bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic regulation of visual system remodeling during flatfish metamorphosis: DNA methylation dynamics in ocular migration and visual adaptation
Authors: Guerrero-Peña Laura , Suarez-Bregua Paula , Sánchez-Baizán Nuria , Piferrer Francesc , Tena Juan J. , Rotllant Josep 
Published: February 2025

AbstractFlatfish metamorphosis is characterized by extensive tissue remodeling, associated with a transition from pelagic to benthic lifestyle, being the migration of one eye the most dramatic change. Epigenetic mechanisms exert a pivotal role in developmental programs. This study investigates the DNA methylation profiles of migrating and non-migrating eyes using reduced-representation bisulfite sequencing (RRBS) during three developmental stages of turbot: pre-metamorphosis, climax and post-metamorphosis. Over 31% of all identified regions were hypermethylated during climax stage in both eyes, coinciding with elevated expression of thednmt3agene, responsible for de novo methylation. Additionally, transcription factors crucial for retinal ganglion cells (RGCs) development, including theeomesaandtbr1b, exhibited differential methylation and expression between the migrating and non-migrating eye during the climax phase. These findings underscore the significance of DNA methylation in the intricate remodeling of the visual system during turbot metamorphosis, particularly regarding RGC-mediated ocular migration and the transmission of visual signals.
C.La.P.: Enhancing transformer-based genomic signal modeling by integrating DNA sequences and chromatin accessibility data
Authors: Nisantzis Panos Firbas , Gonçalves Carolina , de Polavieja Gonzalo 
Published: February 2025

AbstractTransformers have shown promise in chromatin modeling but have primarily relied solely on reference DNA sequences, limiting their utility across multiple biological contexts. In this work we enhance transformer models by integrating reference sequences with ATAC-seq, a chromatin accessibility assay. Our Chromatin LAnguage Processing (CLaP) model combines a convolutional tokenizer, a transformer encoder, and task-specific components to predict multiple genomic signals from a single input. After pre-training with masked nucleotide prediction, CLaP achieved per-token F1 scores exceeding 0.8 for three target ChIP-seq assays in fine-tuning. Attention mechanism analysis revealed that CLaP detects CTCF binding sites with nucleotide-level precision by learning the sequence preference of the CTCF factor and the characteristic ATAC-seq patterns that are caused by protein binding events. Additionally, CLaP predicts protein-DNA binding events not captured by the ChIP-seq ground truth. These findings highlight CLaP’s potential to expand chromatin modeling by incorporating molecular assay data alongside sequence information.
Target-Specificity and Repeatability in Neuro-Cardiac-Guided TMS for Heart-Brain Coupling
Authors: Feng Zi-Jian , Martin Sandra , Numssen Ole , Weise Konstantin , Jing Ying , Gerardos Gerasimos , Martin Carla , Hartwigsen Gesa , Knösche Thomas R. 
Published: February 2025

AbstractThe dorsolateral prefrontal cortex (DLPFC) is a principal target for repetitive transcranial magnetic stimulation (rTMS) in the treatment of major depressive disorder, with therapeutic effects hypothesized to be mediated by the connectivity between the DLPFC and the subgenual anterior cingulate cortex (sgACC). Interestingly, these depression-related hubs are also part of the heart-brain axis, thus potentially rendering the stratification of individual depression targets possible by tapping into short-term heart rate modulation after DLPFC stimulation. Recently, a set of stimulation protocols has been proposed to objectively quantify these downstream effects. While these neuro-cardiac-guided TMS protocols (NCG-TMS) are promising to improve clinical responses, rigorous, third-party assessments of these approaches including replicability, robustness, and the impact of stimulation side-effects are critically missing. Here, we employed a 10 Hz TMS protocol (NCG-TMS 2.0) across three sessions to evaluate the effects of stimulation intensity and DLPFC target specificity on heart–brain coupling (HBC) in a cohort of healthy participants. Our results demonstrate a significant nonlinear increase in HBC with higher stimulation intensity, with the F3 lateral and F3 posterior targets eliciting more robust effects than the sham condition. For the first time, we are able to demonstrate reliable target- and intensity-specific HBC modulation across multiple NCG-TMS 2.0 sessions. Although the repeatability within subjects was limited when including the initial session, subsequent sessions yielded consistent results for the F3 anterior and F3 lateral targets at higher intensities. Although pain and other side effects influenced HBC, they did not fully account for the observed modulation of HBC. These findings underscore the critical role of spatial specificity and stimulation intensity in modulating heart–brain interactions and offer a potential framework for optimizing individualized rTMS treatment protocols for depression.
In vitroandin vivoAntiviral Activity of the Acyclic Nucleoside Phosphonate Prodrug LAVR-289 against Poxvirus and African Swine Fever Virus Replication
Authors: Marcheteau Elie , Mosca Estelle , Frenois-Veyrat Gaelle , Kappler-Gratias Sandrine , Boutin Laetitia , Top Sokunthea , Mathieu Thomas , Colas Cyril , Favetta Patrick , Garnier Tony , Barbe Peggy , Keck Mathilde , Gillet Daniel , Mas Alicia , Alejo Ali , Yu Yinyi , Toth Karoly , Abate Getahun , Roy Vincent , Skerry Janet , Wetzel Kelly S , Joshua Shamblin D , Joseph Golden W , Panchal Rekha G , Mucker Eric M , Mudhasani Rajini , Agrofoglio Luigi A. , Iseni Frederic , Gallardo Franck 
Published: February 2025

