bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA supercoiling enhances DNA condensation by ParB proteins
Authors: Martin Gonzalez Alejandro , Tišma Miloš , Analikwu Brian T. , Barth Anders , Janissen Richard , Antar Hammam , Kemps Gianluca , Gruber Stephan , Dekker Cees 
Published: July 2024

AbstractThe ParABS system plays a critical role in bacterial chromosome segregation. The key component of this system, ParB, loads and spreads along DNA to form a local protein-DNA condensate known as a partition complex. As bacterial chromosomes are heavily supercoiled due to the continuous action of RNA polymerases, gyrases, and nucleoid-associated proteins, it is important to study the impact of DNA supercoiling on the ParB-DNA partition complex formation. Here, we use anin vitrosingle- molecule assay to visualize ParB on supercoiled DNA. Unlike most DNA-binding proteins, individual ParB proteins are found to not pin plectonemes on supercoiled DNA, but freely diffuse along supercoiled DNA. We find that DNA supercoiling enhances ParB-DNA condensation which initiates at lower ParB concentrations than on DNA that is torsionally relaxed. ParB proteins induce a DNA- protein condensate that strikingly absorbs all supercoiling writhe. Our findings provide mechanistic insights that have important implications for our understanding of bacterial chromosome organization and segregation.
Sex-specific DNA methylation signatures of autism spectrum disorder in newborn blood
Authors: Mouat Julia S. , Krigbaum Nickilou Y. , Hakam Sophia , Thrall Emily , Kuodza George E. , Mellis Julia , Yasui Dag H. , Cirillo Piera M. , Ludena Yunin , Schmidt Rebecca J. , La Merrill Michele A. , Hertz-Picciotto Irva , Cohn Barbara A. , LaSalle Janine M. 
Published: July 2024

AbstractBackgroundAutism spectrum disorder(ASD)comprises a group of neurodevelopmental conditions currently diagnosed by behavioral assessment in childhood, although neuropathology begins during gestation. A poorly understood male bias for ASD diagnosis is thought to be due to both biological sex differences and cultural biases against female diagnosis of ASD. Identification of molecular biomarkers of ASD likelihood in newborns would provide more objective screening and early intervention. Epigenetic dysregulation has been reported in multiple tissues from newborns who are later diagnosed with ASD, but this is the first study to investigate sex-specific DNA methylation signatures for ASD in newborn blood, an accessible and widely banked tissue.MethodsDNA methylation was assayed from ASD and typically developing(TD)newborn blood (discovery setn= 196, replication setn= 90) using whole genome bisulfite sequencing(WGBS). Sex-stratified differentially methylated regions(DMRs)were assessed for replication, comparisons by sex, overlaps with DMRs from other tissues, and enrichment for biological processes and SFARI ASD-risk genes.ResultsWe found that newborn blood ASD DMRs from both sexes significantly replicated in an independent cohort and were enriched for hypomethylation in ASD compared to TD samples, as well as location in promoters, CpG islands and CpG shores. Comparing females and males, we found that most DMRs with sex differences amongst TD individuals were also found in ASD individuals, plus many additional DMRs with sex differences that were only found in those with ASD. Newborn blood DMRs from females were enriched for the X chromosome and both sexes showed significant overlap with DMRs from umbilical cord blood and placenta but not post-mortem cortex. DMRs from all tissues were enriched for neurodevelopmental processes (females) and SFARI ASD-risk genes (females and males).LimitationsThis study is primarily limited by sample sizes, particularly amongst females.ConclusionsOverall, we found a highly replicated sex-specific DNA methylation signature of ASD in newborn blood that showed support for the female protective effect and convergence with epigenetic and genetic signatures of ASD in newborns. These results demonstrate the utility of newborn blood in ASD screening and emphasizes the importance of sex-stratification in future studies.
Previously unknown regulatory role of extracellular RNA on bacterial directional migration
Authors: Tetz Victor , Kardava Kristina , Vecherkovskaya Maria , Khodadadi-Jamayran Alireza , Tsirigos Aristotelis , Tetz George 
Published: July 2024

