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Reposted by Nitzan Gonen

Edda Schulz @eddaschulz.bsky.social · 2d

⚠️ 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.

www.nature.com

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Nitzan Gonen @nitzan-gonen.bsky.social · 9d

📢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

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Nitzan Gonen @nitzan-gonen.bsky.social · Aug 4

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 💪

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Nitzan Gonen @nitzan-gonen.bsky.social · Aug 1

Thank you so much Sandra 🙏

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Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

Thanks dear and thank you for all the help and advice 😘

Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

Thanks Rod 🙏

Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

Thanks so much Jen!!

Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

10/n And like any good paper, this is just the beginning for many cool followup projects where we delve into the mechanism and functional exploration of candidate enhancers. Cool stuff in the pipe, stay tuned!!!
We want to thank the reviewers for the constructive advice 🙏

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Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

9/n Last but not least, we performed ATAC TFs footprinting to look for TF occupancy on the regulatory regions. While we found the usual suspects in Sertoli cells: SOX, DMRT, NR5A1, the top occupied motif in granulosa cells was that of Lhx9/Emx2!!

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Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

8/n In addition, we conducted computational linkage analysis linking genes to their regulatory elements in a positive (enhancer) or negative manner (silencer).

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Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

7/n We then applied Promoter Capture HiC on E13.5 Sertoli and granulosa cells and were able to identify physical proximity between enhancers and their target genes. This was done with the superb Lera Malysheva.

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Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

6/n We then focused on regulatory elements. We identified numerous regulatory elements that are specific to the sex (testis/ ovaries) or to the developmental time

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Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

5/n We employed ATAC-seq and RNA-seq on these cells to identify their gene expression and functional regulatory elements. We provide a cool tool that enables you to track the expression of your gene of interest. Check this out:
4ljrl2-roni-weiss.shinyapps.io/tpm_allgenes/

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Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

4/n To start looking at that we started a project 5 years ago that came into completion now. We used existing and new transgenic mouse lines that enable u to purify Sertoli and granulosa cells during 4 key time pints in which the sex is being determined (E11.5-15.5)

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Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

3/n So, I believe that a lot of the action is mediated via the non-coding parts of the genome, but where exactly??? it is 98% of the genome!

a man in a suit and tie is standing in front of a window with blinds

ALT: a man in a suit and tie is standing in front of a window with blinds

media.tenor.com

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Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

2/n So you all know that I am obsessed about my precious Enh13, deletions/duplications of which lead to XY and XX sex reversal in mice and human. And, we know that most DSD patients fail to receive genetic diagnosis even after whole exome sequencing.

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Nitzan Gonen @nitzan-gonen.bsky.social · Jul 27

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

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Nitzan Gonen @nitzan-gonen.bsky.social · Jun 27

Congrats Vicki, super interesting!

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Nitzan Gonen @nitzan-gonen.bsky.social · Jun 26

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

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Reposted by Nitzan Gonen

Nature @nature.com · Jun 4

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

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Nitzan Gonen @nitzan-gonen.bsky.social · Jun 5

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.

www.nature.com

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Reposted by Nitzan Gonen

Daniel Ibrahim @danielibrahim.bsky.social · May 27

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

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Nitzan Gonen @nitzan-gonen.bsky.social · Apr 23

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!

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Reposted by Nitzan Gonen

Evgeny Kvon @evgenykvon.bsky.social · Apr 9

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 ...

www.nature.com

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