bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis
Authors: Syed Sabriya A. , Shqillo Kristina , Nand Ankita , Zhan Ye , Dekker Job , Imbalzano Anthony N. 
Published: June 2023

ABSTRACTProtein arginine methyltransferase 5 (Prmt5) is an essential regulator of embryonic development and adult progenitor cell functions. Prmt5 expression is mis-regulated in many cancers, and the development of Prmt5 inhibitors as cancer therapeutics is an active area of research. Prmt5 functions via effects on gene expression, splicing, DNA repair, and other critical cellular processes. We examined whether Prmt5 functions broadly as a genome-wide regulator of gene transcription and higher-order chromatin interactions during the initial stages of adipogenesis using ChIP-Seq, RNA-seq, and Hi-C using 3T3-L1 cells, a frequently utilized model for adipogenesis. We observed robust genome-wide Prmt5 chromatin-binding at the onset of differentiation. Prmt5 localized to transcriptionally active genomic regions, acting as both a positive and a negative regulator. A subset of Prmt5 binding sites co-localized with mediators of chromatin organization at chromatin loop anchors.Prmt5knockdown decreased insulation strength at the boundaries of topologically associating domains (TADs) adjacent to sites with Prmt5 and CTCF co-localization. Genes overlapping such weakened TAD boundaries showed transcriptional dysregulation. This study identifies Prmt5 as a broad regulator of gene expression, including regulation of early adipogenic factors, and reveals an unappreciated requirement for Prmt5 in maintaining strong insulation at TAD boundaries and overall chromatin organization.
SNPLift: Fast and accurate conversion of genetic variant coordinates across genome assemblies
Authors: Normandeau Eric , de Ronne Maxime , Torkamaneh Davoud 
Published: June 2023

AbstractMotivationThe advent of high-throughput sequencing technologies and the availability of reference genomes have provided an unprecedented opportunity to discover and genotype millions of genetic variants in hundreds or even thousands of samples. Variant calling, the identification of genetic variants from raw sequencing data, is both time-consuming and computationally demanding. Currently, reference genomes are evolving very rapidly and new assembly versions come out more and more frequently. To take advantage of new or improved reference genomes, raw reads alignments, genotype calling, and filtration must typically all be redone. This is a costly and time consuming operation that is not always viable when projects are under time constraints.ResultsHere, we introduce SNPLift, a bioinformatic pipeline that can quickly transfer the coordinate of nucleotide variants (SNPs and Indels) between different versions of reference genomes. We tested SNPLift on nine SNP datasets in VCF format from different species (Homo sapiens, Arabidopsis thaliana, Coregonus clupeaformis, Medicato truncatula, Oriza sativa, Salvelinus namaycush, Solanum lycopersicum, Zea mays, and Glycine max). Depending on the species, we achieved accurate lifting of variants ranging from 92.92% to 99.69%. Importantly, SNPLift significantly reduces the computational resources and time required for variant analysis compared to performing a complete re-analysis using a new reference genome. SNPLift offers a fast and efficient solution to leverage the benefits of updated or improved reference genomes.Availability and implementationSNPLift is available athttps://github.com/enormandeau/snpliftwith its documentation. It contains a script that runs an automated test on a small dataset, composed of 190,443 SNPs in chromosome 1 ofMedicago truncatula. SNPLift uses only common tools that are easy to install and works under Linux and MacOS.
Latent mutations in the ancestries of alleles under selection
Authors: Fan Wai-Tong (Louis) , Wakeley John 
Published: June 2023