ABSTRACTBacterial directional migration plays a significant role in bacterial adaptation. However, the regulation of this process, particularly in young biofilms, remains unclear.Here, we demonstrated the critical role of extracellular RNA as part of the Universal Receptive System in bacterial directional migration using a multidisciplinary approach, including bacterial culture, biochemistry, and genetics.We found that the destruction or inactivation of extracellular RNA with RNase or RNA-specific antibodies in the presence of the chemoattractant triggered the formation of bacterial “runner cells» in what we call a “panic state” capable of directional migration. These cells quickly migrated even on the surface of 1.5% agar and formed evolved colonies that were transcriptionally and biochemically different from the ancestral cells. We have also shown that cell-free DNA from blood plasma can act as a potent bacterial chemoattractant. Our data revealed a previously unknown role of bacterial extracellular RNA in the regulation of bacterial migration and have shown that its destruction or inhibition triggered the directional migration of developing and mature biofilms towards the chemoattractant.
Differential amino acid usage leads to ubiquitous edge effect in proteomes across domains of life that can be explained by amino acid secondary structure propensities
Authors: Morimoto Juliano , Pietras Zuzanna 
Published: July 2024

AbstractBackgroundAmino acids are the building blocks of proteins and enzymes, which are pivotal for life on Earth. Amino acid usage provides critical insights into the functional constraints acting on proteins and illuminates molecular mechanisms underpinning traits. Despite this, we have limited knowledge of the genome-wide signatures of amino acid usage across domains of life, precluding new genome and proteome patterns to being discovered.ResultsHere, we analysed the proteomes of 5,590 species across four domains of life and found that only a small subset of amino acids is most and least frequently used across proteomes. This creates a ubiquitous ‘edge effect’ on amino acid usage diversity by rank that arises from protein secondary structural constrains. This edge effect was not driven by the evolutionary chronology of amino acids, showing that functional rather than evolutionary constrains shape amino acid usage in the proteome. We also tested contemporary hypotheses about similarities in amino acid usage profiles and the relationship between amino acid usage and growth temperature, and found that, contrary to previous beliefs, amino acid usage varies across domains of life and temperature only weakly contributes to variance in amino acid usage.ConclusionWe have described a novel and ubiquitous pattern of amino acid usage signature across genomes, which reveals how structural constrains shape amino acid usage at the proteome level. This can ultimately influence the way in which we probe deep evolutionary relationships of protein families across the tree of life and engineer biology in synthetic biology.
Ribosomal DNA arrays are the most H-DNA rich element in the human genome
Authors: Chantzi Nikol , Patsakis Michail , Nayak Akshatha , Montgomery Austin , Mouratidis Ioannis , Georgakopoulos-Soares Ilias 
Published: July 2024

AbstractRepetitive DNA sequences can form non-canonical structures such as H-DNA which is an intramolecular triplex DNA structure. The new Telomere-to-Telomere (T2T) genome assembly for the human genome has eliminated gaps, enabling the examination of highly repetitive regions including centromeric and pericentromeric repeats and ribosomal DNA arrays. This gapless assembly allows for the examination of the distribution of H-DNA sequences in parts of the human genome that were not previously annotated. We find that H-DNA appears once every 30,000 bps in the human genome. Its distribution is highly inhomogeneous with H-DNA motif hotspots being detectable in acrocentric chromosomes. Ribosomal DNA arrays in acrocentric chromosomes are the genomic element with the highest H-DNA enrichment, with 13.22% of total H-DNA motifs being found in ribosomal DNA arrays, representing a 42.65-fold enrichment over what would be expected by chance. Across the acrocentric chromosomes we report that 55.87% of all H-DNA motifs found in these chromosomes are in rDNA array loci. The H-DNA motifs are primarily found in the intergenic spacer regions of the ribosomal DNA arrays, generating repeated clusters. We also discover that binding sites for PRDM9, a protein that regulates the formation of double-strand breaks and determines the meiotic recombination hotspots in humans and most mammals, are over 5-fold enriched for H-DNA motifs. Finally, we provide evidence that our findings are consistent in other non-human great ape genomes. We conclude that ribosomal DNA arrays are the most enriched genomic loci for H-DNA sequences in human and other great ape genomes.
The mitochondrial Na+/Ca2+exchanger NCLX is implied in the activation of hypoxia-inducible factors
Authors: Choya-Foces Carmen , Hernansanz-Agustín Pablo , Navarro Elisa , López Manuela G. , Egea Javier , Martínez-Ruiz Antonio 
Published: July 2024

