bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromatin interaction maps identify Wnt responsivecis-regulatory elements coordinatingPaupar-Pax6expression in neuronal cells
Authors: Pavlaki Ioanna , Shapiro Michael , Pisignano Giuseppina , Telenius Jelena , Descalzo Silvia Muñoz , Williams Robert J. , Hughes Jim R. , Vance Keith W. 
Published: May 2021

AbstractCentral nervous system-expressed long non-coding RNAs (lncRNAs) are often located in the genome close to protein coding genes involved in transcriptional control. Such lncRNA-protein coding gene pairs are frequently temporally and spatially co-expressed in the nervous system and are predicted to act together to regulate neuronal development and function. Although some of these lncRNAs also bind and modulate the activity of the encoded transcription factors, the regulatory mechanisms controlling co-expression of neighbouring lncRNA-protein coding genes remain unclear. Here, we used high resolution NG Capture-C to map thecis-regulatory interaction landscape of the key neuro-developmentalPaupar-Pax6lncRNA-mRNA locus. The results defined chromatin architecture changes associated with highPaupar-Pax6expression in neurons and identified both promoter selective as well as sharedcis-regulatory interactions with thePauparandPax6promoters involved in regulatingPaupar-Pax6co-expression in neuronal cells. The TCF7L2 transcription factor, a major regulator of chromatin architecture and effector of the Wnt signalling pathway, binds to a subset of these candidatecis-regulatory elements to coordinatePauparandPax6co-expression. We identify a functional TCF7L2 boundcis-regulatory element within thePaupargene, suggesting that thePauparDNA locus itself regulatesPax6expression in addition to its previously described transcriptdependent modes of action. Our work provides important insights into the chromatin interactions, signalling pathways and transcription factors controlling co-expression of adjacent lncRNAs and protein coding genes in the brain.
Standard PBMC cryopreservation selectively decreases detection of nine clinically-relevant T-cell markers
Authors: Capelle Christophe M. , Cire Séverine , Ammerlaan Wim , Konstantinou Maria , Balling Rudi , Betsou Fay , Cosma Antonio , Ollert Markus , Hefeng Feng Q. 
Published: May 2021

AbstractBiobanking is an operational component of various epidemiological studies and clinical trials. Although peripheral blood is routinely acquired and stored in biobanks, the effects of specimen processing on cell composition and clinically-relevant functional markers of T cells still require a systematic evaluation. Here we assessed 25 relevant T-cell markers and showed that the detection of nine membrane markers, e.g., PD-1, CTLA4, KLRG1, CD25, CD122, CD127 and others reflecting exhaustion, senescence and other functions was reduced among at least one T-cell subset following standard processing, although the frequency of CD4, CD8 and regulatory T cells was unaffected. Nevertheless, a six-month-long cryopreservation did not impair the expression levels of many other membrane and all the eight tested intracellular lineage or functional T-cell markers. Our findings uncover that several clinically-relevant markers are particularly affected by processing and the interpretation of those results in clinical trials and translational research should be done with caution.
Permutation-based significance analysis reduces the type 1 error rate in bisulfite sequencing data analysis of human umbilical cord blood samples
Authors: Laajala Essi , Halla-aho Viivi , Grönroos Toni , Ullah Ubaid , Vähä-Mäkilä Mari , Nurmio Mirja , Kallionpää Henna , Lietzén Niina , Mykkänen Juha , Rasool Omid , Toppari Jorma , Orešič Matej , Knip Mikael , Lund Riikka , Lahesmaa Riitta , Lähdesmäki Harri 
Published: May 2021