AbstractWe consider a single genetic locus with two allelesA1andA2in a large haploid population. The locus is subject to selection and two-way, or recurrent, mutation. Assuming the allele frequencies follow a Wright-Fisher diffusion and have reached stationarity, we describe the asymptotic behaviors of the conditional gene genealogy and the latent mutations of a sample with known allele counts, when the countn1of alleleA1is fixed, and when either or both the sample sizenand the selection strength |α| tend to infinity. Our study extends previous work under neutrality to the case of non-neutral rare alleles, asserting that when selection is not too strong relative to the sample size, even if it is strongly positive or strongly negative in the usual sense (α→ −∞ orα→ +∞), the number of latent mutations of then1copies of alleleA1follows the same distribution as the number of alleles in the Ewens sampling formula. On the other hand, very strong positive selection relative to the sample size leads to neutral gene genealogies with a single ancient latent mutation. We also demonstrate robustness of our asymptotic results against changing population sizes, when one of |α| ornis large.
All exons are not created equal - Exon vulnerability determines the effect of exonic mutations on splicing
Authors: Holm Lise L. , Doktor Thomas K. , Flugt Katharina K. , Petersen Ulrika S. S. , Pedersen Rikke , Andresen Brage S. 
Published: June 2023

AbstractIt is now widely accepted that aberrant splicing of constitutive exons is often caused by mutations affectingcis-acting splicing regulatory elements (SREs), but there is a misconception that all exons have an equal dependency on SREs and thus a similar vulnerability to aberrant splicing. We demonstrate that some exons are more likely to be affected by exonic splicing mutations (ESM) due to an inherent vulnerability, which is context-dependent and influenced by the strength of exon definition. We have developed VulExMap, a tool which based on empirical data that can designate whether a constitutive exon is vulnerable. Using VulExMap, we find that only 27% of all exons can be categorized as vulnerable whereas two-thirds of 332 previously reported ESMs in 71 disease genes are located in vulnerable exons. Because VulExMap analysis is based on empirical data on splicing of exons in their endogenous context, it includes all features important in determining the vulnerability. We believe that VulExMap will be an important tool when assessing the effect of exonic mutations by pinpointing whether they are located in exons vulnerable to ESMs.
Incorporation of genome-bound cellular proteins into HIV-1 particles regulates viral infection
Authors: Garcia-Moreno Manuel , Truman Robin , Chen Honglin , Iselin Louisa , Lenz Caroline E. , Lee Jeff , Dicker Kate , Noerenberg Marko , Sohier Thibault J.M. , Palmalux Natasha , Järvelin Aino I. , Kamel Wael , Ruscica Vincenzo , Ricci Emiliano P. , Davis Ilan , Mohammed Shabaz , Castello Alfredo 
Published: June 2023

SUMMARYThe initial steps of the human immunodeficiency virus 1 (HIV-1) lifecycle are regulated by cellular RNA-binding proteins (RBPs). To understand the scope of these early host-virus interactions, we developed in virion RNA interactome capture (ivRIC), which allowed the comprehensive and systematic profiling of the proteins that interact with the HIV-1 genomic (g)RNA inside viral particles. ivRIC identified 104 cellular RBPs within the encapsidated HIV-1 ribonucleoprotein, many of which are typically found in the cellular nucleus. Notably, these nuclear RBPs interact with the HIV-1 RBP Rev, suggesting that they associate with HIV-1 gRNA during its nuclear life. Functional assays show that ivRBPs are important for HIV-1, including PURA and PURB, which control viral gene expression and infectivity through interaction with critical sequences in the gRNA. Our characterisation of the composition of the encapsidated ribonucleoprotein of HIV-1 uncovers new host-virus interactions that invokes new mechanisms for controlling HIV-1 infection.
Polygenic adaptation to overnutrition reveals a role for cholinergic signaling in longevity
Authors: Rundell Thomas B , Brunelli Melina , Alvi Azva , Safian Gabrielle , Capobianco Christina , Tu Wangshu , Subedi Sanjeena , Fiumera Anthony , Musselman Laura Palanker 
Published: June 2023

