• DNA methylation enables recurrent endogenization of giant viruses in an animal relative

  Sarre, Luke A.; Kim, Iana V.; Ovchinnikov, Vladimir; Olivetta, Marine; Suga, Hiroshi; Dudin, Omaya; Sebé-Pedrós, Arnau; Mendoza, Alex de (American Association for the Advancement of Science (AAAS), 2024)

  5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. ...
• The structure and mechanics of the cell cortex depend on the location and adhesion state

  Flormann, Daniel; Kainka, Lucina; Montalvo, Gala; Rheinlaender, Johannes; Thalla, D.; Vesperini, Doriane; Pohland, M. O.; Kaub, K. H.; Schu, M.; Pezzano, Fabio; Ruprecht, Verena; Terriac, Emmanuel; Hawkins, Rhoda; Lautenschläger, Franziska (National Academy of Sciences, 2024)

  Cells exist in different phenotypes and can transition between them. A phenotype may be characterized by many different aspects. Here, we focus on the example of whether the cell is adhered or suspended and choose particular ...
• Common genetic variants associated with urinary phthalate levels in children: A genome-wide study

  Bustamante Pineda, Mariona; Balagué-Dobón, Laura; Casas Sanahuja, Maribel; Maitre, Léa; Nurtdinov, Ramil; González, Juan Ramón; Vrijheid, Martine (Elsevier, 2024)

  Introduction: Phthalates, or dieters of phthalic acid, are a ubiquitous type of plasticizer used in a variety of common consumer and industrial products. They act as endocrine disruptors and are associated with increased ...
• Long non-coding RNAs involved in Drosophila development and regeneration

  Camilleri Robles, Carlos; Amador, Raziel; Tiebe, Marcel; Teleman, Aurelio A.; Serras, Florenci; Guigó Serra, Roderic; Corominas Guiu, Montserrat (Oxford University Press, 2024)

  The discovery of functional long non-coding RNAs (lncRNAs) changed their initial concept as transcriptional noise. LncRNAs have been identified as regulators of multiple biological processes, including chromatin structure, ...
• Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya Virus

  Baquero Pérez, Belinda; Bortoletto, Enrico; Rosani, Umberto; Delgado-Tejedor, Anna; Medina, Rebeca; Novoa, Eva Maria; Venier, Paola; Díez Antón, Juana, 1962- (MDPI, 2024)

  The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus ...
• Modeling the impact of neuromorphological alterations in Down syndrome on fast neural oscillations

  Clusella, Pau; Manubens-Gil, Linus, 1989-; García Ojalvo, Jordi; Dierssen, Mara (Public Library of Science (PLoS), 2024)

  Cognitive disorders, including Down syndrome (DS), present significant morphological alterations in neuron architectural complexity. However, the relationship between neuromorphological alterations and impaired brain ...
• CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing

  Carbonell Sala, Silvia; Perteghella, Tamara; Lagarde, Julien; Nishiyori, Hiromi; Palumbo, Emilio; Arnan Ros, Carme; Takahashi, Hazuki; Carninci, Piero; Uszczynska-Ratajczak, Barbara; Guigó Serra, Roderic (Nature Research, 2024)

  Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts ...
• The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics

  Corominas Guiu, Montserrat; Guigó Serra, Roderic (Oxford University Press, 2024)

  The Catalan Initiative for the Earth BioGenome Project (CBP) is an EBP-affiliated project network aimed at sequencing the genome of the >40 000 eukaryotic species estimated to live in the Catalan-speaking territories ...
• Detection of differential bait proteoforms through immunoprecipitation-mass spectrometry data analysis

  Kourtis, Savvas; Cianferoni, Damiano; Serrano Pubull, Luis, 1982-; Sdelci, Sara (Nature Research, 2024)

  Proteins are often referred to as the workhorses of cells, and their interactions are necessary to facilitate specific cellular functions. Despite the recognition that protein-protein interactions, and thus protein functions, ...
• A dynamic in vitro model of Down syndrome neurogenesis with trisomy 21 gene dosage correction

  Bansal, Prakhar; Banda, Erin C.; Glatt-Deeley, Heather R.; Stoddard, Christopher E.; Linsley, Jeremy W.; Arora, Neha; Deleschaux, Cécile; Ahern, Darcy T.; Kondaveeti, Yuvabharath; Massey, Rachael E.; Nicouleau, Michael; Wang, Shijie; Sabariego Navarro, Miguel; Dierssen, Mara; Finkbeiner, Steven; Pinter, Stefan F. (American Association for the Advancement of Science (AAAS), 2024)