AbstractBackgroundDNA methylation patterns are largely established in-utero and might mediate the impacts of in-utero conditions on later health outcomes. Associations between perinatal DNA methylation marks and pregnancy-related variables, such as maternal age and gestational weight gain, have been earlier studied with methylation microarrays, which typically cover less than 2 % of human CpG sites. To detect such associations outside these regions, we chose the bisulfite sequencing approach.MethodsWe collected and curated all available clinical data on 200 newborn infants; whose umbilical cord blood samples were analyzed with the reduced representation bisulfite sequencing (RRBS) method. A generalized linear mixed effects model was fit for each high coverage CpG site, followed by spatial and multiple testing adjustment of P values to identify differentially methylated cytosines (DMCs) and regions (DMRs) associated with clinical variables such as maternal age, mode of delivery, and birth weight. Type 1 error rate was then evaluated with a permutation analysis.ResultsWe discovered a strong inflation of spatially adjusted P values through the permutation analysis, which we then applied for empirical type 1 error control. Based on empirically estimated significance thresholds, very little differential methylation was associated with any of the studied clinical variables, other than sex. With this analysis workflow, the sex-associated differentially methylated regions were highly reproducible across studies, technologies, and statistical models.ConclusionsThe inflation of P values was caused by a common method for spatial adjustment and DMR detection, implemented in tools comb-p and RADMeth. With standard significance thresholds, type 1 error rates were high with both these implementations, across alternative parameter settings and analysis strategies. We conclude that comb-p and RADMeth are convenient methods for the detection of differentially methylated regions, but the statistical significance should either be determined empirically or before the spatial adjustment. Our RRBS data analysis workflow is available inhttps://github.com/EssiLaajala/RRBS_workflow.
Renal Angiotensinogen is Predominantly Liver-Derived in Nonhuman Primates
Authors: Kukida Masayoshi , Cai Lei , Ye Dien , Sawada Hisashi , Katsumata Yuriko , Franklin Michael K. , Hecker Peter I. , Campbell Kenneth S. , Danser A.H. Jan , Mullick Adam E. , Daugherty Alan , Temel Ryan E. , Lu Hong S. 
Published: May 2021

AbstractAGT (Angiotensinogen) is the unique substrate of the renin-angiotensin system. Liver is the primary source of circulating AGT. The present study determined whether hepatocyte-derived AGT regulates renal AGT accumulation by injecting ASO (antisense oligonucleotides) targeting hepatocyte-derived AGT (GalNAc AGT ASO) into female cynomolgus monkeys. Hepatocyte-specific inhibition of AGT led to profound reductions of plasma AGT concentrations. AGT protein in S1 and S2 of renal proximal tubules was greatly diminished by GalNAc AGT ASO. Given the similarity between nonhuman primates and human, our findings support the notion that renal AGT is predominantly derived from liver, and liver regulates renal angiotensin II production in humans.Abstract Figure
The METTL5-TRMT112N6-methyladenosine methyltransferase complex regulates metabolism and development via translation
Authors: Sepich-Poore Caraline , Zheng Zhong , Schmitt Emily , Wen Kailong , Zhang Zijie Scott , Cui Xiao-Long , Dai Qing , Zhu Allen C. , Zhang Linda , Castillo Arantxa Sanchez , Zhuang Xiaoxi , He Chuan , Nachtergaele Sigrid 
Published: May 2021

ABSTRACTRibosomal RNAs (rRNAs) have long been known to carry modifications, including numerous sites of 2’O-methylation and pseudouridylation, as well asN6-methyladenosine (m6A), andN6,6-dimethyladenosine. While the functions of many of these modifications are unclear, some are highly conserved and occur in regions of the ribosome critical for mRNA decoding. Both 28S rRNA and 18S rRNA carry m6A, and while ZCCHC4 has been identified as the methyltransferase responsible for the 28S rRNA m6A site, the methyltransferase responsible for the 18S rRNA m6A site has remained uncharacterized until recently. Here, we show that the METTL5-TRMT112 complex is the methyltransferase responsible for installing m6A at position 1832 of human 18S rRNA. TRMT112 is required for the metabolic stability of METTL5, and human METTL5 mutations associated with microcephaly and intellectual disability disrupt this interaction. Loss of METTL5 in human cancer lines alters the translation of transcripts associated with mitochondrial biogenesis and function.Mettl5knockout mice display reduced body size and evidence of metabolic defects. This m6A site is located on the 3’ end of 18S rRNA, which may become surface-exposed under some circumstances and thus may play a regulatory role in translation of specific transcripts. While recent work has focused heavily on m6A modifications in mRNA and its roles in mRNA processing and translation, deorphanizing putative methyltransferase enzymes is revealing previously unappreciated regulatory roles for m6A in noncoding RNAs.
Genetics and material culture support repeated expansions into Paleolithic Eurasia from a population hub out of Africa
Authors: Vallini Leonardo , Marciani Giulia , Aneli Serena , Bortolini Eugenio , Benazzi Stefano , Pievani Telmo , Pagani Luca 
Published: May 2021