AbstractOvernutrition by high-sugar (HS) feeding reduces both the lifespan and healthspan across taxa. Pressuring organisms to adapt to overnutrition can highlight genes and pathways important for the healthspan in stressful environments. We used an experimental evolution approach to adapt four replicate, outbred population pairs ofDrosophila melanogasterto a HS or control diet. Sexes were separated and aged on either diet until mid-life, then mated to produce the next generation, allowing enrichment for protective alleles over time. All HS-selected populations increased their lifespan and were therefore used as a platform to compare allele frequencies and gene expression. Pathways functioning in the nervous system were overrepresented in the genomic data and showed evidence for parallel evolution, although very few genes were the same across replicates. Acetylcholine-related genes, including the muscarinic receptormAChR-A,showed significant changes in allele frequency in multiple selected populations and differential expression on a HS diet. Using genetic and pharmacological approaches, we show that cholinergic signaling affects Drosophila feeding in a sugar-specific fashion. Together, these results suggest that adaptation produces changes in allele frequencies that benefit animals under conditions of overnutrition and that it is repeatable at the pathway level.
Correlating phylogenetic and functional diversity of thenod-free but nodulatingBradyrhizobiumphylogroup
Authors: Ling Lu , Camuel Alicia , Wang Sishuo , Wang Xiaojun , Liao Tianhua , Tao Jinjin , Lin Xingqin , Nouwen Nico , Giraud Eric , Luo Haiwei 
Published: June 2023

AbstractBradyrhizobiumis a main rhizobial lineage of which most members nodulate legume plants using Nod factors (NFs) synthetized by thenodgenes. However, members of the Photosynthetic supergroup (phylogroup) withinBradyrhizobium(PB) arenod-free but still capable of establishing nitrogen-fixing nodules with some tropical legumes of theAeschynomenegenus.These unusual findings are based on the genomic sequences of only 13 PB strains, and almost all were isolated fromAeschynomenenodules. Here, we investigate the diversity ofBradyrhizobiumin grassland, forest, and rice field byrpoBamplicon sequencing and report that PB is mainly associated with rice root and rhizosphere. Moreover, we sequenced 209 new PB members isolated mostly from the rice field. The extended PB supergroup comprises three major clades: a basal clade with significant expansion of its diversity, followed by an intermediate clade composed by two strains, and a new clade exclusively represented by our new strains. Although the PB strains universally lack the canonicalnodgenes, all 28 assayed strains covering the broad diversity of these clades induced nodules onAeschynomene indica. Interestingly, the three clades displayed significant differences in the efficiency of symbiosis, aligning well with their phylogenetic branching order. Our strain collection expands the ecological, phylogenetic and functional diversity ofnod-free but nodulatingBradyrhizobium. With this expanded diversity, we conclude that the NF-independent nodulation ofAeschynomeneis a common trait of this supergroup, in contrast to the photosynthetic trait originally thought as its unifying feature.
WITHDRAWN: Widespread but spotty: Atlantic cod is a complex of five species through ecological speciation
Authors: Halldórsdóttir Katrín , Llanos-Garrido Alejandro , Einarsson Axel Wilhelm , Sackton Tim , Árnason Einar 
Published: June 2023

Withdrawal StatementThe authors have withdrawn their manuscript because they have discovered errors in the alignment of parts of the data. Miscommunication with the sequencing center led to a misunderstanding of the pooling design and incorrect merging of sequencing read files from different individuals into single bam files. Thus bam alignments for each individual sample of four out of 12 batches are based on a majority of reads from that individual but also on reads from one or two other individuals. Individuals in eight other batches were not affected by this. However, for this paper, the entire data was jointly genotyped to produce vcf files, and the joint genotyping may thus indirectly affect samples of other batches. Revising the paper by teasing apart the affected and non-affected parts of the data is not an option, and they, therefore, withdraw the preprint. They are reanalyzing the dataset. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
BRI2-mediated regulation of TREM2 processing in microglia and its potential implications for Alzheimer’s disease and related dementias
Authors: Yin Tao , D’Adamio Luciano 
Published: June 2023

