Darío Lupiáñez

VENIRSUS! dirás

🚨 Job Alert - Please share! 🙏

Interested in 3D gene regulation in development & evolution? 🤓🧬

💥 Our lab at @cabd-upo-csic.bsky.social is expanding!

We’re recruiting:
✅ PhD students
✅ Postdocs
💻🧪 Experimental or computational backgrounds welcome

👇 Details below

🚨JOB ALERT🚨PLEASE SPREAD and RT

Searching for a motivated Master’s student @bokelab.bsky.social @crg.eu @prbb.org to investigate how proteostasis in oocytes influences dormancy and fertility.

Reach out to me (adriano.bolondi@crg.es) to join us in sunny Barcelona!

See details below👇

If you want to explore ncRNA dynamics during mammalian development, love microscopy, and are not afaraid of transposons biology, apply‼️
We are looking for a postdoc to join our team at @imbavienna.bsky.social
More details 👇🏻

IRTG 2403 Regulatory Genome

25/n This project was part of the IRTG2403, a graduate school between Berlín Institutions and Duke University, funded by the @dfg.de and led by @uweohler.bsky.social 👏

www.regulatory-genome.hu-berlin.de/en

24/n And to our supporting institutions:
@cabd-upo-csic.bsky.social , @mdc-bimsb.bsky.social , @erc.europa.eu , @ageinves.bsky.social , @embo.org , @csic.es , @csicandalextrem.bsky.social, @pablodeolavide.upo.es , Junta de Andalucía

🙏 Your contributions made this work possible!

23/n 👏👏 Huge thanks to our amazing collaborators:
S. Dupont, A. Hurtado, V. Cadenas, L. Zuber, I. Maceda, O. Lao, J. Jedamzick, R. Kühn, S. Lacadie, A. Garcia-Moreno, @miguel-torres-1963.bsky.social , @fany-real.bsky.social, @rdacemel.bsky.social

22/n These and other interesting observations (as well as many Hi-C maps) can be found in the manuscript

Have a look and get in touch with us for any potential questions!!

21/n In summary, METALoci provide novel insights on #sexdetermination, going from fundamental mechanisms of #generegulation to their relevance in vivo.

This highlights the power of integrative genomic approaches to uncover the molecular underpinnings of developmental processes.

20/n We show that Meis1 and Meis2 act redundantly during sexual development

Through allele deletions in transgenic mice, we show these genes are essential to specify sexual identity in both females and males

The more Meis alleles deleted, regardless of the combination, the stronger the phenotype

20/n Finally, we reconstructed gene-regulatory networks associated to #sexdetermination

These networks are highly dynamic and include key sex-determining factors, as well as novel regulators like Meis genes

19/n Importantly, we demonstrate that METALoci predictions are tissue specific.

The deletion of the Fgf9 gonadal regulatory region causes sex reversal but overcomes the perinatal lung lethality typically associated with complete Fgf9 inactivation.

18/n Mutant gonads displayed two distinct phenotypes with different degrees of male-to-female sex reversal, same as in the full Fgf9 knockout.

Immunofluorescence revealed the simultaneous presence of testicular (SOX9) as well as ovarian (FOXL2) and meiotic markers (SYCP3).

17/n RNA-seq analysis of XY E13.5 gonads revealed a downregulation of Fgf9, as well as of other testicular genes.

In contrast, the female program was activated with the initiation of meiosis and the upregulation of ovarian genes.

16/n We identified a non-coding region located approximately 250 Kb downstream of Fgf9, whose deletion was predicted to be disruptive for its regulation.

To validate it, we generated different transgenic mouse lines carrying deletions of the region.

15/n We tested the potential of METALoci as predictive tool for regulatory activity

We investigated the regulation of Fgf9, a pro-testicular morphogen whose regulation was unknown

We computationally scanned the locus and estimated the effect of 50Kb deletions on Fgf9 metaloci

14/n From a regulatory perspective, we observe fundamental differences between the female and male pathways.

Male differentiation involves increased #enhancer activity and more activation/repression of sex-specific genes than female differentiation.

13/n Focusing on genes that transition from low to highly active 3D environments during Sertoli cell differentiation, we performed enrichment analysis.

This demonstrates that METALoci accurately captures the biology of the underlying process, just based on regulatory activity.

12/n METALoci quantified and compares regulatory activity between samples/conditions
I.e. Sox9 transitions from a 3D environment with low activity to a highly active.

We quantified and compared the temporal and sex-specific regulatory activity for all 24,027 genes in the mouse

11/n Using Hi-C and H3K27Ac data, METALoci reconstructs the 3D enhancer hubs (or metaloci) for each gene during sex determination

I.e. The testis-specific upregulation of Sox9 is associated with formation of a metaloci (in red) including its two known enhancers, TESCO & Enh13

10/n METALoci repurposed this type of analysis to quantify gene regulation, based on the fact that #enhancers and their target genes may cluster within the 3D nuclear space and display similar #epigenetic properties

9/n In the next image, you can see a map of the median household income in Paris. Red color indicates areas with high income surrounded by other blocks with similar income. The blue area shows the same for the low income. In pink-ish areas, there’s not a clear correlation.

8/n METALoci is based on spatial autocorrelation analysis, classically employed in geostatistics already since the 1950’s, to describe how a variable depends on space at a global and local scales.

7/n Here, we applied METALoci, an approach that integrates #3DGenome and #Epigenetics data into a unified framework maps, developed by @jrotwitguez.bsky.social & @mamartirenom.bsky.social from @cnag-eu.bsky.social @crg.eu

a woman says how is that possible in white letters ALT: a woman says how is that possible in white letters

6/n But are conventional tools for Hi-C analysis well suited to identify meaningful changes for #generegulation?

How can such a minor variation in 3D chromatin organization explain a process characterized by major changes in #transcription and cell identity?

5/n Our initial analyses revealed a high degree of conservation in TAD structures and moderate changes in A/B compartments.

3D chromatin structure seems to be mostly preformed before #sexdetermination occurs!

4/n We explored the 3D regulatory landscape of mammalian #sexdetermination in vivo, combining FACS sorting and low-input Hi-C.

Focusing on the cell lineage initiating this process: bipotential supporting cells that differentiate into granulosa (XX) or Sertoli (XY), in mice.

3/n Mammalian #sexdetermination is directed by the gonad, which can differentiate into ovary or testis.

This depends on the presence or absence of a Y chromosome and the SRY gene.

Sex-determining signals induce a physical and behavioral transformation of the entire organism.

a man in a suit and tie is sitting at a table and making a funny face . ALT: a man in a suit and tie is sitting at a table and making a funny face .

2/n Humanity has wondered how sex is determined for more than 2,000 years. Only in the last century we started to understand the genetic basis of this process. But not much is known about its #epigenetic regulation

Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs Nature Structural & Molecular Biology - METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining...

🤩💪 Out now! 3D regulatory hubs in sex determination

With @mamartirenom.bsky.social & Capel labs, led by @imotagom.bsky.social & @jrotwitguez.bsky.social

1️⃣ METALoci – explore #3DGenome 🧬
2️⃣ Non-coding region controlling Fgf9 🧩
3️⃣ Meis genes = new key players 🌟

👉 rdcu.be/e5sm2

1/n Bluetorial 👇