  Excess gene dosage from chromosome 21 (chr21) causes Down syndrome (DS), spanning developmental and acute phenotypes in terminal cell types. Which phenotypes remain amenable to intervention after development is unknown. ...
• An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity

  Faure, Andre J.; Lehner, Ben, 1978-; Miró Pina, Verónica; Serrano Colomé, Clàudia; Weghorn, Donate (Public Library of Science (PLoS), 2024)

  Accurate models describing the relationship between genotype and phenotype are necessary in order to understand and predict how mutations to biological sequences affect the fitness and evolution of living organisms. The ...
• Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images

  Wernersson, Erik; Gelali, Eleni; Girelli, Gabriele; Wang, Su; Castillo, David; Mattsson Langseth, Christoffer; Verron, Quentin; Nguyen, Huy Q.; Chattoraj, Shyamtanu; Martinez Casals, Anna; Blom, Hans; Lundberg, Emma; Nilsson, Mats; Martí Renom, Marc A.; Wu, Chao-Ting; Crosetto, Nicola; Bienko, Magda (Nature Research, 2024)

  Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of ...
• A TdT-driven amplification loop increases CRISPR-Cas12a DNA detection levels

  Zwerus, Jordy T.; Berghuis, Nicole F.; Jacques, Jeroen M.; Mars-Groenendijk, Roos; Busker, Ruud W.; Paauw, Armand; de Jong, Ad L.; van Leeuwen, Hans C. (Elsevier, 2024)

  Recent findings on CRISPR-Cas enzymes with collateral DNAse/RNAse activity have led to new and innovative methods for pathogen detection. However, many CRISPR-Cas assays necessitate DNA pre-amplification to boost sensitivity, ...
• The hepatocyte epidermal growth factor receptor (EGFR) pathway regulates the cellular interactome within the liver fibrotic niche

  Gonzalez-Sanchez, Ester; Vaquero, Javier; Caballero Díaz, Daniel; Grzelak, Jan; Fusté, Noel P.; Bertran, Esther; Amengual, Josep; García Sáez, Juan; Martín-Mur, Beatriz; Gut, Marta; Esteve-Codina, Anna; Alay, Ania; Coulouarn, Cedric; Calero Pérez, Silvia; Valdecantos, Pilar; Valverde, Angela M.; Sánchez, Aránzazu; Herrera, Blanca; Fabregat, Isabel (Wiley, 2024)

  Liver fibrosis is the consequence of chronic liver injury in the presence of an inflammatory component. Although the main executors of this activation are known, the mechanisms that lead to the inflammatory process that ...
• Documenting the de-identification process of clinical and imaging data for AI for health imaging projects

  Kondylakis, Haridimos; Garcia Lezena, Teresa; Tsiknakis, Manolis (Springer, 2024)

  Artificial intelligence (AI) is revolutionizing the field of medical imaging, holding the potential to shift medicine from a reactive "sick-care" approach to a proactive focus on healthcare and prevention. The successful ...
• PHF2-mediated H3K9me balance orchestrates heterochromatin stability and neural progenitor proliferation

  Aguirre, Samuel; Pappa, Stella; Serna Pujol, Núria; Padilla, Natàlia; Iacobucci, Simona; Nacht, A. Silvina; Vicent, Guillermo Pablo; Jordan Vallès, Albert; Cruz, Xavier de la; Martínez Balbás, Marian A. (EMBO Press, 2024)

  Heterochromatin stability is crucial for progenitor proliferation during early neurogenesis. It relays on the maintenance of local hubs of H3K9me. However, understanding the formation of efficient localized levels of H3K9me ...
• Targeting the autophagy-NAD axis protects against cell death in Niemann-Pick type C1 disease models

  Kataura, Tetsushi; Sedlackova, Lucia; Sun, Congxin; Kocak, Gamze; Wilson, Niall; Banks, Peter; Hayat, Faisal; Trushin, Sergey; Trushina, Eugenia; Maddocks, Oliver D. K.; Oblong, John E.; Miwa, Satomi; Imoto, Masaya; Saiki, Shinki; Erskine, Daniel; Migaud, Marie E.; Sarkar, Sovan; Korolchuk, Viktor I. (Nature Research, 2024)

  Impairment of autophagy leads to an accumulation of misfolded proteins and damaged organelles and has been implicated in plethora of human diseases. Loss of autophagy in actively respiring cells has also been shown to ...
• 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 ...

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