What happens when you change the promoter of my favorite gene? Sox9?

Daniel Ibrahim@danielibrahim.bsky.social · 10mo ago

What is a promoter? And how does it work? We very happy to share our latest work trying to understand enhancer-promoter compatibility. I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters www.biorxiv.org/content/10.1...

⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation. 👉 We discover how sex and development signals are decoded at a single gene locus. www.nature.com/articles/s41... 👇 Bluetorial

Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology

Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.

nature.com

📢To all the sex determination lovers! 📢 Get ready for the 10th International Symposium on the Biology of Vertabrate Sex Determination (VSD). We exchange the nostalgic Hawaii beaches with the gorgeous Crete beaches 🏖! The meeting will take place on 23-27 March 2026. biology-of-vsd.my.canva.site

Publishing an exciting paper and getting an ISF grant, both at the same week, is a good justification of Pizza and Prosecco in the middle of the day! 🍾🥂 Huge congrats to Isabelle, Meshi and Elisheva for this superb publication 💪

1/n Very excited to share our recent paper published on @ScienceAdvances where we dissect the gene regulatory landscape guiding mouse sex determination! science.org/doi/10.1126/... A huge well done to @IsabelleStevant.genomic.social.ap.brid.gy, Meshi and Elisheva who spearhead this project!

The gene regulatory landscape driving mouse gonadal supporting cell differentiation

Multiomics analysis revealed the regulatory elements and transcription factors responsible for gonadal sex determination.

science.org

Alpha Genome by DeepMind... Will it be as good as AlphaFold?? deepmind.google/discover/blo...

AlphaGenome: AI for better understanding the genome

Introducing a new, unifying DNA sequence model that advances regulatory variant-effect prediction and promises to shed new light on genome function — now available via API.

deepmind.google

Male mouse fetuses can develop female organs in utero if their mother is iron deficient during pregnancy https://go.nature.com/43N7f4s

Male mice can grow ovaries if their pregnant mums are iron deficient

The study is the first to show that low iron levels can affect fetal sexual development.

go.nature.com

One of the coolest papers in the field of sex determination! It is the first evidence that environmental aspects can affect mammalian sex determination!! www.nature.com/articles/s41...

Maternal iron deficiency causes male-to-female sex reversal in mouse embryos - Nature

Iron-deficient conditions in pregnant mice can cause XY mouse embryos to develop female rather than male genitalia, revealing that iron metabolism has a role in determining male sex in mice.

nature.com

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭 Check out our paper - fresh off the press!!! We find widespread functional conservation of enhancers in absence of sequence homology Including: a bioinformatic tool to map sequence-diverged enhancers! rdcu.be/enVDN github.com/tobiaszehnde...

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances

Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...

rdcu.be

Had the best time in Geneva, visiting my friend and collaborator Serge Nef. I saw the beautiful city of Geneva, gave a seminar at the Medicine Faculty of Geneva University and met many brilliant scientists!! Heading next to Zurich for the #TT2025 meeting to hear about transgenic mice technologies!

A tour de force study from Taipale&Yin labs. It expands the vocabulary of the Regulatory Code by adding 1131 TF:TF composite motifs that are different from the individual TF motifs. The new composite motifs are enriched in cell-type specific elements and active in vivo www.nature.com/articles/s41...

DNA-guided transcription factor interactions extend human gene regulatory code - Nature

A large-scale analysis of DNA-bound transcription factors (TFs) shows how the presence of DNA markedly affects the landscape of TF interactions, and identifies composite motifs that are recognized by ...

nature.com

Very cool and about time! www.sciencealert.com/hormone-free...

Hormone-Free Male Birth Control Pill Enters Clinical Trials For The First Time

A hormone-free male birth control pill is undergoing clinical testing for the first time ever.

sciencealert.com

Highly recommend all scientist to watch the movie Joy on Netflix! It tells the story of IVF and the birth of Louise Joy Brown in 1978 and all the scientific endeavour behind. Millions of failures for 1 amazing success! This is what science is all about m.imdb.com/title/tt1024...