AbstractITM2B/BRI2mutations cause familial forms of Alzheimer’s disease (AD)-related dementias by disrupting BRI2’s protein function and leading to the accumulation of amyloidogenic peptides. Although typically studied in neurons, our findings show that BRI2 is highly expressed in microglia, which are crucial in AD pathogenesis due to the association of variants in the microglial gene TREM2 with increased AD risk. Our single-cell RNAseq (scRNAseq) analysis revealed a microglia cluster that depends on a Trem2 activity that is inhibited by Bri2, pointing to a functional interaction betweenItm2b/Bri2andTrem2. Given that the AD-related Amyloid-β Precursor protein (APP) and TREM2 undergo similar proteolytic processing, and that BRI2 inhibits APP processing, we hypothesized that BRI2 may also regulate TREM2 processing. We found that BRI2 interacts with Trem2 and inhibits its processing by α-secretase in transfected cells. In mice lacking Bri2 expression, we observed increased central nervous system (CNS) levels of Trem2-CTF and sTrem2, which are the products of α-secretase processing of Trem2, indicating increased Trem2 processing by α-secretasein vivo. Reducing Bri2 expression only in microglia resulted in increased sTrem2 levels, suggesting a cell-autonomous effect of Bri2 on α-secretase processing of Trem2. Our study reveals a previously unknow role of BRI2 in regulating TREM2-related neurodegenerative mechanisms. The ability of BRI2 to regulate the processing of both APP and TREM2, combined with its cell-autonomous role in neurons and microglia, makes it a promising candidate for the development of AD and AD-related dementias therapeutics.
Cell Cycle Dependent Orchestration of Surface Layer Biogenesis inCaulobacter crescentus
Authors: Herdman Matthew , von Kügelgen Andriko , Schulze Ulrike , Wainman Alan , Bharat Tanmay A.M. 
Published: June 2023

ABSTRACTSurface layers (S-layers) are proteinaceous, two-dimensional crystals that constitute the outermost components of many prokaryotic cell envelopes. In this study, we investigated principles of S-layer biogenesis on the outer membrane in the bacterial model organismCaulobacter crescentus. Fluorescent microscopy revealed localised incorporation of new S-layer at the poles and mid-cell, consistent with elongation and division phases of the cell cycle. Next, light microscopy and electron cryotomography investigations of drug-treated bacteria revealed that bacterial actin homologue MreB is crucial for localised S-layer insertion. We further uncovered that S-layer biogenesis follows new peptidoglycan synthesis and localises to regions of high cell wall turnover. Finally, correlated cryo-light microscopy and electron cryotomographic analysis of regions of S-layer insertion showed the presence of gaps in the hexagonal S-layer lattice, contrasting with other S-layers completed by defined symmetric defects. Our findings provide insight into howC. crescentuscells form an ordered S-layer on their surface, providing evidence for coordination between the biogenesis of the cell envelope at multiple levels.
What lies behind the people? An approach to the 2019 mobilizations in Hong Kong and Chile through sociological discourse analysis
Authors: Osorio Solano Susana Alejandra , Serrano-Moreno Juan Enrique 
Published: June 2023

PurposeThis study analyzes how the notion of the people emerged in two (neo)liberal societies during the crisis in 2019: Hong Kong and Chile.Design/methodology/approachFrom a qualitative and comparative perspective, 131 middle-class individuals were interviewed during heightened contentious activity in Hong Kong and Chile. The interviews were analyzed based on Ruiz's model for sociological discourse analysis.FindingsThe study shows that in contexts strongly influenced by liberalism, the notion of “people” is not advertised antagonistically against the individual but as complementary, and to this end, it emphasizes the heterogeneity of repertoires or demands. The comparison of these two movements highlighted the importance of democratic institutions in shaping the outcomes and effectiveness of protests.Research limitations/implicationsEnacting the National Security Law in Hong Kong and the mandatory blockade imposed by both governments in response to the COVID-19 pandemic required an adaptation in the design and execution of the interviews, adopting a hybrid format. The volatility that characterizes periods of political crisis requires longitudinal follow-up. This article does not capture but can be explored in associated research publications.Originality/valueThe research offers two significant contributions: it addresses the immediate context by conducting on-site research during the most significant contemporary crises in Hong Kong and Chile. Secondly, it problematizes the understanding of the people in liberal societies and proposes it as a complementary (and not antagonistic) concept to that of the individual.
Exploring the quality of corporate governance disclosure under an “apply and explain” regime
Authors: Gowry Yuveshna , Soobaroyen Teerooven , Agathee Ushad Subadar 
Published: June 2023

