@dariloops.bsky.social
A bit of 3D gene regulation, single-cell omics and transgenic models. Born and raised in the bay of Algeciras. Enjoying Science and Flamenco at CABD, Seville. Lab website: https://lupianezlab.github.io/Website/ Email: dario.lupianez@csic.es
✉️ Research Briefing by @mamartirenom.bsky.social and I on our recent study, where we employ a new method, METALoci, to explore the 3D regulatory landscape of sex determination.
👏Thanks to @mcgambetta.bsky.social & @dimitristypas.bsky.social for their insights.
👉 Full manuscript: rdcu.be/e5sm2
Ever wondered how a eukaryotic transcription factor finds its specific DNA motif in the vast genome? In this preprint, we directly measured the dynamics of this search process in living cells, revealing a cooperative mechanism mediated by disordered regions. 1/10 doi.org/10.64898/202...
@csic.es @csicandalextrem.bsky.social @pablodeolavide.upo.es @embo.org @erc.europa.eu @ageinves.bsky.social
🐟How does the Amazon molly defy all evolutionary odds and overcome the detrimental costs of asexual reproduction?🧬
😊Glad that @rdacemel.bsky.social and I could contribute to this fascinating study, brilliantly led by Ed Ricemeyer @nature.com
👏Congrats to all authors!
@cabd-upo-csic.bsky.social
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 👇🏻
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
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!