• The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development

  Nakagawa, Shoma; Carnevali, Davide; Tan, Xiangtian; Alvarez, Mariano J.; Parfitt, David-Emlyn; Di Vicino, Umberto; Arumugam, Karthik; Shin, William; Aranda, Sergi; Normanno, Davide; Sebastián Pérez, Rubén; Cannatá, Chiara; Cortes, Paola; Neguembor, Maria Victoria; Shen, Michael M.; Califano, Andrea; Cosma, Maria Pia (Elsevier, 2024)

  Embryo size, specification, and homeostasis are regulated by a complex gene regulatory and signaling network. Here we used gene expression signatures of Wnt-activated mouse embryonic stem cell (mESC) clones to reverse ...
• TANGO1 inhibitors reduce collagen secretion and limit tissue scarring

  Raote, Ishier; Häkkinen, Hanna-Maria; Vibe, Carine; Broadbent, Katrina; Carolis, Carlo; Ruprecht, Verena; Malhotra, Vivek (Nature Research, 2024)

  Uncontrolled secretion of ECM proteins, such as collagen, can lead to excessive scarring and fibrosis and compromise tissue function. Despite the widespread occurrence of fibrotic diseases and scarring, effective therapies ...
• Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization

  Kant, Aayush; Guo, Zixian; Vinayak, Vinayak; Neguembor, Maria Victoria; Li, Wing Shun; Agrawal, Vasundhara; Pujadas, Emily; Almassalha, Luay; Backman, Vadim; Lakadamyali, Melike; Cosma, Maria Pia; Shenoy, Vivek B. (Nature Research, 2024)

  In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this ...
• Developing a platform for secretion of biomolecules in Mycoplasma feriruminatoris

  Gonzalez de Miguel, Javier; Montero-Blay, Ariadna, 1994-; Ciampi, Ludovica; Rodriguez-Arce, Irene; Serrano Pubull, Luis, 1982- (BioMed Central, 2024)

  Background: Having a simple and fast dividing organism capable of producing and exposing at its surface or secreting functional complex biomolecules with disulphide bridges is of great interest. The mycoplasma bacterial ...
• Engineering Mycoplasma pneumoniae to bypass the association with Guillain-Barré syndrome

  Broto, Alicia; Piñero-Lambea, Carlos; Segura-Morales, Carolina; Tio-Gillen, Anne P.; Unger, Wendy W. J.; Burgos, Raul; Mazzolini, Rocco; Miravet Verde, Samuel; Jacobs, Bart C.; Casas, Josefina; Huizinga, Ruth; Lluch-Senar, Maria 1982-; Serrano Pubull, Luis, 1982- (Elsevier, 2024)

  A non-pathogenic Mycoplasma pneumoniae-based chassis is leading the development of live biotherapeutic products (LBPs) for respiratory diseases. However, reports connecting Guillain-Barré syndrome (GBS) cases to prior M. ...
• Systematic mapping of organism-scale gene-regulatory networks in aging using population asynchrony

  Eder, Matthias; Martin, Olivier M. F.; Oswal, Natasha; Sedlackova, Lucia; Moutinho, Catia; Carmen Fabregat, Andrea del; Menéndez Bravo, Simón; Sebé-Pedrós, Arnau; Heyn, Holger; Stroustrup, Nicholas (Elsevier, 2024)

  In aging, physiologic networks decline in function at rates that differ between individuals, producing a wide distribution of lifespan. Though 70% of human lifespan variance remains unexplained by heritable factors, little ...
• Staying on track - Keeping things running in a high-end scientific imaging core facility

  Renaud, Oliver; Aulner, Nathalie; Salles, Audrey; Halidi, Nadia; Brunstein, Maia; Mallet, Adeline; Aumayr, Karin; Terjung, Stefan; Levy, Daniel; Lippens, Saskia; Verbavatz, Jean-Marc; Heuser, Thomas; Santarella-Mellwig, Rachel; Tinevez, Jean-Yves; Woller, Tatiana; Botzki, Alexander; Cawthorne, Christopher; Core4Life Consortium; Munck, Sebastian (Wiley, 2024)

  Modern life science research is a collaborative effort. Few research groups can single-handedly support the necessary equipment, expertise and personnel needed for the ever-expanding portfolio of technologies that are ...
• Non-canonical role for the BAF complex subunit DPF3 in mitosis and ciliogenesis

  Verrillo, Giulia; Obeid, Anna Maria; Genco, Alexia; Scrofani, Jacopo, 1984-; Orange, François; Hanache, Sarah; Mignon, Julien; Leyder, Tanguy; Michaux, Catherine; Kempeneers, Céline; Bricmont, Noëmie; Herkenne, Stephanie; Vernos, Isabelle, 1959-; Martin, Maud; Mottet, Denis (Company of Biologists, 2024)

  DPF3, along with other subunits, is a well-known component of the BAF chromatin remodeling complex, which plays a key role in regulating chromatin remodeling activity and gene expression. Here, we elucidated a non-canonical ...
• Characterization of the common genetic variation in the spanish population of Navarre

  Maillo, Alberto; Beltran, Sergi; Gómez Cabrero, David (MDPI, 2024)

  Large-scale genomic studies have significantly increased our knowledge of genetic variability across populations. Regional genetic profiling is essential for distinguishing common benign variants from disease-causing ones. ...
• Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic β-cell survival and function