AbstractEukaryotic cells and organisms depend on oxygen for basic living functions, and they display a panoply of adaptations to situations in which oxygen availability is diminished (hypoxia). A number of these responses in animals are mediated by changes in gene expression programs directed by hypoxia-inducible factors (HIFs), whose main mechanism of stabilization and functional activation in response to decreased cytosolic oxygen concentration was elucidated two decades ago. Human acute responses to hypoxia have been known for decades, although their precise molecular mechanism for oxygen sensing is not fully understood. It is already known that a redox component, linked with reactive oxygen species (ROS) production of mitochondrial origin, is implied in these responses. We have recently described a mechanism by which the mitochondrial sodium/calcium exchanger, NCLX, participates in mitochondrial electron transport chain regulation and ROS production in response to acute hypoxia.Here we show that NCLX is also implied in the response to hypoxia mediated by the HIFs. By using a NCLX inhibitor and interference RNA we show that NCLX activity is necessary for HIF-α subunits stabilization in hypoxia and for HIF-1-dependent transcriptional activity. We also show that hypoxic mitochondrial ROS production is not required for HIF-1α stabilization under all circumstances, suggesting that other mechanism(s) could be operating in the NCLX-mediated response to hypoxia that operates through HIF-α stabilization. This finding provides a link between acute and medium-term responses to hypoxia, reinforcing a central role of mitochondrial cell signalling in the response to hypoxia.
The association between metabolite concentrations and wellbeing in adults
Authors: Azcona-Granada Natalia , Geijsen Anne J.M.R. , Pool René , Pelt Dirk H. M. , Bartels Meike 
Published: July 2024

AbstractThe biological complexity of wellbeing is studied from various perspectives, including genetics and epigenetics. However, there is a knowledge gap concerning other layers, such as metabolomics, which is dynamic and changes throughout life. This study explores the association between metabolites and wellbeing in a sample (N = 4748) drawn from the Netherlands Twin Register. A latent factor score for wellbeing was constructed based on: Quality of Life, Life Satisfaction, and Subjective Happiness. A total of 231 blood metabolites were analyzed using1HNMR technique. Linear regression models were performed for each metabolite, while correcting for family clustering, relevant covariates, and multiple testing. None of the metabolites were significantly associated with wellbeing after multiple testing correction. Despite the lack of significant findings, the 34 metabolites with the lowestp-value (0.25) pointed to the same metabolic pathway: endogenous lipid metabolism. This pathway has previously been linked to wellbeing in a GWAS and associated with related phenotypes in other metabolomic studies. In conclusion, this study confirms the biological complexity of wellbeing and speculates on a potential role of lipids. Further research is needed to confirm these hypotheses.
Exploring Anatomical Links Between the Crow’s Nidopallium Caudolaterale and its Song System
Authors: Moll Felix W. , Kersten Ylva , Erdle Saskia , Nieder Andreas 
Published: July 2024

AbstractCrows are corvid songbirds that exhibit remarkable cognitive control over their actions, including their vocalizations. They can learn to vocalize on command and the activity of single neurons from the crow’s associative telencephalic structure nidopallium caudolaterale (NCL) is correlated with the execution of this vocal and many non-vocal skilled behaviors. However, it remains unknown if specific anatomical adaptations that directly link the crow NCL to any of the nuclei of the crow’s “song system” exist. To address this issue, we used fluorescent tracers along with histological staining methods (Nissl-, myelin-, and anti tyrosine hydroxylase) to characterize the connectivity of the crow’s NCL in relation to its song system nuclei. We found that the NCL sends dense projections into the dorsal intermediate arcopallium (AID) directly adjacent to and engulfing the robust nucleus of the arcopallium (RA), which is the telencephalic motor output of the song system. Similarly, we demonstrate dense NCL projections into the striatum surrounding the basal ganglia song nucleus “area X”. Both of these descending projections mirror the projections of the nidopallial song nucleus HVC (proper name) into RA and area X, with extremely sparse NCL fibers extending into area X. Furthermore, we characterized the distribution of cells projecting from the lateral part of the magnocellular nucleus of the anterior nidopallium (MAN) to NCL. Notably, a separate medial population of MAN cells projects to HVC. These two sets of connections—MAN to NCL and MAN to HVC—run in parallel but do not overlap. Taken together, our findings support the hypothesis that the NCL is part of a “general motor system” that parallels the song system but exhibits only minimal monosynaptic interconnections with it.
Fromin vitrotoin silico: a pipeline for generating virtual tissue simulations from real image data
Authors: Nürnberg Elina , Vitacolonna Mario , Bruch Roman , Reischl Markus , Rudolf Rüdiger , Sauer Simeon 
Published: July 2024

