago

Have you ever looked at a gene in IGV or a genome browser and wondered “What are all those (ATAC-seq/H3K27ac/CTCF ChIP-seq/…) peaks doing?” 🤔 I’m thrilled to share that we developed a new technology called Swap-seq to answer that exact question. Swap-seq: www.biorxiv.org/content/10.6...

c0nc0rdance@c0nc0rdance.bsky.social · last wk.

Let's talk about the HALLOWEEN GENES (really). 1979: It was a dark & stormy night⛈️& a scientist (Eric Wieschaus) is laboring over a microscope🔬, observing the dead remains of ... a fruitfly🪰. But not just ANY fruitfly. This was a TWISTED & MUTATED fruitfly with a GHOSTLY, transparent appearance.

Mad Scientist Working in a Laboratory

Alt: Mad Scientist Working in a Laboratory. A man in a lab coat works on a large cabinet sized device covered in proper dials and levers and blinky lights. We used to be researchers. PROPER researchers.

static.klipy.com

Philippe Batut@philippebatut.bsky.social · last mo.

🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇

Noncoding transcription controls the developmental dynamics of long-range gene regulation

The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...

science.org

Kazuhiro Maeshima@kazu-maeshima.bsky.social · 2w ago

🧬 Highly related @natgenet.nature.com paper from @binzmit.bsky.social group, using nucleosome-resolution chromatin modeling: Euchromatin forms condensed domains with short active regions on the surface www.nature.com/articles/s41... Congratulations! 🎉

Euchromatin forms condensed domains with short active regions on the surface - Nature Genetics

Simulations integrating micro-C and imaging data provide a coherent view of chromatin organization from nucleosomes to clutches to domains, revealing that most regions form compact domains but short r...

nature.com

Kazuhiro Maeshima@kazu-maeshima.bsky.social · last mo.

Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)

Dorien Pastoors@dpastoors.bsky.social · last mo.

Congratulations, this sounds very cool and interesting!! Makes me continie to wonder what the true meaning is of atac-seq signal

Kazuhiro Maeshima@kazu-maeshima.bsky.social · last mo.

Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)

Vijay G. Sankaran@bloodgenes.bsky.social · 2mo ago

🚨👇 Check out this wonderful collaborative work identifying a new 3D genome regulator - Matchmakers - with the incredible @andersshansen.bsky.social ! Fantastic work led by Varshini Ramanathan and Chun-Jie Guo!

Anders Sejr Hansen@andersshansen.bsky.social · 2mo ago

(1/n) Excited to share close collab w @bloodgenes.bsky.social led by Varshini & Chun-jie et al How to induce expression of key genes while silencing much of the genome during Erythropoiesis? A: Matchmaker CREs load cohesin near key genes to promote looping & exp: www.biorxiv.org/content/10.6...

Elzo de Wit lab @ NKI@dewitlab.bsky.social · 3mo ago

(1/10) The majority of human genetic variation is located in non-coding regions. The great challenge of the post-genomic era is to assign function to these variants. We reasoned that combining haplotyping with allele-specific multiomics can help pinpoint the functional ones: rdcu.be/fgr5W. A thread:

Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning

Nature Communications - How non-coding mutations in DNA contribute to phenotypes is a largely unresolved question. Here the authors integrate personal genomics and machine learning to identify...

rdcu.be

Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 4mo ago

Interested in hearing about mechanisms of cohesin-dependent vs. -independent enhancer regulation? @karissalhansen.bsky.social will be presenting her work **Tues June 23rd 8am CET** www.biorxiv.org/content/10.6... www.science.org/doi/10.1126/... Thank you @genome-org-aus.bsky.social ! 👇

GOA - Genome Organisation Australia@genome-org-aus.bsky.social · 4mo ago

Only one week to go until our next GOA seminar! @karissalhansen.bsky.social will present here work on the mechanisms of long-range enhancer-promoter communication. Registration link: unimelb.zoom.us/webinar/regi...

Total Internal Reflection🇬🇧🇺🇸🇺🇦@tirscienceblog.bsky.social · 4mo ago

The #ThermoFisher #antibody scandal is an ugly reminder, I think, of how few people (including those at TF, it seems) are trained to properly validate antibodies before use. Some advice on antibody validation in the posting 👇 totalinternalreflectionblog.com/2022/09/18/h...