AbstractThe population dynamics that followed the out of Africa expansion (OoA) and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macro populations have long been debated. Shedding light on these events may, in turn, provide clues to better understand cultural evolution in Eurasia between 50kya and 35kya.Here we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust’Ishim, Bacho Kiro and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 kya, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 kya, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones while moving through Siberia (Yana, Mal’ta).
Single-dose immunisation with a multimerised SARS-CoV-2 receptor binding domain (RBD) induces an enhanced and protective response in mice
Authors: Salzer Ralf , Clark Jordan J. , Vaysburd Marina , Chang Veronica T. , Albecka Anna , Kiss Leo , Sharma Parul , Llamazares Andres Gonzalez , Kipar Anja , Hiscox Julian A. , Owen Andrew , Aricescu A. Radu , Stewart James P. , James Leo C. , Löwe Jan 
Published: May 2021

ABSTRACTThe COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, has triggered a worldwide health emergency. So far, several different types of vaccines have shown strong efficacy. However, both the emergence of new SARS-CoV-2 variants and the need to vaccinate a large fraction of the world’s population necessitate the development of alternative vaccines, especially those that are simple and easy to store, transport and administer. Here, we showed that ferritin-like Dps protein from hyperthermophilic Sulfolobus islandicus can be covalently coupled with different SARS-CoV-2 antigens via the SpyCatcher system, to form extremely stable and defined multivalent dodecameric vaccine nanoparticles that remain intact even after lyophilisation. Immunisation experiments in mice demonstrated that the SARS-CoV-2 receptor binding domain (RBD) coupled to Dps (RBD-S-Dps) shows particular promise as it elicited a higher antibody titre and an enhanced neutralising antibody response compared to the monomeric RBD. Furthermore, we showed that a single immunisation with the multivalent RBD-S-Dps completely protected hACE2-expressing mice from serious illness and led to efficient viral clearance from the lungs upon SARS-CoV-2 infection. Our data highlight that multimerised SARS-CoV-2 subunit vaccines are a highly efficacious modality, particularly when combined with an ultra-stable scaffold.
Quantitative reverse transcription PCR assay to detect pyrethroid resistance in Culex mosquitoes
Authors: Hager Kelli M. , Gaona Erick , Kistler Amy , Ratnasiri Kalani , Retallack Hanna , Barretto Miguel , Wheeler Sarah S. , Hoover Christopher M. , Haas-Stapleton Eric J. 
Published: May 2021

AbstractPyrethroid insecticides are widely used to control mosquitoes that transmit diseases such as West Nile virus (WNV) to humans. A single nucleotide polymorphism (SNP) in the knockdown resistance locus (kdr) of the voltage gated sodium channel (Vgsc) gene of Culex mosquitoes confers knockdown resistance to pyrethroids. PCR-based assays that detect these SNPs in Culex species are currently available for Culex pipiens Linnaeus and Culex quinquefasciatus Say. RNAseq was employed to sequence the coding region of Vgsc for Culex tarsalis Coquillett and Culex erythrothorax Dyar, two WNV vectors. We utilized the cDNA sequence to develop a quantitative reverse transcriptase PCR assay that detects the L1014F mutation in the kdr of Vgsc. Because this locus is conserved, the assay successfully detected the SNPs in multiple Culex spp. vectors of WNV in the United States. The resulting Culex RTkdr assay was validated using quantitative PCR, CDC bottle bioassays, and sequencing of PCR products. Using sequencing, we determined the accuracy of the Culex RTkdr assay was 99%. Pyrethroid resistance was more common among Cx. pipiens than other Culex spp. and co-occured with agriculture. We anticipate that public health and vector control agencies may utilize the Culex RTkdr assay to map the distribution of pyrethroid resistance in Culex species to more efficiently control mosquitoes and the diseases they transmit.
Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors
Authors: Pöll Gisela , Pilsl Michael , Griesenbeck Joachim , Tschochner Herbert , Milkereit Philipp 
Published: May 2021