Abstract3D cell culture models replicate tissue complexity, aiming to study cellular interactions and responses in a more physiologically relevant environment compared to traditional 2D cultures. However, the spherical structure of these models makes it difficult to extract meaningful data, necessitating advanced techniques for proper analysis. In silico simulations enhance research by predicting cellular behaviors and therapeutic responses, providing a powerful tool to complement experimental approaches. Despite their potential, these simulations often require advanced computational skills and significant resources, creating a barrier for many researchers.To address these challenges, we developed an accessible pipeline using open-source software to facilitate virtual tissue simulations. Our approach employs the Cellular Potts Model, a versatile framework for simulating cellular behaviors in tissues. The simulations are constructed from real world 3D image stacks of cancer spheroids, ensuring the virtual models are rooted in experimental data. By introducing a new metric for parameter optimization, we enable the creation of realistic simulations without requiring extensive computational expertise. This pipeline benefits researchers wanting to incorporate computational biology into their methods, even if they do not possess extensive expertise in this area. By reducing the technical barriers associated with advanced computational modeling, our pipeline allows more researchers to utilize these powerful tools. Our approach aims to foster broader use ofin silicomethods in disease research, contributing to a deeper understanding of disease biology and the refinement of therapeutic interventions.
PP1 PNUTS binds the “restrictor” and dephosphorylates RNA pol II CTD Ser5 to stimulate transcription termination
Authors: Erickson Benjamin , Fedoryshchak Roman , Fong Nova , Sheridan Ryan , Larson Keira Y. , Saviola Anthony J. , Mouilleron Stephane , Hansen Kirk C. , Treisman Richard , Bentley David L. 
Published: July 2024

AbstractThe restrictor, ZC3H4/WDR82, is the major termination factor for antisense transcription from bidirectional promoters, but its mechanism is poorly understood. We report that ZC3H4/WDR82 co-purifies with PP1 phosphatase and PP1 phosphatase nuclear targeting subunit, PNUTS, which binds directly to the WDR82 subunit of restrictor. AlphaFold predicts a quaternary complex, PPWZ, in whichPP1-associatedPNUTS andZC3H4 both contactWDR82. To investigate the role of protein dephosphorylation in PPWZ activity, we expressed a substrate trap comprising inactive PP1H66Klinked to the PNUTS C-terminus. PP1H66K-PNUTS binds pol II large subunit and nuclear exosome components. PP1H66K-PNUTS, but not PP1WT-PNUTS, functions as a dominant-negative inhibitor of antisense termination and CTD Ser5 dephosphorylation. Both these activities require the PNUTS WDR82 binding domain that interacts with restrictor. We show that CTD Ser5 hyperphosphorylation is associated with higher processivity and reduced pausing that would counteract termination, and propose that Ser5 dephosphorylation by PPWZ is coupled to termination. In summary, we identify the PP1 phosphatase activity of the PPWZ complex as essential for terminator function and propose that this heterotetramer is the physiologically relevant form of restrictor.
RqcH supports survival in the absence of non-stop ribosome rescue factors
Authors: Callan Katrina , Prince Cassidy R. , Feaga Heather A. 
Published: July 2024