Joy (2024) ⭐ 7.1 | Biography, Drama, History

1h 55m | PG-13

m.imdb.com

Exonic enhancers are a widespread class of dual-function regulatory elements x.com/biorxiv_geno...

bioRxiv Genomics on X: "Exonic enhancers are a widespread class of dual-function regulatory elements https://t.co/Ho0TdalAsu #biorxiv_genomic" / X

Exonic enhancers are a widespread class of dual-function regulatory elements https://t.co/Ho0TdalAsu #biorxiv_genomic

x.com

Among the fun parts of being a scientist is going to conferences!! A first time in Washington D.C where I will present our work at the #asa_ica25conf tomorrow. Come and hear me if you are here

Ready for it??? To all the **sex determination lovers** 📢 Save the date to the 10th International Symposium on the Biology of Vertebrate Sex Determination (VSD) held in the beautiful Hawaii!! Great community, amazing science, excellent speakers and superb location 🏝 📢 March 23-26, 2026 📢

Israeli friends! Interested in learning & practicing the thinking tools of the creative process in science? Join the Night Science workshop in Tel Aviv University next week! Register here: forms.office.com/r/xVhzcHTy1t Thank you @judithberman11.bsky.social for organizing! @odedrechavi.bsky.social

📣 We are advertising for a postdoc to join our team at the University of Edinburgh! Our lab studies gene regulatory mechanisms in development, and how genetic changes may impact these processes to alter development and shape human craniofacial form and function 🧬🧪

An excellent article about the biology of sex and how it is being regarded by the US government thehill.com/opinion/whit...

Me and all my XYs... Love them!

After many postpones due to war, military service and just general depression, we went out today for a super fun day in Tel Aviv. I have such an AMAZING lab and I am so happy to be thier friend, mentor, and just doing science and fun togerher ❤️

It will be very bad if this will happen. Far less research on females in many topics that will eventually harm 50% of the population www.thetransmitter.org/policy/exclu...

Exclusive: NIH appears to archive policy requiring female animals in studies

Such a shift would “put us back in the dark ages in terms of our science,” says neuroscientist Anne Murphy, who helped to formulate the original policy.

thetransmitter.org

www.ynet.co.il/environment-... ושום גרנט לא יוקרתי כמו פרסום ב YNET 🤣 שמחה להיות ה XX היחידה ברשימה יוקרתית ונכבדת של 11 XY.

ממיפוי עננים ועד גידול אשכים במעבדה: מענק יוקרתי ל-12 פרופסורים מישראל

שלושה חוקרים ממכון ויצמן למדע, שלושה מהאוניברסיטה העברית, שניים מהטכניון, שניים מבית החולים שיבא, חוקר מאוניברסיטת תל אביב וחוקרת מאוניברסיטת בר-אילן יקבלו מהאיחוד האירופי מענק "הוכחת היתכנות", שנועד ...

ynet.co.il

Thankful for the @ERC_Research for their continuous support in our research with an ERC PoC. We plan to generate testis organoids from pre-pubertal boys testis biopsies, taken prior to chemotherapy.

How to test the functional impact of non-coding variants in vivo? We developed a new method called dual-enSERT, which can quantitatively compare the effects of enhancer variants in live mouse embryos in under two weeks. www.nature.com/articles/s41... 1/n

The Gonen Lab lighting the fifth Chanukah candle together ❤️

Makhtesh Ramon in the Negev Desert. Beautiful and peaceful place. Apparently 80/96 of the chemical elements in the periodic table can be found here!!!

It was great to gather around today all the PIs at the Life Sciences Faculty @Bar_ilan, light the second Candle of Hanukkah, have our dean Cyrille Cohen playing, and giving a talk about my lab science in my home base. Superb Faculty and such a great feeling of home

Scared to share this after 10 freaking years of waiting, but here we go: We found that temperature *perception* can change the biology of the next generations, even when “it’s just in the parents' head”. Read how C. elegans neurons control epigenetic inheritance! www.biorxiv.org/content/10.1...

Perception of Temperature Even in the Absence of Actual Change is Sufficient to Drive Transgenerational Epigenetic Inheritance

Can processes occurring in one individuals nervous system influence the physiology of the descendants? Here we explored the provocative hypothesis that parents sensation or perception of environmental...

biorxiv.org