AbstractPoxviruses are double-stranded DNA viruses including relevant zoonotic pathogens with high morbidity. Although African swine fever virus (ASFV) belongs to theAsfarviridaefamily and is not strictly classified as a member of thePoxviridae, both fall within the same class ofPokkesviricetesthat replicate in the cytoplasm, and some poxviruses pose potential biological warfare threats. Among compounds targeting these viruses, acyclic nucleoside phosphonate prodrugs are nucleoside analogues inhibitors of viral DNA polymerases that have been identified as promising agents. However, some limitations related to their toxicity and the rapid emergence of resistance highlight the need for new antiviral molecules. In this study, the new nucleoside analogue LAVR-289 was shown to effectively inhibit the viral replication by intervening early in the viral replication step, targeting a specific domain of the poxvirus DNA polymerase. Using monkeypox virus models, the subcutaneous or oral administration of LAVR-289 demonstrates protective efficacy in infected animal models without toxicity or behavioral modification. The stabilityin vivo, long shelf-life and efficacy make LAVR-289 a promising candidate for further development and stockpiling as a medical countermeasure against dsDNA virus outbreaks. Its broad-spectrum efficacy is a real asset in a context of recurrent viral epidemics, risk of bioterrorism and emergence of resistance strains in the population.HighlightsLAVR-289 is a unique acyclic nucleoside phosphonate prodrug targeting viral DNA polymerases.LAVR-289 displays antiviral activity against dsDNA viruses, ASFV and poxviruses.First report ofin vivoevaluation of LAVR-289 against MPXV by subcutaneous and oral administration.LAVR-289 reduces clinical signs and increase survival in animal models.
Discovery of non-opioid receptor protein targets of fentanyl and remifentanil by affinity-based protein profiling in diverse animal model and human tissues
Authors: Lin Vivian S. , Suazo Kiall F. , Kim Doo Nam , Leach Damon T. , Sveistyte Agne , Walker Jennifer , Gorham Leo J. , Schultz Katherine J. , Mo Kai-For , Callister Stephen J. , Stratton Kelly G. , Lomas Gerard X. , Nelson William C. , Colburn Heather A. , Paurus Vanessa L. , Lalli Priscila M. , Moore Ronald J. , Powell Samantha M. , Rodriguez Oscar , Cort John R. , Wright Aaron T. 
Published: February 2025

AbstractSynthetic opioids such as fentanyl and related analogs have been widely used for pain management. However, their negative side effects, including respiratory depression and high potential for addiction, underscore the need for a deeper understanding of fentanyl’s interactions with proteins throughout the human body. Fentanyl analogs bind and activate opioid receptors in the central and peripheral nervous systems, triggering numerous downstream signaling pathways. Increasingly, fentanyl has been shown to interact with non-opioid receptors, and elucidation of these non-canonical fentanyl-protein interactions may provide insights into the mechanisms contributing to fentanyl’s adverse effects and illuminate novel countermeasure strategies. To identify proteins in mammalian tissues that may interact with fentanyl, we designed and synthesized three affinity-based probes (AfBPs) that include the fentanyl core and feature a diazirine photoaffinity group and alkyne handle for click chemistry at different positions. Molecular docking simulations predicted that these AfBPs bind the mu opioid receptor similarly to fentanyl.Affinity-based protein profiling using the FA-T1 probein vitroin tissues from six animal species identified histamine N-methyltransferase (HNMT), endophilin-B1 (SH3GLB1), fructosamine-3-kinase (FN3K), cutA divalent cation tolerance analog (CUTA), and monoamine oxidase B (MAOB) among the top proteins that bind fentanyl in multiple species and tissue types. Molecular docking of fentanyl and remifentanil with these protein structures identified putative binding sites. The interaction of fentanyl with specific proteins was empirically assessed through protein structural analyses. These findings highlight potential fentanyl-protein interactions that may contribute to the acute and long-term impacts of fentanyl exposures.
Chemical inhibition of a bacterial immune system
Authors: Zang Zhiyu , Duncan Olivia K. , Sabonis Dziugas , Shi Yun , Miraj Gause , Fedorova Iana , Le Shuai , Deng Jun , Zhu Yuhao , Cai Yanyao , Zhang Chengqian , Arya Garima , Duerkop Breck A. , Liang Haihua , Bondy-Denomy Joseph , Ve Thomas , Tamulaitiene Giedre , Gerdt Joseph P. 
Published: February 2025