Hitting the target (a short guide to validating antibody specificity)

Antibodies are essential and ubiquitous tools in biology, but their unguarded usage can easily lead to error. Here’s how to validate their specificity, and ensure that they’re hitting the rig…

totalinternalreflectionblog.com

Reese Richardson@reeserichardson.bsky.social · 4mo ago

The Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)

Mark Peifer (He, him)@peiferlabunc.bsky.social · 5mo ago

By the way, @dshb-antibodies.bsky.social is a non-profit that sells quality antibodies to many proteins at exceptionally reasonable prices, without AI generated faux-validation images. Check them out. dshb.biology.uiowa.edu

Developmental Studies Hybridoma Bank - DSHB

High quality, low cost antibodies.

dshb.biology.uiowa.edu

Mark Peifer (He, him)@peiferlabunc.bsky.social · 5mo ago

Someone in the news departments of @nature.com or @science.org needs to take a look at this--its a huge scandal from the scientific supplier that has become a monopoly

Anders Sejr Hansen@andersshansen.bsky.social · 5mo ago

(1/n) Super excited to share that our preprint is out today in @natsmb.nature.com with a new name "Integrated MINFLUX tracking reveals two distinct chromatin dynamics classes across cell types" and more than 2x more data: www.nature.com/articles/s41... See also MIT News news.mit.edu/2026/how-chr...

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Anders Sejr Hansen@andersshansen.bsky.social · last yr.

(1/n) Thread @matteomazzocca.bsky.social @domenicnarducci.bsky.social Simon Grosse-Holz @jessematthias.bsky.social preprint Q: how does chromatin move? Using MINFLUX, SPT & SRLCI, we track chromatin dynamics across 7 orders of magnitude in time to provide answers www.biorxiv.org/content/10.1...

Dorien Pastoors@dpastoors.bsky.social · 6mo ago

I am very happy to have been awarded a Rubicon Postdoctoral fellowship from the NWO (Dutch Science Council) (Science/Life Sciences domain) for my postdoc in the @tothovalab.bsky.social at @danafarber.bsky.social / @broadinstitute.org! www.nwo.nl/en/news/thir...

Thirteen early-career researchers set to cross borders thanks to Rubicon grants | NWO

No fewer than thirteen talented researchers who have recently completed their PhDs are being given the opportunity to gain valuable research experience abroad. The Rubicon round, organised by NWO, had...

nwo.nl

Elzo de Wit lab @ NKI@dewitlab.bsky.social · 7mo ago

🧵 CTCF is essential for embryonic development, but why has remained unclear. By combining gastruloids with a temporal degron system, we uncovered a surprising dual function — and it changes how we think about CTCF's role in development. 1/8 www.biorxiv.org/content/10.6...

A dual role for CTCF in development

CTCF is an essential DNA binding protein whose absence leads to embryonic lethality. CTCF is primarily known for its role in 3D genome organization where its N-terminal domain interacts with cohesin to anchor chromatin loops. How CTCF facilitates proper embryonic development remains unclear, necessitating temporal control to resolve its stage-specific functions. By combining gastruloids, an in vitro model of embryonic development, with a degron system to rapidly deplete CTCF at defined timepoints, we show that early CTCF depletion impairs early gastruloid morphogenesis. Surprisingly, ATAC-seq and time-resolved RNA-seq revealed that differentiation was unaffected. CTCF binding is strongly enriched at promoters of downregulated genes. Re-expression of a CTCF variant with an N-terminal truncation, incapable of looping, was sufficient to rescue the expression of CTCF-promoter bound genes and the defects in morphogenesis. However, extended culture (up to 168 hours) of gastruloids reconstituted with N-terminal truncated CTCF led to their collapse. Our work shows that CTCF has a dual function in early mammalian development: at early stages CTCF regulates developmentally important genes through promoter binding, while at later stages its looping function is required for correct development. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 637587, 865459 Dutch Research Council, https://ror.org/04jsz6e67, 016.161.316, VI.C.222.049 Dutch Cancer Society, https://ror.org/0368jnd28, N/A

biorxiv.org

Dorien Pastoors@dpastoors.bsky.social · 8mo ago

having a look at my HemeSky feed for the first time in a while (have been on an off bluesky a bit) but this looks so interesting! my HemeSky feed picks up interesting papers as well podcasts such as this one, and also blood-themed valentine cards 👀 (@ash.hematology.org ) : bsky.app/profile/dpas...

Bloody Minded Pod@bloodyminded.bsky.social · 8mo ago

Bringing it back to basics this week with a chat on myelopoiesis to set up our upcoming run on myeloid disorders. Sorry but the gimp jokes are necessary fundamental knowledge #hemesky #meded #thefactorymustgrow www.bloodyminded.com.au/allepisodes/...