  Hu, Ming; Kim, Innah; Morán, Ignasi; Peng, Weicong; Sun, Orien; Bonnefond, Amélie; Khamis, Amna; Bonàs-Guarch, Silvia; Froguel, Philippe; Rutter, Guy A. (Wiley, 2024)

  Variants at the SLC30A8 locus are associated with type 2 diabetes (T2D) risk. The lead variant, rs13266634, encodes an amino acid change, Arg325Trp (R325W), at the C-terminus of the secretory granule-enriched zinc transporter, ...
• Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data

  Otalora Acevedo, Katherin Eliana; Riera, Joan Lluís; Tavecchia, Giacomo; Rotger, Andreu; Igual, José Manuel; Trotta, Jean-Remi Paul; Baldo, Laura (Wiley, 2024)

  Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized ...
• Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming

  Martínez Sarmiento, José A.; Cosma, Maria Pia; Lakadamyali, Melike (Elsevier, 2024)

  During cell fate transitions, cells remodel their transcriptome, chromatin, and epigenome; however, it has been difficult to determine the temporal dynamics and cause-effect relationship between these changes at the ...
• Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster

  Sklias, Athena; Cruciani, Sonia; Marchand, Virginie; Spagnuolo, Mariangela; Lavergne, Guillaume; Bourguignon, Valérie; Brambilla, Alessandro; Dreos, René; Marygold, Steven J.; Novoa Pardo, Ana María; Motorin, Yuri; Roignant, Jean-Yves (Oxford University Press, 2024)

  During their maturation, ribosomal RNAs (rRNAs) are decorated by hundreds of chemical modifications that participate in proper folding of rRNA secondary structures and therefore in ribosomal function. Along with pseudouridine, ...
• Membrane to cortex attachment determines different mechanical phenotypes in LGR5+ and LGR5- colorectal cancer cells

  Conti, Sefora; Venturini, Valeria; Cañellas Socias, Adrià; Cortina Duran, Carme; Abenza, Juan F.; Stephan-Otto Attolini, Camille; Middendorp Guerra, Emily; Xu, Catherine K.; Li, Jia Hui; Rossetti, Leone; Stassi, Giorgio; Roca-Cusachs, Pere; Diz-Muñoz, Alba; Ruprecht, Verena; Guck, Jochen; Batlle Gómez, Eduard; Labernadie, Anna; Trepat, Xavier (Nature Research, 2024)

  Colorectal cancer (CRC) tumors are composed of heterogeneous and plastic cell populations, including a pool of cancer stem cells that express LGR5. Whether these distinct cell populations display different mechanical ...
• Intron detention tightly regulates the stemness/differentiation switch in the adult neurogenic niche

  González Iglesias, Ainara; Arcas Mantas, Aida; Domingo Muelas, Ana; Mancini, Estefanía; Galcerán, Joan; Valcárcel, J. (Juan); Fariñas, Isabel; Nieto, M. Ángela (Nature Research, 2024)

  The adult mammalian brain retains some capacity to replenish neurons and glia, holding promise for brain regeneration. Thus, understanding the mechanisms controlling adult neural stem cell (NSC) differentiation is crucial. ...
• CSDE1: a versatile regulator of gene expression in cancer

  Ciocia, Annagiulia; Mestre Farràs, Neus; Vicent Nacht, Ignacio; Guitart, Tanit; Gebauer, Fátima (Oxford University Press, 2024)

  RNA-binding proteins (RBPs) have garnered significant attention in the field of cancer due to their ability to modulate diverse tumor traits. Once considered untargetable, RBPs have sparked renewed interest in drug ...
• Beyond quiescent and active: Intermediate microglial transcriptomic states in a mouse model of down syndrome

  Fernández Blanco, Álvaro; Sierra, Cesar; Tejido, Clara; Dierssen, Mara (MDPI, 2024)

  Research on microglia in Down syndrome (DS) has shown that microglial activation, increased inflammatory gene expression, and oxidative stress occur at different ages in DS brains. However, most studies resulted in simplistic ...
• YY1 binding is a gene-intrinsic barrier to Xist-mediated gene silencing

  Bowness, Joseph S.; Almeida, Mafalda; Nesterova, Tatyana B.; Brockdorff, Neil (Nature Research, 2024)

  X chromosome inactivation (XCI) in mammals is mediated by Xist RNA which functions in cis to silence genes on a single X chromosome in XX female cells, thereby equalising levels of X-linked gene expression relative to XY ...
• LATS1 controls CTCF chromatin occupancy and hormonal response of 3D-grown breast cancer cells

  Ramírez Cuéllar, Angélica Julieta; Ferrari, Roberto; Sanz, Rosario T.; Valverde Santiago, Marta; García García, Judith; Nacht, A. Silvina; Castillo, David; Le Dily, François; Neguembor, Maria Victoria; Malatesta, Marco; Bonnin, Sarah; Martí Renom, Marc A.; Beato, Miguel; Vicent, Guillermo Pablo (Nature Research, 2024)

  The cancer epigenome has been studied in cells cultured in two-dimensional (2D) monolayers, but recent studies highlight the impact of the extracellular matrix and the three-dimensional (3D) environment on multiple cellular ...
• Integrating physics in deep learning algorithms: a force field as a PyTorch module

  Orlando, Gabriele; Serrano Pubull, Luis, 1982-; Schymkowitz, Joost; Rousseau, Frédéric (Oxford University Press, 2024)

  Motivation: Deep learning algorithms applied to structural biology often struggle to converge to meaningful solutions when limited data is available, since they are required to learn complex physical rules from examples. ...

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