AbstractThe rise of antibiotic resistance motivates a revived interest in phage therapy. However, bacteria possess dozens of anti-bacteriophage immune systems that confer resistance to therapeutic phages. Chemical inhibitors of these anti-phage immune systems could be employed as adjuvants to overcome resistance in phage-based therapies. Here, we report that anti-phage systems can be selectively inhibited by small molecules, thereby sensitizing phage-resistant bacteria to phages. We discovered a class of chemical inhibitors that inhibit the type II Thoeris anti-phage immune system. These inhibitors block the biosynthesis of a histidine-ADPR intracellular ‘alarm’ signal by ThsB and prevent ThsA from arresting phage replication. These inhibitors promiscuously inhibit type II Thoeris systems from diverse bacteria—including antibiotic-resistant pathogens. Chemical inhibition of the Thoeris defense improved the efficacy of a model phage therapy against a phage-resistant strain ofP. aeruginosain a mouse infection, suggesting a therapeutic potential. Furthermore, these inhibitors may be employed as chemical tools to dissect the importance of the Thoeris system for phage defense in natural microbial communities.
RNA-guided nucleases enable a gene drive of insertion sequences in plasmids
Authors: Mears Kepler S. , Rossine Fernando W. , Quinones-Olvera Natalia , Souque Célia , Baym Michael 
Published: February 2025

AbstractMobile genetic elements (MGEs) and the interactions between them are a major source of evolutionary innovation. Insertion sequences, the simplest MGEs usually encoding only the necessary genes for transposition and maintenance, are widespread in bacterial genomes, and are particularly common in plasmids. Plasmids, self-replicating extrachromosomal DNA elements, often exist in multiple copies imparting a stochastic barrier to the fixation of an insertion sequence by limiting the proportion of the plasmid population harboring the IS. In this work we demonstrate that to overcome this, the IS200/605 family of insertion sequences utilizes programmable RNA guided nucleases as gene drive to spread the IS through the plasmid population. TnpB, the likely ancestor of Cas12, records the specific insertion site of the IS in its RNA guide to prevent loss of the IS during transposition. When introduced to a plasmid TnpB will be reprogrammed to target and cleave IS-plasmids, resulting in biased replication of IS+ plasmids. Furthermore, the gene drive activity is critical for the IS to invade high copy plasmid populations. Because TnpB can only be mobilized between microbes on other mobile genetic elements, this advantage to fixing in plasmids may help explain the prevalence of TnpB across the tree of life. More generally, the unique pressures arising from movement between genetic contexts with different multiplicities shapes the evolution of strategies for MGE spread.
AnNlrp5-null mutation leads to attenuatedde novomethylation in oocytes, accompanied by a significant reduction in DNMT3L
Authors: Nic Aodha Leah , Pokhilko Alexandra , Rosen Leah U , Galatidou Styliani , Walewska Edyta , Belton Christian , Galvao Antonio , Okkenhaug Hanneke , Yu Lu , Nakhuda Asif , Mansfield Bill , Khan Soumen , Oxley David , Barragán Montserrat , Kelsey Gavin 
Published: February 2025