Purpose
This study aims to explore the quality of corporate governance disclosure under an “apply and explain” regime in the context of an emerging economy (Mauritius), following a transition from the traditional “comply or explain” approach within the national code of corporate governance.

Design/methodology/approach
The research relies on a content analysis of corporate governance disclosure in 86 annual reports of companies listed on the Stock Exchange of Mauritius for the financial periods 2018–2019 and 2019–2020, one-way analysis of variance tests and draws on the typology of corporate governance explanations developed by Shrives and Brennan (2015), focusing on specificity, location and comprehensiveness dimensions. This paper draws on legitimacy theory and the concepts of substantive and symbolic disclosures to guide the interpretation of the findings.

Findings
From a specificity point of view, the disclosure index revealed significant variations, with the highest score being four times the lowest score. With regards to location and comprehensiveness, only around half of companies are making optimum use of a corporate governance report and providing explanations by principles. This paper also illustrated how some firms provided symbolic disclosures. Overall, there are disparities in the application of the code by companies, reflected in a blend of substantive and symbolic disclosures to maintain their legitimacy.

Originality/Implications
This study examines “apply and explain” disclosures in a emerging economy in contrast to the “comply or explain” approach studied so far in the literature. Merely professing a “well intended” shift to the “apply and explain” approach does not necessarily lead to improvements in the quality of corporate governance disclosures. Companies, governance professionals and regulatory bodies could formulate disclosure guidance to better underpin the implications of the “apply and explain” approach.
Impact of institutional ownership on environmental disclosure in Indonesian companies
Authors: Wicaksono Aditya Pandu , Kusuma Hadri , Cahaya Fitra Roman , Rosjidi Anis Al , Rahman Arief , Rahayu Isti 
Published: June 2023

Purpose
This study aims to investigate the effect of the classification of origin country of institutional shareholder (domestic, developed and developing country) and its status on stock exchange (listed and unlisted) on environmental disclosure level in Indonesian companies.

Design/methodology/approach
The data set comprises 474 non-financial firms listed in Indonesian Stock Exchange (IDX) for the period of 2017 to 2019. The study uses an environmental disclosure checklist to measure the extent of environmental disclosure in companies’ reports. Panel regression analysis technique is adopted to investigate the association between total percentage of shares held by institutional shareholders based on the classification of origin country and the status in stock exchange, and the extent of environmental disclosure.

Findings
The study reveals that the extent of environmental disclosure is positively and significantly associated with institutional investors from domestic, developed countries, listed and unlisted institutional investors. Further analysis shows interesting results that institutions from developing countries have a negative and significant relationship with environmental disclosure in non-sensitive industries.

Research limitations/implications
The authors recognize the issue of authors’ subjectivity in the measurement process of environmental disclosure. The sample for this study encompasses Indonesian listed firms. Thus, the results may not be generalized to Indonesian unlisted firms and other countries or regions.

Practical implications
This study suggests managers to engage more with institutional shareholders because they have greater concern for environmental disclosure practices. The current study also suggests managers to make strong environmental policies as they are important to ensure that institutional shareholders’ investments are safe.

Social implications
Given the positive impact institutional shareholders have on the level of environmental disclosure, it indirectly indicates that institutional shareholders have a strong motivation to make the world a better place.

Originality/value
This study offers in-depth insights into the effect of institutional ownership on environmental disclosure based on the classification of origin country and listing status of institutional investors.