AbstractIn yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with the stabilisation and maturation of subunit precursors potentially promotes the production of ribosomes with defined composition. To further decipher mechanisms of such an intrinsic quality control pathway we analysed here the contribution of three yeast large ribosomal subunit r-proteins for intermediate nuclear subunit folding steps. Structure models obtained from single particle cryo-electron microscopy analyses provided evidence for specific and hierarchic effects on the stable positioning and remodelling of large ribosomal subunit domains. Based on these structural and previous biochemical data we discuss possible mechanisms of r-protein dependent hierarchic domain arrangement and the resulting impact on the stability of misassembled subunits.
Inhibiting BCKDK in triple negative breast cancer suppress protein translation, impair mitochondrial function, and potentiate doxorubicin cytotoxicity
Authors: Biswas Dipsikha , Slade Logan , Duffley Luke , Mueller Neil , Dao Khoi Thien , Mercer Angella , Hiani Yassine El , Kienesberger Petra , Pulinilkunnil Thomas 
Published: May 2021

AbstractTriple-negative breast cancers (TNBCs) are characterized by poor survival, prognosis and gradual resistance to cytotoxic chemotherapeutics, like doxorubicin (DOX), which is limited by its cardiotoxic and chemoresistant effects that manifest over time. TNBC growth and survival are fuelled by reprogramming branched-chain amino acids (BCAAs) metabolism, which rewires oncogenic gene expression and cell signaling pathways. A regulatory kinase of the rate-limiting enzyme of the BCAA catabolic pathway, branched-chain ketoacid dehydrogenase kinase (BCKDK), have recently been implicated in driving tumor cell proliferation and conferring drug resistance by activating RAS/RAF/MEK/ERK signaling. However it remains unexplored if BCKDK remodels TNBC proliferation, survival and susceptibility to DOX-induced genotoxic stress. TNBC cell lines exhibited reduced BCKDK expression in response to DOX. Genetic and pharmacological inhibition of BCKDK in TNBC cell lines displayed reduced intracellular and secreted BCKAs. Moreover, BCKDK inhibition with concurrent DOX treatment exacerbated apoptosis, caspase activity and loss of TNBC proliferation. Transcriptome analysis of BCKDK silenced cells confirmed a marked upregulation of the apoptotic signaling pathway with increased protein ubiquitylation and compromised mitochondrial metabolism. BCKDK silencing in TNBC downregulated mitochondrial metabolism genes, reduced electron complex protein expression, oxygen consumption and ATP production. Silencing BCKDK in TNBC upregulated sestrin 2 and concurrently decreased protein synthesis and mTORC1 signaling. Inhibiting BCKDK in TNBC remodel BCAA flux, reduces protein translation triggering cell death, ATP insufficiency and susceptibility to genotoxic stress.Graphical abstract
An immature subset of neuroblastoma cells synthesizes retinoic acid and depends on this metabolite
Authors: van Groningen Tim , Niklasson Camilla U. , Chan Alvin , Akogul Nurdan , Westerhout Ellen M. , von Stedingk Kristoffer , Hamdi Mohamed , Valentijn Linda J. , Mohlin Sofie , Stroeken Peter , Hasselt Nancy E. , Haneveld Franciska , Lakeman Arjan , Zwijnenburg Danny A. , van Sluis Peter , Bexell Daniel , Adameyko Igor , Jansky Selina , Westermann Frank , Wigerup Caroline , Påhlman Sven , Koster Jan , Versteeg Rogier , van Nes Johan 
Published: May 2021

AbstractNeuroblastoma is a pediatric tumor of the adrenergic sympathetic lineage. Most high risk neuroblastoma go in complete clinical remission by chemotherapy, which is subsequently complemented by retinoic acid (RA) maintenance therapy. However, by unresolved mechanisms most tumors ultimately relapse as therapy-resistant disease. Neuroblastoma cell lines were recently found to include, besides lineage committed adrenergic (ADRN) tumor cells, also immature mesenchymal (MES) tumor cells. Here, we report that MES-type cells synthesize RA and require this metabolite for proliferation and motility. MES cells are even resistant to RAin vitro. MES cells appear to resemble Schwann Cell Precursors (SCP), which are motile precursors of the adrenergic lineage. MES and SCP cells express shared RA-synthesis and RA-target genes. Endogenous RA synthesis and RA resistance thus stem from normal programs of lineage precursors that are maintained in an immature tumor cell fraction. These cells are fully malignant in orthotopic patient-derived xenograft models and may mediate development of drug-resistant relapses.
The draft genome sequence ofEucalyptus polybracteabased on hybrid assembly with short- and long-reads reads
Authors: Li Teng , Kainer David , Foley William J. , Rodrigo Allen , Külheim Carsten 
Published: May 2021