AbstractNlrp5encodes a core component of the subcortical maternal complex (SCMC) a cytoplasmic protein structure unique to the mammalian oocyte and cleavage-stage embryo.NLRP5mutations have been identified in patients presenting with early embryo arrest, recurrent molar pregnancies and imprinting disorders. Correct patterning of DNA methylation over imprinted domains during oogenesis is necessary for faithful imprinting of genes. It was previously shown that oocytes with mutation in the human SCMC geneKHDC3Lhad globally impaired methylation, indicating that integrity of the SCMC is essential for correct establishment of DNA methylation at imprinted regions. Here, we present a multi-omic analysis of anNlrp5- null mouse model, which in GV oocytes displays a misregulation of a broad range of maternal proteins, including proteins involved in several key developmental processes. This misregulation likely underlies impaired oocyte developmental competence. Amongst impacted proteins are several epigenetic modifiers, including a substantial reduction in DNMT3L; we show thatde novoDNA methylation is attenuated inNlrp5-null oocytes. This provides evidence for mechanisms leading to downstream misregulation of imprinted genes, which in turn, may result in imprinting syndromes, multi-locus imprinting disturbances (MLID) and hydatidiform moles.
Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci
Authors: Hecker Dennis , Song Xiaoning , Baumgarten Nina , Diagel Anastasiia , Katsaouni Nikoletta , Li Ling , Li Shuangyue , Kumar Maji Ranjan , Behjati Ardakani Fatemeh , Ma Lijiang , Tews Daniel , Wabitsch Martin , Björkegren Johan L.M. , Schunkert Heribert , Chen Zhifen , Schulz Marcel H. 
Published: February 2025

AbstractCoronary artery disease (CAD) is the leading cause of death worldwide. Recently, hundreds of genomic loci have been shown to increase CAD risk, however, the molecular mechanisms underlying signals from CAD risk loci remain largely unclear. We sought to pinpoint the candidate causal coding and non-coding genes of CAD risk loci in a cell type-specific fashion. We integrated the latest statistics of CAD genetics from over one million individuals with epigenetic data from 45 relevant cell types to identify genes whose regulation is affected by CAD-associated single nucleotide variants (SNVs) via epigenetic mechanisms. Applying two statistical approaches, we identified 1,580 genes likely involved in CAD, about half of which have not been associated with the disease so far. Enrichment analysis and phenome-wide association studies linked the novel candidate genes to disease-specific pathways and CAD risk factors, corroborating their disease relevance. We showed that CAD-SNVs are enriched to regulate gene expression by affecting the binding of transcription factors (TFs) with cellular specificity. Of all the candidate genes, 23.5% represented non-coding RNAs (ncRNA), which likewise showed strong cell type specificity. We conducted a proof-of-concept biological validation for the novel CAD ncRNA geneIQCH-AS1. CRISPR/Cas9-based gene knockout ofIQCH-AS1, in a human preadipocyte strain, resulted in reduced preadipocyte proliferation, less adipocyte lipid accumulation, and atherogenic cytokine profile. The cellular data are in line with the reduction ofIQCH-AS1in adipose tissues of CAD patients and the negative impact of risk alleles on its expression, suggestingIQCH-AS1to be protective for CAD. Our study not only pinpoints CAD candidate genes in a cell type-specific fashion but also spotlights the roles of the understudied ncRNA genes in CAD genetics.
A non-catalytic role for MLL2 in controlling chromatin organisation and mobility during the priming of pluripotent cells for differentiation
Authors: Steindel Maike , Davis Oliver , Neumann Katrin , Pirvan Liviu , Agsu Gökçe , Kranz Andrea , Adhya Dwaipayan , Morf Jorg , Yang Shuyue , Zhang Ziwei , Fu Jun , Barile Melania , Wurmser Annabelle , Strawbridge Stanley E. , Mohorianu Irina , Madapura Pradeepa , Huntly Brian , Göttgens Berthold , Holcman David , Samarajiwa Shamith A. , Klenerman David , Anastassiadis Konstantinos , Francis Stewart A. , Basu Srinjan 
Published: February 2025

AbstractThe chromatin regulator MLL2 (KMT2B) is the primary histone 3 lysine 4 (H3K4) trimethyltransferase acting at bivalent promoters in embryonic stem cells (ESCs) and is required for differentiation toward neuroectoderm. Here, we demonstrate that this requirement occurs during exit from naïve pluripotency, days before neuroectoderm differentiation is impaired. During exit, the effect of MLL2 on transcription is subtle, increasing the expression of a few important neuroectodermal transcription factors. In contrast, MLL2’s effect on chromatin architecture is substantial, stabilising loops associated with bivalent promoters in primed ESCs. MLL2 H3K4 catalytic activity is dispensable for stabilising these loops during ESC exit and for neuroectoderm differentiation. We therefore identify a non-catalytic function for MLL2 in stabilising 3D chromatin architecture, which has implications for lineage specification. Because MLL2 shares features with all four MLLs, we propose that chromatin tethering, rather than H3K4 methylation, represents a primary function for MLLs during lineage commitment decisions.
Random guide-independent DNA cleavage from the Argonaute ofExiguobacteriumsp. AB2
Authors: Cañiza Miguel Antonio M. , Dy Ron Leonard V. 
Published: February 2025