AbstractRibosomes frequently translate truncated or damaged mRNAs due to the extremely short half-life of mRNAs in bacteria. When ribosomes translate mRNA that lacks a stop codon (non-stop mRNA), specialized pathways are required to rescue the ribosome from the 3’ end of the mRNA. The most highly conserved non-stop rescue pathway istrans-translation, which is found in greater than 95% of bacterial genomes. In all Proteobacteria that have been studied, the alternative non-stop ribosome rescue factors, ArfA and ArfB, are essential in the absence oftrans-translation. Here, we investigate the interaction between non-stop rescue pathways and RqcH, a ribosome quality control factor that is broadly conserved outside of Proteobacteria. RqcH does not act directly on non-stop ribosomes but adds a degron tag to stalled peptides that obstruct the large ribosomal subunit, which allows the stalled peptide to be cleared from the ribosome by peptidyl-tRNA hydrolase (PTH). We show thatBacillus subtiliscan survive withouttrans-translation and BrfA (Bacillus ArfA homolog), due to the presence of RqcH. We also show that expression of RqcH and its helper protein RqcP rescues the synthetic lethality of ΔssrAΔarfAinEscherichia coli. These results suggest that non-stop ribosome complexes can be disassembled and then cleared because of the tagging activity of RqcH, and that this process is essential in the absence of non-stop ribosome rescue pathways. Moreover, we surveyed the conservation of ribosome rescue pathways in >14,000 bacterial genomes. Our analysis reveals a broad distribution of non-stop rescue pathways, especiallytrans-translation and RqcH, and a strong co-occurrence between the ribosome splitting factor MutS2 and RqcH. Altogether, our results support a role for RqcH in non-stop ribosome rescue and provide a broad survey of ribosome rescue pathways in diverse bacterial species.ImportanceRibosome stalling on damaged mRNA is a major problem in bacteria. It is estimated that 2-4% of all translation reactions terminate with the ribosome stalled on a damaged mRNA lacking a stop codon. Mechanisms that rescue these ribosomes, such astrans-translation, are often essential for viability. We investigated the functional overlap between RqcH and the non-stop ribosome rescue systems (ArfA andtrans-translation) that are present in bothE. coliandB. subtilis. Since these two species are extremely distant relatives, our work is likely to have wider implications for understanding ribosome rescue in bacteria. Furthermore, we used a bioinformatics approach to examine the conservation and overlap of various ribosome rescue systems in >14,000 species throughout the bacterial domain. These results provide key insights into ribosome rescue in diverse phyla.
Measles virus co-opts epithelial-to-mesenchymal transition and live cell extrusion to exit human airway epithelia
Authors: Hippee Camilla E. , Durnell Lorellin A. , Kaufman Justin W. , Murray Eileen , Singh Brajesh K. , Sinn Patrick L. 
Published: July 2024

ABSTRACTMeasles virus (MeV) is a highly contagious respiratory virus transmitted via aerosols. To understand how MeV exits the airways of an infected host, we use unpassaged primary cultures of human airway epithelial cells (HAE). MeV typically remains cell-associated in HAE and forms foci of infection, termed infectious centers, by directly spreading cell-to-cell. We previously described the phenomenon in which infectious centers detachen massefrom HAE and remain viable. Here we investigate the mechanism of this cellular detachment. Via immunostaining, we observed loss of tight junction and cell adhesion proteins within infectious centers. These morphological changes indicate activation of epithelial-to-mesenchymal transition (EMT). EMT can contribute to wound healing in respiratory epithelia by mobilizing nearby cells. Inhibiting TGF-β, and thus EMT, reduced infectious center detachment. Compared to uninfected cells, MeV-infected cells also expressed increased levels of sphingosine kinase 1 (SK1), a regulator of live cell extrusion. Live cell extrusion encourages cells to detach from respiratory epithelia by contracting the actomyosin of neighboring cells. Inhibition or induction of live cell extrusion impacted infectious center detachment rates. Thus, these two related pathways contributed to infectious center detachment in HAE. Detached infectious centers contained high titers of virus that may be protected from the environment, allowing the virus to live on surfaces longer and infect more hosts. This mechanism may contribute to the highly contagious nature of MeV.IMPORTANCEMeasles virus (MeV) is an extremely contagious respiratory pathogen that continues to cause large, disruptive outbreaks each year. Here, we examine a phenomenon that may help explain the contagious nature of MeV: detachment of MeV-infected cells. MeV spreads cell-to-cell in human airway epithelial cells (HAE) to form groups of infected cells, termed “infectious centers”. We reported that infectious centers ultimately detach from HAE as a unit, carrying high titers of virus. Viral particles within cells may be more protected from environmental conditions, such as ultraviolet radiation and desiccation. We identified two host pathways, epithelial-to-mesenchymal transition and live cell extrusion, that contribute to infectious center detachment. Perturbing these pathways altered the kinetics of infectious centers detachment. These pathways influence one another and contribute to epithelial wound healing, suggesting infectious center detachment may be a usurped consequence of the host’s response to infection that benefits MeV by increasing its transmissibility between hosts.