AbstractEucalyptus polybracteais a small, multi-stemmed tree, which is widely cultivated in Australia for the production of Eucalyptus oil. We report the hybrid assembly of theE. polybracteagenome utilizing both short- and long-read technology. We generated 44 Gb of Illumina HiSeq short reads and 8 Gb of Nanopore long reads, representing approximately 83× and 15× genome coverage, respectively. The hybrid-assembled genome, after polishing, contained 24,864 scaffolds with an accumulated length of 523 Mb (N50 = 40.3 kb; BUSCO-calculated genome completeness of 94.3%). The genome contained 35,385 predicted protein-coding genes detected by combining homology-based and de novo approaches. We have provided the first assembled genome based on hybrid sequences from the highly diverseEucalyptussubgenusSymphyomyrtus, and revealed the value of including long-reads from Nanopore technology for enhancing the contiguity of the assembled genome, as well as for improving its completeness. We anticipate that theE. polybracteagenome will be an invaluable resource supporting a range of studies in genetics, population genomics and evolution of related species inEucalyptus.
Mechanosensitive calcium signaling in response to cell shape changes promotes epithelial tight junction remodeling by activating RhoA
Authors: Varadarajan Saranyaraajan , Stephenson Rachel E. , Misterovich Eileen R. , Wu Jessica L. , Erofeev Ivan S. , Goryachev Andrew B. , Miller Ann L. 
Published: May 2021

AbstractEpithelia maintain an effective barrier by actively remodeling cell-cell junctions in response to mechanical stimuli. Cells often respond to mechanical stress through activation of RhoA and dynamic remodeling of actomyosin. Previously, we found that local leaks in the epithelial tight junction barrier are rapidly repaired by localized, transient activation of RhoA, a process we termed “Rho flares”, but how Rho flares are initiated remains unknown. Here, we discovered that intracellular calcium flashes occur in Xenopus laevis embryonic epithelial cells undergoing rapid remodeling of tight junctions via activation of Rho flares. Calcium flashes originate at the site of leaks and propagate into the cell. Depletion of intracellular calcium or inhibition of mechanosensitive calcium channels (MSC) reduced the amplitude of calcium flashes and diminished the activation of Rho flares. Furthermore, MSC-dependent calcium influx was necessary to maintain global barrier function by regulating repair of local tight junction proteins through efficient contraction of junctions. Collectively, we propose that MSC-dependent calcium flashes are an important mechanism allowing epithelial cells to sense and respond to local leaks induced by mechanical stimuli.
Rad52 oligomeric N-terminal domain stabilizes Rad51 nucleoprotein filaments and contributes to their protection against Srs2
Authors: Ma Emilie , Maloisel Laurent , Falher Léa Le , Guérois Raphaël , Coïc Eric 
Published: May 2021

AbstractHomologous recombination (HR) depends on the formation of a nucleoprotein filament of the recombinase Rad51 to scan the genome and invade the homologous sequence used as template for DNA repair synthesis. Therefore, HR is highly accurate and crucial for genome stability. Rad51 filament formation is controlled by positive and negative factors. In Saccharomyces cerevisiae, the mediator protein Rad52 catalyzes Rad51 filament formation and stabilizes them, mostly by counteracting the disruptive activity of the translocase Srs2. Srs2 activity is essential to avoid the formation of toxic Rad51 filaments, as revealed by Srs2-deficient cells. We previously reported that Rad52 SUMOylation or mutations disrupting the Rad52-Rad51 interaction suppress Rad51 filament toxicity because they disengage Rad52 from Rad51 filaments and reduce their stability. Here, we found that mutations in Rad52 N-terminal domain also suppress the DNA damage sensitivity of Srs2-deficient cells. Structural studies showed that these mutations affect the Rad52 oligomeric ring structure. Overall, in vivo and in vitro analyzes of these mutants indicate that Rad52 ring structure is important for protecting Rad51 filaments from Srs2, but can increase Rad51 filament stability and toxicity in Srs2-deficient cells. This stabilization function is distinct from Rad52 mediator and annealing activities.