ABSTRACTBackgroundBacteria and bacteriophages (phages) are locked in a coevolutionary “arms race” to outcompete one another with novel systems and strategies. Regularly outnumbered tenfold by phages, bacteria have responded to the constant threat of phage predation by evolving a vast array of sophisticated defense systems. Among these, prokaryotic Argonautes (pAgos) are nucleic acid-guided endonucleases that target complementary sequences of invading mobile genetic elements (MGEs). However, as the preference for targeting MGE sequences has been demonstrated in only a limited number of pAgos, their precise physiological functions remain elusive. Here, we discovered a pAgo inExiguobacteriumsp. AB2, EsAgo, encoded in close proximity to other putative defense systems on theE. AB2 genome. Such clustering into genomic “defense islands” is a common phenomenon among prokaryotic defense systems, further implicating pAgos with a role in host defense. Accordingly, we had sought to characterize EsAgo as a nucleic acid-guided nucleic acid-targeting nuclease against MGEs for bacterial defense in this study.ResultsUsing sequence to structure homology tools, we show that the predicted model of EsAgo exhibits the structural characteristics typical of a full-length, catalytically active, DNA-guided pAgo. Akin to other pAgos, EsAgo uses a divalent cation cofactor to indiscriminately “chop” plasmidsin vitro. Furthermore, a site-directed double mutant of EsAgo bearing two missense mutations at the catalytic site exhibited significantly reduced levels of this random plasmid-degrading activity. Lastly, when EsAgo was supplied with synthetic 5’-P ssDNA guides, random nuclease activity was attenuated and may have resulted in the sequence-specific cleavage of dsDNA at 37°C.ConclusionsThese findings suggest that EsAgo functions as a DNA-interfering nuclease with or without DNA guides. Within the cell, it is possible that EsAgo utilizes this mechanism to screen and destroy foreign genetic elements. Moreover, the potential capacity for specific dsDNA cleavage at moderate temperatures gives rise to intriguing possibilities of repurposing EsAgo as a programmable nuclease for future biotechnological use.
EpiMolBio: A Novel User-Friendly Bioinformatic Program for Genetic Variability Analysis
Authors: Reinosa Roberto , Troyano-Hernáez Paloma , Valadés-Alcaráz Ana , Holguín África 
Published: February 2025

AbstractMotivationGenetic sequence analysis has become essential in many medicine, biology, and epidemiology fields. However, the currently available tools can pose a challenge for users without advanced computational skills.ResultsWe present EpiMolBio, a free-to-use software designed with an intuitive, user-friendly interface that enables a broad spectrum of users to explore genetic variability. Its diverse toolkit encompasses sequence processing, conservation and variability analysis, consensus sequence generation, and genome mutation or amino acid changes identification, including specialized tools for HIV and SARS-CoV-2 analysis.AvailabilityFreely available on the web athttps://www.epimolbio.comandhttps://github.com/EpiMolBio/EpiMolBio.Contactafrica.holguin@salud.madrid.org;roberto117343@gmail.comSupplementary informationSupplementary Table 1, 2, and Supplementary Text 1.
Phosphatase specificity influences phosphorylation timing of CDK substrates during the cell cycle
Authors: Zeisner Theresa U. , Auchynnikava Tania , Nurse Paul 
Published: February 2025

AbstractCell cycle events are ordered by cyclin-dependent kinases (CDKs), which phosphorylate hundreds of substrates. Multiple phosphatases oppose CDK substrate phosphorylation, yet a systematic understanding of how these phosphatases collectively influence phosphorylation timing is lacking. Here, we show that phosphatases influence the timing of CDK substrate phosphorylation during G2 and mitosis in fission yeast. We identify substrates of four phosphatases (PP2A-B55, PP2A-B56, CDC14, and PP1), showing that each phosphatase targets a distinct subset of CDK substrate sites. On average, sites dephosphorylated by CDC14 and PP2A-B56 are phosphorylated earlier during G2, followed by sites dephosphorylated by PP1 and then PP2A-B55. This suggests that the identity of the phosphatase impacts the timing of CDK substrate phosphorylation, establishing different phosphorylation thresholds at the G2/M transition. Consistent with this, depletion of PP2A-B55 and CDC14 advances mitotic onset independently of CDK activity regulation, likely due to the earlier phosphorylation of their respective CDK substrates.